2024/07/18 更新

写真a

エンドウ マサユキ
遠藤 政幸
ENDO,Masayuki
所属
研究推進部 特別任命教授
職名
特別任命教授
プロフィール

DNAは優れた超分子で自己集合によってナノスケール及びメゾスケールの複雑な構造やパターンを形成させることが可能です。また、配列のプログラムにしたがって機能性分子やナノ材料を配置することも可能です。本グループでは、さまざまな平面構造と立体構造の構築を行える「DNAオリガミ」法を用いて、DNA配列の設計を行い、ナノ構造体やナノ空間の構築を行うことで、 (1) 新規な2次元及び3次元ナノ構造体の構築とその操作、(2) 2次元DNA構造体の配列プログラムに従った精密な配列と機能化、(3) DNAナノ空間内での生体分子反応の制御と操作、(4) DNAナノ空間での1分子の挙動や反応の可視化と解析、(5) DNAナノ空間での生体分子の物性の解明、(6) 新規DNA結晶の開発、(7)1分子で動作する分子デバイスの開発、(8) 光学材料への応用、(9) 分子ロボットへの応用、(10) 細胞へのデリバリーシステムの開発、(11) 診断・治療への応用を検討しています。 本グループでは、目的に応じたDNAナノ構造体の設計・構築、ナノスケールで新規機能を発揮する分子デバイス・分子システムの開発、生体機能解明のための1分子イメージング・分析システムの開発、新規バイオナノマテリアルによる生体への応用を目指しています。これらの研究のため、本グループでは、実時間測定可能な高速原子間力顕微鏡(AFM)を備えています。

外部リンク

学位

  • 博士(工学) ( 1997年3月   東京大学 )

  • 修士(工学) ( 1994年3月   東京大学 )

  • 工学学士 ( 1992年3月   京都大学 )

研究キーワード

  • ケミカルバイオロジー

  • ナノテクノロジー

  • 核酸化学

  • 1分子イメージング

  • 細胞工学

  • 光化学

  • タンパク質工学

研究分野

  • ナノテク・材料 / ナノ材料科学

  • ナノテク・材料 / ナノバイオサイエンス

  • ナノテク・材料 / 生体化学

  • ライフサイエンス / 機能生物化学

学歴

  • 東京大学   大学院工学系研究科   化学生命工学専攻

    1997年

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    備考: 博士後期課程

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  • 京都大学   工学部   合成化学科

    1992年

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    国名: 日本国

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  • 東京大学   大学院工学系研究科   工業化学専攻

    1994年

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    国名: 日本国

    備考: 博士後期課程

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経歴

  • 京都大学   高等研究院 物質―細胞統合システム拠点   客員教授

    2021年 - 現在

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  • 関西大学   先端科学技術推進機構   特任教授

    2021年 - 現在

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  • 京都大学   大学院理学研究科 化学専攻   特定准教授

    2018年

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  • 京都大学   物質-細胞統合システム拠点   准教授

    2008年

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  • 大阪大学   産業科学研究所   特任准教授

    2005年

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  • 大阪大学   産業科学研究所   助手

    2001年

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  • 理化学研究所   ゲノム科学総合研究センター   基礎科学特別研究員

    2000年

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  • ハーバード大学   化学・ケミカルバイオロジー学科   博士研究員

    1998年

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  • 東京医科歯科大学   医用器材研究所   日本学術振興会特別研究員

    1997年

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▼全件表示

所属学協会

論文

  • Structural Expansion of Catalytic RNA Nanostructures through Oligomerization of a Cyclic Trimer of Engineered Ribozymes

    Mst. Ayesha Siddika, Hiroki Oi, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    Molecules   28 ( 18 )   6465 - 6465   2023年9月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:MDPI AG  

    The multimolecular assembly of three-dimensionally structured proteins forms their quaternary structures, some of which have high geometric symmetry. The size and complexity of protein quaternary structures often increase in a hierarchical manner, with simpler, smaller structures serving as units for larger quaternary structures. In this study, we exploited oligomerization of a ribozyme cyclic trimer to achieve larger ribozyme-based RNA assembly. By installing kissing loop (KL) interacting units to one-, two-, or three-unit RNA molecules in the ribozyme trimer, we constructed dimers, open-chain oligomers, and branched oligomers of ribozyme trimer units. One type of open-chain oligomer preferentially formed a closed tetramer containing 12 component RNAs to provide 12 ribozyme units. We also observed large assembly of ribozyme trimers, which reached 1000 nm in size.

    DOI: 10.3390/molecules28186465

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  • Isothermal self-assembly of multicomponent and evolutive DNA nanostructures 査読

    Caroline Rossi-Gendron, Farah El Fakih, Laura Bourdon, Koyomi Nakazawa, Julie Finkel, Nicolas Triomphe, Léa Chocron, Masayuki Endo, Hiroshi Sugiyama, Gaëtan Bellot, Mathieu Morel, Sergii Rudiuk, Damien Baigl

    Nature Nanotechnology   2023年7月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    Abstract

    Thermal annealing is usually needed to direct the assembly of multiple complementary DNA strands into desired entities. We show that, with a magnesium-free buffer containing NaCl, complex cocktails of DNA strands and proteins can self-assemble isothermally, at room or physiological temperature, into user-defined nanostructures, such as DNA origamis, single-stranded tile assemblies and nanogrids. In situ, time-resolved observation reveals that this self-assembly is thermodynamically controlled, proceeds through multiple folding pathways and leads to highly reconfigurable nanostructures. It allows a given system to self-select its most stable shape in a large pool of competitive DNA strands. Strikingly, upon the appearance of a new energy minimum, DNA origamis isothermally shift from one initially stable shape to a radically different one, by massive exchange of their constitutive staple strands. This method expands the repertoire of shapes and functions attainable by isothermal self-assembly and creates a basis for adaptive nanomachines and nanostructure discovery by evolution.

    DOI: 10.1038/s41565-023-01468-2

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    その他リンク: https://www.nature.com/articles/s41565-023-01468-2

  • Two-Dimensional DNA Origami Lattices Assembled on Lipid Bilayer Membranes

    Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo

    Methods in Molecular Biology   83 - 90   2023年5月

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    掲載種別:論文集(書籍)内論文   出版者・発行元:Springer US  

    DOI: 10.1007/978-1-0716-3028-0_5

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  • Single-Molecule Visualization of B–Z Transition in DNA Origami Using High-Speed AFM 招待 査読

    Masayuki Endo, Hiroshi Sugiyama

    Methods in Molecular Biology   2651   241 - 250   2023年3月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:論文集(書籍)内論文  

    DOI: 10.1007/978-1-0716-3084-6_17

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  • Photocontrolled DNA nanotubes as stiffness tunable matrices for controlling cellular behavior 査読

    Soumya Sethi, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    Nanoscale   15 ( 6 )   2904 - 2910   2023年1月

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    担当区分:最終著者, 責任著者   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1039/d2nr05202d

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  • Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes

    Mst. Ayesha Siddika,Takahiro Yamada, Risako Aoyama, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    Molecules   27 ( 23 )   8298 - 8298   2022年11月

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    掲載種別:研究論文(学術雑誌)  

    DOI: 10.3390/molecules27238298

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  • Zeptoliter DNA Origami Reactor to Reveal Cosolute Effects on Nanoconfined G-Quadruplexes 査読

    Shankar Pandey, Sagun Jonchhe, Shubham Mishra, Tomoko Emura, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao

    The Journal of Physical Chemistry Letters   8692 - 8698   2022年9月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpclett.2c02253

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  • Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers

    Md Dobirul Islam, Kumi Hidaka, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    Journal of Bioscience and Bioengineering   134 ( 3 )   195 - 202   2022年9月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.jbiosc.2022.06.008

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  • Surface Assembly of DNA Origami on A Lipid Bilayer Observed Using High-Speed Atomic Force Microscopy 招待 査読

    Masayuki Endo

    Molecules   27   4224   2022年6月

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    記述言語:英語  

    DOI: 10.3390/molecules27134224

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  • DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion 査読

    Shengtao Yao, Yongyun Chang, Zanjing Zhai, Hiroshi Sugiyama, Masayuki Endo, Weiping Zhu, Yufang Xu, Yangyang Yang, Xuhong Qian

    ACS Appl. Mater. Interfaces   14   20739 - 20748   2022年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/acsami.2c03265

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  • Biomimetic DNA Nanotechnology to Understand and Control Cellular Responses

    Soumya Sethi, Hiroshi Sugiyama, Masayuki Endo

    ChemBioChem   23 ( 6 )   2022年3月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/cbic.202100446

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    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cbic.202100446

  • A Hexameric Ribozyme Nanostructure Formed by Double‐Decker Assembly of a Pair of Triangular Ribozyme Trimers

    Kai Yu, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    ChemBioChem   23 ( 6 )   2022年3月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/cbic.202100573

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    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cbic.202100573

  • Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity

    Sagun Jonchhe, Shankar Pandey, Christian Beneze, Tomoko Emura, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao

    Nucleic Acids Research   50 ( 2 )   697 - 703   2022年1月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    Abstract

    Both ligand binding and nanocavity can increase the stability of a biomolecular structure. Using mechanical unfolding in optical tweezers, here we found that a DNA origami nanobowl drastically increased the stability of a human telomeric G-quadruplex bound with a pyridostatin (PDS) ligand. Such a stability change is equivalent to >4 orders of magnitude increase (upper limit) in binding affinity (Kd: 490 nM → 10 pM (lower limit)). Since confined space can assist the binding through a proximity effect between the ligand-receptor pair and a nanoconfinement effect that is mediated by water molecules, we named such a binding as mechanochemical binding. After minimizing the proximity effect by using PDS that can enter or leave the DNA nanobowl freely, we attributed the increased affinity to the nanoconfinement effect (22%) and the proximity effect (78%). This represents the first quantification to dissect the effects of proximity and nanoconfinement on binding events in nanocavities. We anticipate these DNA nanoassemblies can deliver both chemical (i.e. ligand) and mechanical (i.e. nanocavity) milieus to facilitate robust mechanochemical binding in various biological systems.

    DOI: 10.1093/nar/gkab1298

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  • Non‐invasive Regulation of Cellular Morphology Using a Photoswitchable Mechanical DNA Polymer 査読

    Soumya Sethi, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    Angewandte Chemie International Edition   60 ( 37 )   20342 - 20349   2021年9月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/anie.202105425

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    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/anie.202105425

  • HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in Chlamydomonas reinhardtii 査読

    Mari Takusagawa, Yusuke Kobayashi, Yoichiro Fukao, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, Takashi Hamaji, Yoshinobu Kato, Isamu Miyakawa, Osami Misumi, Toshiharu Shikanai, Yoshiki Nishimura

    Proceedings of the National Academy of Sciences   118 ( 20 )   e2021053118 - e2021053118   2021年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Proceedings of the National Academy of Sciences  

    Compaction of bulky DNA is a universal issue for all DNA-based life forms. Chloroplast nucleoids (chloroplast DNA–protein complexes) are critical for chloroplast DNA maintenance and transcription, thereby supporting photosynthesis, but their detailed structure remains enigmatic. Our proteomic analysis of chloroplast nucleoids of the green alga <italic>Chlamydomonas reinhardtii</italic> identified a protein (HBD1) with a tandem repeat of two DNA-binding high mobility group box (HMG-box) domains, which is structurally similar to major mitochondrial nucleoid proteins transcription factor A, mitochondrial (TFAM), and ARS binding factor 2 protein (Abf2p). Disruption of the <italic>HBD1</italic> gene by CRISPR-Cas9–mediated genome editing resulted in the scattering of chloroplast nucleoids. This phenotype was complemented when intact HBD1 was reintroduced, whereas a truncated HBD1 with a single HMG-box domain failed to complement the phenotype. Furthermore, ectopic expression of HBD1 in the mitochondria of yeast <italic>Δabf2</italic> mutant successfully complemented the defects, suggesting functional similarity between HBD1 and Abf2p. Furthermore, in vitro assays of HBD1, including the electrophoretic mobility shift assay and DNA origami/atomic force microscopy, showed that HBD1 is capable of introducing U-turns and cross-strand bridges, indicating that proteins with two HMG-box domains would function as DNA clips to compact DNA in both chloroplast and mitochondrial nucleoids.

    DOI: 10.1073/pnas.2021053118

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    その他リンク: https://syndication.highwire.org/content/doi/10.1073/pnas.2021053118

  • Flexible Assembly of Engineered Tetrahymena Ribozymes Forming Polygonal RNA Nanostructures with Catalytic Ability 査読

    Yuki Mori, Hiroki Oi, Yuki Suzuki, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    ChemBioChem   22 ( 12 )   2168 - 2176   2021年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/cbic.202100109

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    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cbic.202100109

  • An RNA Triangle with Six Ribozyme Units Can Promote a Trans-Splicing Reaction through Trimerization of Unit Ribozyme Dimers 査読

    Junya Akagi, Takahiro Yamada, Kumi Hidaka, Yoshihiko Fujita, Hirohide Saito, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    Applied Sciences   11 ( 6 )   2583 - 2583   2021年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:MDPI AG  

    Ribozymes are catalytic RNAs that are attractive platforms for the construction of nanoscale objects with biological functions. We designed a dimeric form of the Tetrahymena group I ribozyme as a unit structure in which two ribozymes were connected in a tail-to-tail manner with a linker element. We introduced a kink-turn motif as a bent linker element of the ribozyme dimer to design a closed trimer with a triangular shape. The oligomeric states of the resulting ribozyme dimers (kUrds) were analyzed biochemically and observed directly by atomic force microscopy (AFM). Formation of kUrd oligomers also triggered trans-splicing reactions, which could be monitored with a reporter system to yield a fluorescent RNA aptamer as the trans-splicing product.

    DOI: 10.3390/app11062583

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  • Micro-homology intermediates: RecA’s transient sampling revealed at the single molecule level 査読

    Andrew J Lee, Masayuki Endo, Jamie K Hobbs, A Giles Davies, Christoph Wälti

    Nucleic Acids Research   49 ( 3 )   1426 - 1435   2021年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    <title>Abstract</title>
    Recombinase A (RecA) is central to homologous recombination. However, despite significant advances, the mechanism with which RecA is able to orchestrate a search for homology remains elusive. DNA nanostructure-augmented high-speed AFM offers the spatial and temporal resolutions required to study the RecA recombination mechanism directly and at the single molecule level. We present the direct in situ observation of RecA-orchestrated alignment of homologous DNA strands to form a stable recombination product within a supporting DNA nanostructure. We show the existence of subtle and short-lived states in the interaction landscape, which suggests that RecA transiently samples micro-homology at the single RecA monomer-level throughout the search for sequence alignment. These transient interactions form the early steps in the search for sequence homology, prior to the formation of stable pairings at &amp;gt;8 nucleotide seeds. The removal of sequence micro-homology results in the loss of the associated transient sampling at that location.

    DOI: 10.1093/nar/gkaa1258

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  • Short intrinsically disordered polypeptide–oligonucleotide conjugates for programmed self-assembly of nanospheres with temperature-dependent size controllability 査読 国際誌

    Bin Wang, Rizhao Pan, Weiping Zhu, Yufang Xu, Ye Tian, Masayuki Endo, Hiroshi Sugiyama, Yangyang Yang, Xuhong Qian

    Soft Matter   17 ( 5 )   1184 - 1188   2021年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    <p>A new type of thermoresponsive nanospheres was successfully developed by using a series of short intrinsically disordered polypeptide conjugated oligonucleotides as assembling building blocks.</p>

    DOI: 10.1039/d0sm01817a

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  • Photocontrolled DNA Origami Assembly by Using Two Photoswitches 査読 国際誌

    Shubham Mishra, Soyoung Park, Tomoko Emura, Hidaka Kumi, Hiroshi Sugiyama, Masayuki Endo

    Chemistry – A European Journal   27 ( 2 )   778 - 784   2021年1月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    Stimuli-responsive switching molecules have been widely investigated for the purpose of the mechanical control of biomolecules. Recently developed arylazopyrazole (AAP) shows photoisomerization activity, displaying a faster response to light-induced conformational changes and unique absorption spectral properties compared with those of conventionally used azobenzene. Herein, it is demonstrated that AAP can be used as a photoswitching molecule to control photoinduced assembly and disassembly of DNA origami nanostructures. An AAP-modified DNA origami has been designed and constructed. It is observed that the repeated assembly and disassembly of AAP-modified X-shaped DNA origami and hexagonal origami with complementary strands can be achieved by alternating UV and visible-light irradiation. Closed and linear assemblies of AAP-modified X-shaped origami were successfully formed by photoirradiation, and more than 1 μm linear assemblies were formed. Finally, it is shown that the two photoswitches, AAP and azobenzene, can be used in tandem to independently control different assembly configurations by using different irradiation wavelengths. AAP can extend the variety of available wavelengths of photoswitches and stably result in the assembly and disassembly of various DNA origami nanostructures.

    DOI: 10.1002/chem.202004135

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    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/chem.202004135

  • Nanoscopic observation of DNA crystal surface and its dynamic formation and degradation using atomic force microscopy 査読

    Haruhiko Eki, Katsuhiko Abe, Hiroshi Sugiyama, Masayuki Endo

    Chemical Communications   57 ( 13 )   1651 - 1654   2021年1月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    <p>We report the direct observation of formation and degradation of tensegrity triangle DNA crystals using atomic force microscopy (AFM). We observed crystal surface by AFM and characterized the lattice coordination...</p>

    DOI: 10.1039/d0cc07458f

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  • Folding RNA–Protein Complex into Designed Nanostructures

    Tomonori Shibata, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, Hirohide Saito

    Methods in Molecular Biology   2323   221 - 232   2021年

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    記述言語:英語   掲載種別:論文集(書籍)内論文   出版者・発行元:Humana Press Inc.  

    RNA–protein (RNP) complexes are promising biomaterials for the fields of nanotechnology and synthetic biology. Protein-responsive RNA sequences (RNP motifs) can be integrated into various RNAs, such as messenger RNA, short-hairpin RNA, and synthetic RNA nanoobjects for a variety of purposes. Direct observation of RNP interaction in solution at high resolution is important in the design and construction of RNP-mediated nanostructures. Here we describe a method to construct and visualize RNP nanostructures that precisely arrange a target protein on the RNA scaffold with nanometer scale. High-speed AFM (HS-AFM) images of RNP nanostructures show that the folding of RNP complexes of defined sizes can be directly visualized at single RNP resolution in solution.

    DOI: 10.1007/978-1-0716-1499-0_16

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  • Construction of an optically controllable CRISPR-Cas9 system using a DNA origami nanostructure 査読

    Katsuhiko Abe, Hiroshi Sugiyama, Masayuki Endo

    Chemical Communications   57 ( 45 )   5594 - 5596   2021年

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    <p>We demonstrated the photo-controlled sequence-selective dsDNA cleavage using a DNA origami structure with Cas9 nuclease.</p>

    DOI: 10.1039/d1cc00876e

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  • Nucleosomes and Epigenetics from a Chemical Perspective 査読

    Yihong Feng, Masayuki Endo, Hiroshi Sugiyama

    ChemBioChem   22 ( 4 )   595 - 612   2020年10月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/cbic.202000332

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  • Direct Observation of Dynamic Interactions between Orientation‐Controlled Nucleosomes in a DNA Origami Frame 査読

    Yihong Feng, Fumitaka Hashiya, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    Chemistry – A European Journal   26 ( 66 )   15282 - 15289   2020年10月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/chem.202003071

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  • DNA Nanostructures for Targeted Antimicrobial Delivery 査読 国際誌

    Ioanna Mela, Pedro P. Vallejo‐Ramirez, Stanislaw Makarchuk, Graham Christie, David Bailey, Robert M. Henderson, Hiroshi Sugiyama, Masayuki Endo, Clemens F. Kaminski

    Angewandte Chemie International Edition   59 ( 31 )   12698 - 12702   2020年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    We report the use of DNA origami nanostructures, functionalized with aptamers, as a vehicle for delivering the antibacterial enzyme lysozyme in a specific and efficient manner. We test the system against Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) targets. We use direct stochastic optical reconstruction microscopy (dSTORM) and atomic force microscopy (AFM) to characterize the DNA origami nanostructures and structured illumination microscopy (SIM) to assess the binding of the origami to the bacteria. We show that treatment with lysozyme-functionalized origami slows bacterial growth more effectively than treatment with free lysozyme. Our study introduces DNA origami as a tool in the fight against antibiotic resistance, and our results demonstrate the specificity and efficiency of the nanostructure as a drug delivery vehicle.

    DOI: 10.1002/anie.202002740

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  • Duplex DNA Is Weakened in Nanoconfinement 査読

    Sagun Jonchhe, Shankar Pandey, Deepak Karna, Pravin Pokhrel, Yunxi Cui, Shubham Mishra, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao

    Journal of the American Chemical Society   142 ( 22 )   10042 - 10049   2020年6月

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    担当区分:責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jacs.0c01978

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  • X-ray Crystal Structure of a Cyclic-PIP–DNA Complex in the Reverse-Binding Orientation 査読

    Katsuhiko Abe, Yuki Hirose, Haruhiko Eki, Kazuki Takeda, Toshikazu Bando, Masayuki Endo, Hiroshi Sugiyama

    Journal of the American Chemical Society   142 ( 23 )   10544 - 10549   2020年5月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jacs.0c03972

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  • Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures 査読

    Ryuji Kiyooka, Junya Akagi, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    Journal of Bioscience and Bioengineering   130 ( 3 )   253 - 259   2020年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    Ribozymes with modular structures are attractive platforms for the construction of nanoscale RNA objects with biological functions. We designed group I ribozyme dimers as unit ribozyme dimers (Urds), which self-assembled to form their polymeric states and also oligomeric states with defined numbers of Urds. Assembly of Urds yielded catalytic ability of a pair of distinct ribozyme units to cleave two distinct substrates. The morphologies of the assembled ribozyme structures were observed directly by atomic force microscopy (AFM).

    DOI: 10.1016/j.jbiosc.2020.04.010

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  • Direct observation and analysis of TET-mediated oxidation processes in a DNA origami nanochip 査読 国際誌

    Xiwen Xing, Shinsuke Sato, Nai-Kei Wong, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    Nucleic Acids Research   48 ( 8 )   4041 - 4051   2020年5月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    <title>Abstract</title>
    DNA methylation and demethylation play a key role in the epigenetic regulation of gene expression; however, a series of oxidation reactions of 5-methyl cytosine (5mC) mediated by ten-eleven translocation (TET) enzymes driving demethylation process are yet to be uncovered. To elucidate the relationship between the oxidative processes and structural factors of DNA, we analysed the behavior of TET-mediated 5mC-oxidation by incorporating structural stress onto a substrate double-stranded DNA (dsDNA) using a DNA origami nanochip. The reactions and behaviors of TET enzymes were systematically monitored by biochemical analysis and single-molecule observation using atomic force microscopy (AFM). A reformative frame-like DNA origami was established to allow the incorporation of dsDNAs as 5mC-containing substrates in parallel orientations. We tested the potential effect of dsDNAs present in the tense and relaxed states within a DNA nanochip on TET oxidation. Based on enzyme binding and the detection of oxidation reactions within the DNA nanochip, it was revealed that TET preferred a relaxed substrate regardless of the modification types of 5-oxidated-methyl cytosine. Strikingly, when a multi-5mCG sites model was deployed to further characterize substrate preferences of TET, TET preferred the fully methylated site over the hemi-methylated site. This analytical modality also permits the direct observations of dynamic movements of TET such as sliding and interstrand transfer by high-speed AFM. In addition, the thymine DNA glycosylase-mediated base excision repair process was characterized in the DNA nanochip. Thus, we have convincingly established the system's ability to physically regulate enzymatic reactions, which could prove useful for the observation and characterization of coordinated DNA demethylation processes at the nanoscale.

    DOI: 10.1093/nar/gkaa137

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  • Advances in DNA Origami–Cell Interfaces 査読

    Shubham Mishra, Yihong Feng, Masayuki Endo, Hiroshi Sugiyama

    ChemBioChem   21 ( 1-2 )   33 - 44   2020年1月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/cbic.201900481

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  • DNAオリガミによるプラズモニック構造体の構築 招待 査読

    遠藤 政幸

    光学   49 ( 4 )   152 - 158   2020年

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    担当区分:筆頭著者, 最終著者, 責任著者  

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  • DNA density-dependent uptake of DNA origami-based two-or three-dimensional nanostructures by immune cells

    Tatsuoki Maezawa, Shozo Ohtsuki, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Yuki Takahashi, Yoshinobu Takakura, Makiya Nishikawa

    Nanoscale   12 ( 27 )   14818 - 14824   2020年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    <p>Using DNA nanostructures with almost identical molecular weight and structural flexibility, this work clearly showed that compactly packaged DNA nanostructures with high DNA density are suitable for the delivery to immune cells.</p>

    DOI: 10.1039/d0nr02361b

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  • A photocaged DNA nanocapsule for delivery and manipulation in cells

    Yihong Feng, Takeshi Tohgasaki, Yasuyuki Shitomi, Hiroshi Sugiyama, Masayuki Endo

    Methods in Enzymology   329 - 342   2020年

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    掲載種別:論文集(書籍)内論文   出版者・発行元:Elsevier  

    DOI: 10.1016/bs.mie.2020.04.045

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  • DNAオリガミを使った分子ナノマシン 招待 査読

    遠藤 政幸

    電気学会誌   140 ( 4 )   579 - 581   2020年

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    担当区分:筆頭著者, 最終著者, 責任著者   掲載種別:研究論文(学術雑誌)  

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  • Folding of single-stranded circular DNA into rigid rectangular DNA accelerates its cellular uptake. 査読 国際誌

    Shozo Ohtsuki, Yukako Shiba, Tatsuoki Maezawa, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Yuki Takahashi, Yoshinobu Takakura, Makiya Nishikawa

    Nanoscale   11 ( 48 )   23416 - 23422   2019年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Despite the importance of the interaction between DNA and cells for its biological activity, little is known about exactly how DNA interacts with cells. To elucidate the relationship between the structural properties of DNA and its cellular uptake, a single-stranded circular DNA of 1801 bases was designed and folded into a series of rectangular DNA (RecDNA) nanostructures with different rigidities using DNA origami technology. Interactions between these structures and cells were evaluated using mouse macrophage-like RAW264.7 cells. RecDNA with 50 staple DNAs, including four that were Alexa Fluor 488-labeled, was designed. RecDNA with fewer staples, down to four staples (all Alexa Fluor 488-labeled), was also prepared. Electrophoresis and atomic force microscopy showed that all DNA nanostructures were successfully obtained with a sufficiently high yield. Flow cytometry analysis showed that folding of the single-stranded circular DNA into RecDNA significantly increased its cellular uptake. In addition, there was a positive correlation between uptake and the number of staples. These results indicate that highly folded DNA nanostructures interact more efficiently with RAW264.7 cells than loosely folded structures do. Based on these results, it was concluded that the interaction of DNA with cells can be controlled by folding using DNA origami technology.

    DOI: 10.1039/c9nr08695a

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  • Effects of Physical Damage in the Intermediate Phase on the Progression of Amyloid β Fibrillization 査読

    Ryu Tashiro, Hiroaki Taguchi, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama

    Chemistry – An Asian Journal   14 ( 23 )   4140 - 4145   2019年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/asia.201901193

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  • DNA Origami Nanoplate‐Based Emulsion with Nanopore Function 査読

    Daisuke Ishikawa, Yuki Suzuki, Chikako Kurokawa, Masayuki Ohara, Misato Tsuchiya, Masamune Morita, Miho Yanagisawa, Masayuki Endo, Ryuji Kawano, Masahiro Takinoue

    Angewandte Chemie International Edition   58 ( 43 )   15299 - 15303   2019年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/anie.201908392

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  • Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA–RNA interface between two structural modules 査読

    Ryusei Tsuruga, Narumi Uehara, Yuki Suzuki, Hiroyuki Furuta, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    Journal of Bioscience and Bioengineering   128 ( 4 )   410 - 415   2019年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.jbiosc.2019.04.003

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  • AFM-based single-molecule observation of the conformational changes of DNA structures 招待 査読

    Masayuki Endo

    Methods   169   3 - 10   2019年10月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.ymeth.2019.04.007

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  • Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs 査読

    Takashi Mino, Noriki Iwai, Masayuki Endo, Kentaro Inoue, Kotaro Akaki, Fabian Hia, Takuya Uehata, Tomoko Emura, Kumi Hidaka, Yutaka Suzuki, Daron M. Standley, Mariko Okada-Hatakeyama, Shigeo Ohno, Hiroshi Sugiyama, Akio Yamashita, Osamu Takeuchi

    Nucleic acids research   47 ( 16 )   8838 - 8859   2019年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. Regnase-1-mediated mRNA decay (RMD), in which inflammatory mRNAs harboring specific stem-loop structures are degraded, is a critical part of proper immune homeostasis. Prior to initial translation, Regnase-1 associates with target stem-loops but does not carry out endoribonucleolytic cleavage. Single molecule imaging revealed that UPF1 is required to first unwind the stem-loops, thus licensing Regnase-1 to proceed with RNA degradation. Following translation, Regnase-1 physically associates with UPF1 using two distinct points of interaction: The Regnase-1 RNase domain binds to SMG1-phosphorylated residue T28 in UPF1; in addition, an intrinsically disordered segment in Regnase-1 binds to the UPF1 RecA domain, enhancing the helicase activity of UPF1. The SMG1-UPF1-Regnase-1 axis targets pioneer rounds of translation and is critical for rapid resolution of inflammation through restriction of the number of proteins translated by a given mRNA. Furthermore, small-molecule inhibition of SMG1 prevents RNA unwinding in dendritic cells, allowing post-transcriptional control of innate immune responses.

    DOI: 10.1093/nar/gkz628

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  • A Photocaged DNA Nanocapsule for Controlled Unlocking and Opening inside the Cell 査読

    Takeshi Tohgasaki, Yasuyuki Shitomi, Yihong Feng, Saisei Honna, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    Bioconjugate Chemistry   30 ( 7 )   1860 - 1863   2019年7月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.bioconjchem.9b00040

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  • Direct Observation and Analysis of the Dynamics of the Photoresponsive Transcription Factor GAL4 査読

    Guruprasad Raghavan, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    Angewandte Chemie International Edition   58 ( 23 )   7626 - 7630   2019年6月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/anie.201900610

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  • Colloidal plasmonic DNA-origami with photo-switchable chirality in liquid crystals 査読

    Qingkun Liu, Anton Kuzyk, Masayuki Endo, Ivan I. Smalyukh

    Optics Letters   44 ( 11 )   2831 - 2831   2019年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:The Optical Society  

    DOI: 10.1364/ol.44.002831

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    その他リンク: https://www.osapublishing.org/viewmedia.cfm?URI=ol-44-11-2831&seq=0

  • Programming Rotary Motions with a Hexagonal DNA Nanomachine 査読

    Yangyang Yang, Shiwei Zhang, Shengtao Yao, Rizhao Pan, Kumi Hidaka, Tomoko Emura, Chunhai Fan, Hiroshi Sugiyama, Yufang Xu, Masayuki Endo, Xuhong Qian

    Chemistry – A European Journal   25 ( 20 )   5158 - 5162   2019年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/chem.201900221

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  • Direct Observation of the Double-Stranded DNA Formation through Metal Ion-Mediated Base Pairing in the Nanoscale Structure 査読

    Xiwen Xing, Yihong Feng, Zutao Yu, Kumi Hidaka, Fenyong Liu, Akira Ono, Hiroshi Sugiyama, Masayuki Endo

    Chemistry - A European Journal   25 ( 6 )   1446 - 1450   2019年1月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/chem.201805394

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  • Direct Observation of the Formation and Dissociation of Double-Stranded DNA Containing G-Quadruplex/i-Motif Sequences in the DNA Origami Frame Using High-Speed AFM 査読

    Masayuki Endo, Xiwen Xing, Hiroshi Sugiyama

    Methods in Molecular Biology   2035   299 - 308   2019年

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:論文集(書籍)内論文   出版者・発行元:Springer New York  

    DOI: 10.1007/978-1-4939-9666-7_17

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  • Using DNA Origami to Contextualize Direct Observations of Enzymes in Action 査読

    A. Lee, M. Endo, J. Hobbs, C. Walti

    Imaging & Microscopy   21 ( 2 )   42 - 44   2019年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

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  • 脂質膜表面におけるDNAオリガミの二次元自己集合化 招待 査読

    鈴木 勇揮, 遠藤 政幸, 杉山 弘

    生物物理   59 ( 2 )   103 - 105   2019年

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  • Construction of integrated gene logic-chip 査読

    Takeya Masubuchi, Masayuki Endo, Ryo Iizuka, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Hao Qi, Ryosuke Iinuma, Yuya Miyazono, Shuichi Shoji, Takashi Funatsu, Hiroshi Sugiyama, Yoshie Harada, Takuya Ueda, Hisashi Tadakuma

    Nature Nanotechnology   13 ( 10 )   933 - 940   2018年10月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    In synthetic biology, the control of gene expression requires a multistep processing of biological signals. The key steps are sensing the environment, computing information and outputting products1. To achieve such functions, the laborious, combinational networking of enzymes and substrate-genes is required, and to resolve problems, sophisticated design automation tools have been introduced2. However, the complexity of genetic circuits remains low because it is difficult to completely avoid crosstalk between the circuits. Here, we have made an orthogonal self-contained device by integrating an actuator and sensors onto a DNA origami-based nanochip that contains an enzyme, T7 RNA polymerase (RNAP) and multiple target-gene substrates. This gene nanochip orthogonally transcribes its own genes, and the nano-layout ability of DNA origami allows us to rationally design gene expression levels by controlling the intermolecular distances between the enzyme and the target genes. We further integrated reprogrammable logic gates so that the nanochip responds to water-in-oil droplets and computes their small RNA (miRNA) profiles, which demonstrates that the nanochip can function as a gene logic-chip. Our approach to component integration on a nanochip may provide a basis for large-scale, integrated genetic circuits.

    DOI: 10.1038/s41565-018-0202-3

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  • Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures 査読

    Sagun Jonchhe, Shankar Pandey, Tomoko Emura, Kumi Hidaka, Mohammad Akter Hossain, Prakash Shrestha, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao

    Proceedings of the National Academy of Sciences   115 ( 38 )   9539 - 9544   2018年9月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Proceedings of the National Academy of Sciences  

    Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.

    DOI: 10.1073/pnas.1805939115

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  • DNA Origami Nanomachines 査読

    Masayuki Endo, Hiroshi Sugiyama

    Molecules   23 ( 7 )   1766 - 1766   2018年7月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:MDPI AG  

    DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

    DOI: 10.3390/molecules23071766

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  • Environment-Dependent Self-Assembly of DNA Origami Lattices on Phase-Separated Lipid Membranes 査読

    Yusuke Sato, Masayuki Endo, Masamune Morita, Masahiro Takinoue, Hiroshi Sugiyama, Satoshi Murata, Shin-ichiro M. Nomura, Yuki Suzuki

    Advanced Materials Interfaces   5 ( 14 )   1800437 - 1800437   2018年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/admi.201800437

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  • Complexing DNA Origami Frameworks through Sequential Self-Assembly Based on Directed Docking 査読

    Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo

    Angewandte Chemie - International Edition   57 ( 24 )   7061 - 7065   2018年6月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley-VCH Verlag  

    Ordered DNA origami arrays have the potential to compartmentalize space into distinct periodic domains that can incorporate a variety of nanoscale objects. Herein, we used the cavities of a preassembled 2D DNA origami framework to incorporate square-shaped DNA origami structures (SQ-origamis). The framework was self-assembled on a lipid bilayer membrane from cross-shaped DNA origami structures (CR-origamis) and subsequently exposed to the SQ-origamis. High-speed AFM revealed the dynamic adsorption/desorption behavior of the SQ-origamis, which resulted in continuous changing of their arrangements in the framework. These dynamic SQ-origamis were trapped in the cavities by increasing the Mg2+ concentration or by introducing sticky-ended cohesions between extended staples, both from the SQ- and CR-origamis, which enabled the directed docking of the SQ-origamis. Our study offers a platform to create supramolecular structures or systems consisting of multiple DNA origami components.

    DOI: 10.1002/anie.201801983

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  • DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K+ Channels 査読

    Tatsuki Kurokawa, Shigeki Kiyonaka, Eiji Nakata, Masayuki Endo, Shohei Koyama, Emiko Mori, Nam Ha Tran, Huyen Dinh, Yuki Suzuki, Kumi Hidaka, Masaaki Kawata, Chikara Sato, Hiroshi Sugiyama, Takashi Morii, Yasuo Mori

    Angewandte Chemie - International Edition   57 ( 10 )   2586 - 2591   2018年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley-VCH Verlag  

    In native systems, scaffolding proteins play important roles in assembling proteins into complexes to transduce signals. This concept is yet to be applied to the assembly of functional transmembrane protein complexes in artificial systems. To address this issue, DNA origami has the potential to serve as scaffolds that arrange proteins at specific positions in complexes. Herein, we report that Kir3 K+ channel proteins are assembled through zinc-finger protein (ZFP)-adaptors at specific locations on DNA origami scaffolds. Specific binding of the ZFP-fused Kir3 channels and ZFP-based adaptors on DNA origami were confirmed by atomic force microscopy and gel electrophoresis. Furthermore, the DNA origami with ZFP binding sites nearly tripled the K+ channel current activity elicited by heterotetrameric Kir3 channels in HEK293T cells. Thus, our method provides a useful template to control the oligomerization states of membrane protein complexes in vitro and in living cells.

    DOI: 10.1002/anie.201709982

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  • Triggering nucleic acid nanostructure assembly by conditional kissing interactions 査読

    Laurent Azéma, Servane Bonnet-Salomon, Masayuki Endo, Yosuke Takeuchi, Guillaume Durand, Tomoko Emura, Kumi Hidaka, Eric Dausse, Hiroshi Sugiyama, Jean-Jacques Toulmé

    Nucleic Acids Research   46 ( 3 )   1052 - 1058   2018年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    DOI: 10.1093/nar/gkx1267

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  • Direct Single-Molecule Observation of Mode and Geometry of RecA-Mediated Homology Search 査読

    Andrew J. Lee, Masayuki Endo, Jamie K. Hobbs, Christoph Wälti

    ACS Nano   12 ( 1 )   272 - 278   2018年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acsnano.7b06208

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  • DNAから作るナノスケールの構造体―そのデザインと作成― 査読

    遠藤 政幸

    化学と教育   66 ( 2 )   88 - 91   2018年

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  • Direct Observation of Dynamic Movement of DNA Molecules in DNA Origami Imaged Using High-Speed AFM 査読

    Masayuki Endo, Hiroshi Sugiyama

    Methods in Molecular Biology   1814   213 - 224   2018年

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:論文集(書籍)内論文   出版者・発行元:Springer New York  

    DOI: 10.1007/978-1-4939-8591-3_13

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  • Confined space facilitates G-quadruplex formation 査読

    Prakash Shrestha, Sagun Jonchhe, Tomoko Emura, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, Hanbin Mao

    Nature Nanotechnology   12 ( 6 )   582 - 588   2017年6月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Nature Publishing Group  

    Molecular simulations suggest that the stability of a folded macromolecule increases in a confined space due to entropic effects. However, due to the interactions between the confined molecular structure and the walls of the container, clear-cut experimental evidence for this prediction is lacking. Here, using DNA origami nanocages, we show the pure effect of confined space on the property of individual human telomeric DNA G-quadruplexes. We induce targeted mechanical unfolding of the G-quadruplex while leaving the nanocage unperturbed. We find that the mechanical and thermodynamic stabilities of the G-quadruplex inside the nanocage increase with decreasing cage size. Compared to the case of diluted or molecularly crowded buffer solutions, the G-quadruplex inside the nanocage is significantly more stable, showing a 100 times faster folding rate. Our findings suggest the possibility of co-replicational or co-transcriptional folding of G-quadruplex inside the polymerase machinery in cells.

    DOI: 10.1038/nnano.2017.29

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    その他リンク: http://www.nature.com/articles/nnano.2017.29

  • A Photoregulated DNA-Based Rotary System and Direct Observation of Its Rotational Movement 査読

    Yangyang Yang, Ryu Tashiro, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    CHEMISTRY-A EUROPEAN JOURNAL   23 ( 16 )   3979 - 3985   2017年3月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1002/chem.201605616

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  • DNA分子マシン 査読

    遠藤 政幸, 杉山 弘

    日本化学会編『CSJカレントレビュー 分子マシンの展開』   140 - 148   2017年

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  • Single-Molecule Observation of the Photoregulated Conformational Dynamics of DNA Origami Nanoscissors 査読

    Elena M. Willner, Yuu Kamada, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hendrik Dietz, Hiroshi Sugiyama, Masayuki Endo

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   56 ( 48 )   15324 - 15328   2017年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    We demonstrate direct observation of the dynamic opening and closing behavior of photocontrollable DNA origami nanoscissors using high-speed atomic force microscopy (HS-AFM). First the conformational change between the open and closed state controlled by adjustment of surrounding salt concentration could be directly observed during AFM scanning. Then light-responsive moieties were incorporated into the nanoscissors to control these structural changes by photoirradiation. Using photoswitchable DNA strands, we created a photoresponsive nanoscissors variant and were able to distinguish between the open and closed conformations after respective irradiation with ultraviolet (UV) and visible (Vis) light by gel electrophoresis and AFM imaging. Additionally, these reversible changes in shape during photoirradiation were directly visualized using HS-AFM. Moreover, four photoswitchable nanoscissors were assembled into a scissor-actuator-like higher-order object, the configuration of which could be controlled by the open and closed switching induced by irradiation with UV and Vis light.

    DOI: 10.1002/anie.201708722

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  • Holliday junction resolvases mediate chloroplast nucleoid segregation 査読

    Yusuke Kobayashi, Osami Misumi, Masaki Odahara, Kota Ishibashi, Masafumi Hirono, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, Hiroshi Iwasaki, Tsuneyoshi Kuroiwa, Toshiharu Shikanai, Yoshiki Nishimura

    SCIENCE   356 ( 6338 )   631 - 634   2017年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER ASSOC ADVANCEMENT SCIENCE  

    Holliday junctions, four-stranded DNA structures formed during homologous recombination, are disentangled by resolvases that have been found in prokaryotes and eukaryotes but not in plant organelles. Here, we identify monokaryotic chloroplast 1 (MOC1) as a Holliday junction resolvase in chloroplasts by analyzing a green alga Chlamydomonas reinhardtii mutant defective in chloroplast nucleoid (DNA-protein complex) segregation. MOC1 is structurally similar to a bacterial Holliday junction resolvase, resistance to ultraviolet (Ruv) C, and genetically conserved among green plants. Reduced or no expression of MOC1 in Arabidopsis thaliana leads to growth defects and aberrant chloroplast nucleoid segregation. In vitro biochemical analysis and high-speed atomic force microscopic analysis revealed that A. thaliana MOC 1 (AtMOC1) binds and cleaves the core of Holliday junctions symmetrically. MOC1 may mediate chloroplast nucleoid segregation in green plants by resolving Holliday junctions.

    DOI: 10.1126/science.aan0038

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  • Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes 査読

    Hiroki Oi, Daisuke Fujita, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa

    JOURNAL OF BIOCHEMISTRY   161 ( 5 )   451 - 462   2017年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    RNA is a biopolymer that is attractive for constructing nano-scale objects with complex structures. Three-dimensional (3D) structures of naturally occurring RNAs often have modular architectures. The 3D structure of a group I (GI) ribozyme from Tetrahymena has a typical modular architecture, which can be separated into two structural modules (Delta P5 and P5abc). The fully active ribozyme can be reconstructed by assembling the two separately prepared modules through highly specific and strong assembly between Delta P5 ribozyme and P5abc RNA. Such non-covalent assembly of the two modules allows the design of polygonal RNA nano-structures. Through rational redesign of the parent GI ribozyme, we constructed variant GI ribozymes as unit RNAs for polygonal-shaped (closed) oligomers with catalytic activity. Programmed trimerization and tetramerization of the unit RNAs afforded catalytically active nano-sized RNA triangles and squares, the structures of which were directly observed by atomic force microscopy (AFM).

    DOI: 10.1093/jb/mvw093

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  • High-Resolution Imaging of a Single Gliding Protofilament of Tubulins by HS-AFM 査読

    Jakia Jannat Keya, Daisuke Inoue, Yuki Suzuki, Toshiya Kozai, Daiki Ishikuro, Noriyuki Kodera, Takayuki Uchihashi, Arif Md. Rashedul Kabir, Masayuki Endo, Kazuki Sada, Akira Kakugo

    SCIENTIFIC REPORTS   7   6166   2017年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    In vitro gliding assay of microtubules (MTs) on kinesins has provided us with valuable biophysical and chemo-mechanical insights of this biomolecular motor system. Visualization of MTs in an in vitro gliding assay has been mainly dependent on optical microscopes, limited resolution of which often render them insufficient sources of desired information. In this work, using high speed atomic force microscopy (HS-AFM), which allows imaging with higher resolution, we monitored MTs and protofilaments (PFs) of tubulins while gliding on kinesins. Moreover, under the HS-AFM, we also observed splitting of gliding MTs into single PFs at their leading ends. The split single PFs interacted with kinesins and exhibited translational motion, but with a slower velocity than the MTs. Our investigation at the molecular level, using the HS-AFM, would provide new insights to the mechanics of MTs in dynamic systems and their interaction with motor proteins.

    DOI: 10.1038/s41598-017-06249-1

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  • Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate 査読

    Tomonori Shibata, Yoshihiko Fujita, Hirohisa Ohno, Yuki Suzuki, Karin Hayashi, Kaoru R. Komatsu, Shunsuke Kawasaki, Kumi Hidaka, Shin Yonehara, Hiroshi Sugiyama, Masayuki Endo, Hirohide Saito

    NATURE COMMUNICATIONS   8   540   2017年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA-protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA-protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA-protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour.

    DOI: 10.1038/s41467-017-00459-x

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  • Self-Assembled Microcapsule of Amphiphilic Janus DNA Nanoplates at the Water-Oil Interface 査読

    Daisuke Ishikawa, Yuki Suzuki, Chikako Kurokawa, Masayuki Ohara, Masamune Morita, Miho Yanagisawa, Ryuji Kawano, Masayuki Endo, Masahiro Takinoue

    Proceedings of The 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences (microTAS2016)   1   116 - 117   2016年10月

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    記述言語:英語   掲載種別:研究論文(大学,研究機関等紀要)  

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  • Torsional Constraints of DNA Substrates Impact Cas9 Cleavage 査読

    Michael H. Raz, Kumi Hidaka, Shana J. Sturla, Hiroshi Sugiyama, Masayuki Endo

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   138 ( 42 )   13842 - 13845   2016年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    To examine the effect of the torsional constraints imposed on DNA substrates on Cas9 cleavage, we prepared constrained DNA substrates using a DNA origami frame. By fixing the dsDNA at the connectors of the DNA frame, we created torsionally constrained or relaxed substrates. We quantified the cleavage of constrained and relaxed substrates by Cas9 with qPCR. Moreover, we observed the Cas9/sgRNA complex bound to the DNA substrates and characterized the dissociation of the complex with high-speed atomic force microscopy. The results revealed that the constrained nontarget strand reduced the cleavage efficiency of Cas9 drastically, whereas torsional constraints on the target strand had little effect on the cleavage. The present study suggests that highly ordered and constrained DNA structures could be obstacles for Cas9 and additionally provides insights in Cas9 dissociation at a single molecule level.

    DOI: 10.1021/jacs.6b08915

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  • Examining cooperative binding of Sox2 on DC5 regulatory element upon complex formation with Pax6 through excess electron transfer assay 査読

    Abhijit Saha, Seiichiro Kizaki, Debojyoti De, Masayuki Endo, Kyeong Kyu Kim, Hiroshi Sugiyama

    NUCLEIC ACIDS RESEARCH   44 ( 14 )   e125   2016年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    Functional cooperativity among transcription factors on regulatory genetic elements is pivotal for milestone decision-making in various cellular processes including mammalian development. However, their molecular interaction during the cooperative binding cannot be precisely understood due to lack of efficient tools for the analyses of protein-DNA interaction in the transcription complex. Here, we demonstrate that photoinduced excess electron transfer assay can be used for analysing cooperativity of proteins in transcription complex using cooperative binding of Pax6 to Sox2 on the regulatory DNA element (DC5 enhancer) as an example. In this assay, U-Br-labelled DC5 was introduced for the efficient detection of transferred electrons from Sox2 and Pax6 to the DNA, and guanine base in the complementary strand was replaced with hypoxanthine (I) to block intra-strand electron transfer at the Sox2-binding site. By examining DNA cleavage occurred as a result of the electron transfer process, from tryptophan residues of Sox2 and Pax6 to DNA after irradiation at 280 nm, we not only confirmed their binding to DNA but also observed their increased occupancy on DC5 with respect to that of Sox2 and Pax6 alone as a result of their cooperative interaction.

    DOI: 10.1093/nar/gkw478

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  • Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores 査読

    Prakash Shrestha, Tomoko Emura, Deepak Koirala, Yunxi Cui, Kumi Hidaka, William J. Maximuck, Masayuki Endo, Hiroshi Sugiyama, Hanbin Mao

    NUCLEIC ACIDS RESEARCH   44 ( 14 )   6574 - 6582   2016年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10-35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as 'mechanophores' that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators.

    DOI: 10.1093/nar/gkw610

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  • Triple Helix Formation in a Topologically Controlled DNA Nanosystem 査読

    Yutaro Yamagata, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo

    CHEMISTRY-A EUROPEAN JOURNAL   22 ( 16 )   5494 - 5498   2016年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.

    DOI: 10.1002/chem.201505030

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  • A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function 査読

    Anton Kuzyk, Yangyang Yang, Xiaoyang Duan, Simon Stoll, Alexander O. Govorov, Hiroshi Sugiyama, Masayuki Endo, Na Liu

    NATURE COMMUNICATIONS   7   10591   2016年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of their synthetic analogues. However, synthetic molecular machines typically operate at the nanometre scale or below. Translating controlled operation of individual molecular machines to a larger dimension, for example, to 10-100 nm, which features many practical applications, is highly important but remains challenging. Here we demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through the host nanostructure and consequently translate it into reversible chiroptical function with large amplitude modulation. Light is exploited as both energy source and information probe. Our plasmonic nanosystem bears unique features of optical addressability, reversibility and modulability, which are crucial for developing all-optical molecular devices with desired functionalities.

    DOI: 10.1038/ncomms10591

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  • Self-assembling DNA hydrogel-based delivery of immunoinhibitory nucleic acids to immune cells 査読

    Yu Nishida, Shozo Ohtsuki, Yuki Araie, Yuka Umeki, Masayuki Endo, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Yuki Takahashi, Yoshinobu Takakura, Makiya Nishikawa

    NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE   12 ( 1 )   123 - 130   2016年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    Immunoinhibitory oligodeoxynucleotides (INH-ODNs) are promising inhibitors of Toll-like receptor 9 (TLR9) activation. To efficiently deliver INH-ODNs to TLR9-positive cells, we designed a Takumi-shaped DNA (Takumi) consisting of two partially complementary ODNs as the main component of a DNA hydrogel. Polyacrylamide gel electrophoresis showed that Takumi-containing INH-ODNs (iTakumi) and iTakumi-based DNA hydrogel (iTakumiGel) were successfully generated. Their activity was examined in murine macrophage-like RAW264.7 cells and DC2.4 dendritic cells by measuring tumor necrosis factor-alpha and interleukin-6 release after the addition of a TLR9 ligand (CpG ODN). Cytokine release was efficiently inhibited by the iTakumiGel. Flow cytometry analysis and confocal microscopy showed that cellular uptake of INH-ODN was greatly increased by the iTakumiGel. These results indicate that a Takumi-based DNA hydrogel is useful for the delivery of INH-ODNs to immune cells to inhibit TLR9-mediated hyperinduction of proinflammatory cytokines.
    From the Clinical Editor: Toll-like receptor 9 activation has been reported to be associated with many autoimmune diseases. DNA inhibition using oligodeoxynucleotides is one of the potential treatments. In this article, the authors described hydrogel-based platform for the delivery of the inhibitory oligodeoxynucleotides for enhanced efficacy. The positive findings could indicate a way for the future. (C) 2015 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.nano.2015.08.004

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  • DNAオリガミの応用 構造から機能へ 査読

    遠藤 政幸

    現代化学   ( 544 )   40 - 45   2016年

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  • Single-Molecule Visualization of Biomolecules in the designed DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy 招待 査読

    Masayuki Endo

    RNA Technologies (V. A. Erdmann, S. Jurga, J. Barciszewski Eds.) Modified Nucleic Acids in Biology and Medicine, Springer   7   403 - 427   2016年

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  • Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure 査読

    Yosuke Takeuchi, Masayuki Endo, Yuki Suzuki, Kumi Hidaka, Guillaume Durand, Eric Dausse, Jean-Jacques Toulme, Hiroshi Sugiyama

    BIOMATERIALS SCIENCE   4 ( 1 )   130 - 135   2016年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.

    DOI: 10.1039/c5bm00274e

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  • Atomic force microscopy analysis of orientation and bending of oligodeoxynucleotides in polypod-like structured DNA 査読

    Tomoki Shiomi, Mengmeng Tan, Natsuki Takahashi, Masayuki Endo, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Yuki Takahashi, Yoshinobu Takakura, Makiya Nishikawa

    NANO RESEARCH   8 ( 12 )   3764 - 3771   2015年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:TSINGHUA UNIV PRESS  

    We previously demonstrated that polypod-like structured DNA, or polypodna, constructed with three or more oligodeoxynucleotides (ODNs), is efficiently taken up by immune cells such as dendritic cells and macrophages, depending on its structural complexity. The ODNs comprising the polypodna should bend to form the polypod-like structure, and may do so by adopting either a bendtype conformation or a cross-type conformation. Here, we tried to elucidate the orientation and bending of ODNs in polypodnas using atomic force microscopy (AFM). We designed two types of pentapodnas (i.e., a polypodna with five pods) using 60- to 88-base ODNs, which were then immobilized on DNA origami frames. AFM imaging showed that the ODNs in the pentapodna adopted bend-type conformations. Tetrapodna and hexapodna also adopted bend-type conformations when they were immobilized on frames under unconstrained conditions. These findings provide useful information toward the coherent design of, and the structure-activity relationships for, a variety of DNA nanostructures.

    DOI: 10.1007/s12274-015-0875-y

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  • Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures 査読

    Yuki Suzuki, Masayuki Endo, Hiroshi Sugiyama

    Nature Communications   6 ( 1 )   2015年11月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    Self-assembly is a ubiquitous approach to the design and fabrication of novel supermolecular architectures. Here we report a strategy termed 'lipid-bilayer-assisted self-assembly' that is used to assemble DNA origami nanostructures into two-dimensional lattices. DNA origami structures are electrostatically adsorbed onto a mica-supported zwitterionic lipid bilayer in the presence of divalent cations. We demonstrate that the bilayer-adsorbed origami units are mobile on the surface and self-assembled into large micrometre-sized lattices in their lateral dimensions. Using high-speed atomic force microscopy imaging, a variety of dynamic processes involved in the formation of the lattice, such as fusion, reorganization and defect filling, are successfully visualized. The surface modifiability of the assembled lattice is also demonstrated by in situ decoration with streptavidin molecules. Our approach provides a new strategy for preparing versatile scaffolds for nanofabrication and paves the way for organizing functional nanodevices in a micrometer space.

    DOI: 10.1038/ncomms9052

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    その他リンク: http://www.nature.com/articles/ncomms9052

  • Single-Molecule Manipulation of the Duplex Formation and Dissociation at the G-Quadruplex/i-Motif Site in the DNA Nanostructure 査読

    Masayuki Endo, Xiwen Xing, Xiang Zhou, Tomoko Emura, Kumi Hidaka, Bodin Tuesuwan, Hiroshi Sugiyama

    ACS NANO   9 ( 10 )   9922 - 9929   2015年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    We demonstrate the single-molecule operation and observation of the formation and resolution of double-stranded DNA (dsDNA) containing a G-quadruplex (GQ) forming and counterpart i-motif forming sequence in the DNA nanostructure. Sequential manipulation of DNA strands in the DNA frame was performed to prepare a topologically controlled GQ/i-motif dsDNA. Using strand displacement and the addition and removal of K+, the topologically controlled GQ/i-motif dsDNA in the DNA frame was obtained in high yield. The dsDNA was resolved into the single-stranded DNA, GQ, and i-motif by the addition of K-F and operation in acidic conditions. The dissociation of the dsDNA under the GQ and i-motif formation condition was monitored by high-speed atomic force microscopy. The results indicate that the dsDNA containing the GQ- and i-motif sequence is effectively dissolved when the duplex is helically loosened in the DNA nanoscaffold.

    DOI: 10.1021/acsnano.5b03413

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  • Optimal Arrangement of Four Short DNA Strands for Delivery of Immunostimulatory Nucleic Acids to Immune Cells 査読

    Shozo Ohtsuki, Noriyuki Matsuzaki, Kohta Mohri, Masayuki Endo, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Yuki Takahashi, Kenichi Ishiyama, Norimitsu Kadowaki, Yoshinobu Takakura, Makiya Nishikawa

    NUCLEIC ACID THERAPEUTICS   25 ( 5 )   245 - 253   2015年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:MARY ANN LIEBERT, INC  

    Nanosized DNA assemblies are useful for delivering immunostimulatory cytosine-phosphate-guanine (CpG) DNA to immune cells, but little is known about the optimal structure for such delivery. In this study, we designed three different DNA nanostructures using four 55-mer oligodeoxynucleotides (ODNs), that is, tetrapod-like structured DNA (tetrapodna), tetrahedral DNA (tetrahedron), and tetragonal DNA (tetragon), and compared their potencies. Electrophoresis showed that tetrapodna was obtained with high yield and purity, whereas tetrahedron formed multimers at high ODN concentrations. Atomic force microscopy revealed that all preparations were properly constructed under optimal conditions. The thermal stability of tetrapodna was higher than those of the others. Dynamic light scattering analysis showed that all of the assemblies were about 8nm in diameter. Upon addition to mouse macrophage-like RAW264.7 cells, tetrahedron was most efficiently taken up by the cells. Then, a CpG DNA, a ligand for toll-like receptor 9, was linked to these DNA nanostructures and added to RAW264.7 cells. CpG tetrahedron induced the largest amount of tumor necrosis factor-, followed by CpG tetrapodna. Similar results were obtained using human peripheral blood mononuclear cells. Taken together, these results indicate that tetrapodna is the best assembly with the highest yield and high immunostimulatory activity, and tetrahedron can be another useful assembly for cellular delivery if its preparation yield is improved.

    DOI: 10.1089/nat.2014.0524

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  • Direct Visualization of Walking Motions of Photocontrolled Nanomachine on the DNA Nanostructure 査読

    Yangyang Yang, Marisa A. Goetzfried, Kumi Hidaka, Mingxu You, Weihong Tan, Hiroshi Sugiyama, Masayuki Endo

    NANO LETTERS   15 ( 10 )   6672 - 6676   2015年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    A light-driven artificial molecular nanomachine was constructed based on DNA scaffolding. Pyrene-modified walking strands and disulfide bond-connected stator strands, employed as anchorage sites to support walker movement, were assembled into a 2D DNA tile. Pyrene molecules excited by photoirradiation at 350 nm induced cleavage of disulfide bond-connected stator strands, enabling the DNA walker to migrate from one cleaved stator to the next on the DNA tile. The time-dependent movement of the walker was observed and the entire walking process of the walker was characterized by distribution of the walker-stator duplex at four anchorage sites on the tile under different irradiation times. Importantly, the light-fuelled mechanical movements on DNA tile were first visualized in real time during UV irradiation using high-speed atomic force microscopy (HS-AFM).

    DOI: 10.1021/acs.nanolett.5b02502

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  • Efficient amplification of self-gelling polypod-like structured DNA by rolling circle amplification and enzymatic digestion 査読

    Tomoya Yata, Yuki Takahashi, Mengmeng Tan, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Yoshinobu Takakura, Makiya Nishikawa

    SCIENTIFIC REPORTS   5   14979   2015年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    The application of DNA as a functional material such as DNA hydrogel has attracted much attention. Despite an increasing interest, the high cost of DNA synthesis is a limiting factor for its utilization. To reduce the cost, we report here a highly efficient amplification technique for polypod-like structured DNA (polypodna) with adhesive ends that spontaneously forms DNA hydrogel. Two types of polypodna with three (tripodna) and four (tetrapodna) pods were selected, and a template oligodeoxynucleotide, containing a tandem sequence of a looped tripodna or tetrapodna, respectively, along with restriction enzyme (TspRI) sites, was designed. The template was circularized using T4 DNA ligase, and amplified by rolling circle amplification (RCA). The RCA product was highly viscous and resistant to restriction digestion. Observation under an electron microscope revealed microflower-like structures. These structures were composed of long DNA and magnesium pyrophosphate, and their treatment with EDTA followed by restriction digestion with TspRI resulted in numerous copies of polypodna with adhesive ends, which formed a DNA hydrogel. Thus, we believe this technique provides a new approach to produce DNA nanostructures, and helps in expanding their practical applications.

    DOI: 10.1038/srep14979

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  • Studying RNAP–promoter interactions using atomic force microscopy 査読

    Y. Suzuki, M. Endo, H. Sugiyama

    Methods   86   4 - 9   2015年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.ymeth.2015.05.018

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  • Single-Molecule Visualization of the Activity of a Zn2+-Dependent DNAzyme 査読

    Masayuki Endo, Yosuke Takeuchi, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Fuan Wang, Itamar Willner, Hiroshi Sugiyama

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   54 ( 36 )   10550 - 10554   2015年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    We demonstrate the single-molecule imaging of the catalytic reaction of a Zn2+-dependent DNAzyme in a DNA origami nanostructure. The single-molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high-speed atomic force microscopy (AFM). This nanostructure-based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single-molecule level.

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  • Linking two DNA duplexes with a rigid linker for DNA nanotechnology 査読

    Ryu Tashiro, Masahiro Iwamoto, Hironobu Morinaga, Tomoko Emura, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama

    NUCLEIC ACIDS RESEARCH   43 ( 14 )   6692 - 6700   2015年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers.

    DOI: 10.1093/nar/gkv662

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  • DNA NANOTECHNOLOGY Measuring chloride in live cells 査読

    Masayuki Endo, Hiroshi Sugiyama

    NATURE NANOTECHNOLOGY   10 ( 7 )   569 - 570   2015年7月

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    記述言語:英語   出版者・発行元:NATURE PUBLISHING GROUP  

    DOI: 10.1038/nnano.2015.142

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  • Self-Assembling DNA Dendrimer for Effective Delivery of Immunostimulatory CpG DNA to Immune Cells 査読

    Kohta Mohri, Eri Kusuki, Shozo Ohtsuki, Natsuki Takahashi, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama, Yuki Takahashi, Yoshinobu Takakura, Makiya Nishikawa

    BIOMACROMOLECULES   16 ( 4 )   1095 - 1101   2015年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    DNA dendrimers consisting of several branched DNA units connected to each other using DNA ligase were quite effective for the delivery of immunostimulatory CpG DNA to immune cells. Therapeutic application of such DNA dendrimers, however, is hampered by the use of the ligase. Here, we report that self-assembling DNA dendrimers with high immunostimulatory potency can be prepared without DNA ligases. Annealing of DNA consisting of DNA units with elongated adhesive ends resulted in the formation of DNA dendrimers. Atomic force microscopy revealed that the several preparations of DNA dendrimers resulted in dendritic structures as designed. The cellular uptake of DNA dendrimers by mouse macrophage-like RAW264.7 cells and subsequent release of tumor necrosis factor-alpha were dependent on the structural complexity of the dendrimers. These results indicate that the ligation-free, self-assembling DNA dendrimers are a potent system for the delivery of immunostimulatory CpG DNA to immune cells.

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  • Mimicking Membrane-Related Biological Events by DNA Origami Nanotechnology 査読

    Yuki Suzuki, Masayuki Endo, Hiroshi Sugiyama

    ACS NANO   9 ( 4 )   3418 - 3420   2015年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    One of the potential applications of DNA nanotechnology is the construction of two- or three-dimensional nanostructures that mimic the function of existing biological molecules. In this issue of ACS Nano, Kocabey et aL demonstrate that lipid-bilayer-anchored DNA origami structures can be assembled into prescribed superstructures in a programmed manner. The reported DNA-based artificial system can mimic the dynamic assembly of membrane-associated protein clusters that play an essential role in deformation of cellular membranes.

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  • Direct Observation of G-Quadruplexes and their Folding Intermediates 査読

    A. Rajendran, Y. Li, M. Endo, H. Sugiyama

    DNA G-quadruplexes as new anticancer targets (R. De Vooght-Johnson Ed.), Future Science   38 - 54   2015年

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  • Folding RNA–Protein Complex into Designed Nanostructures 査読 国際誌

    T. Shibata, Y. Suzuki, H. Sugiyama, M. Endo, H. Saito

    Methods in Molecular Biology   1316   169 - 79   2015年

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  • Small molecule binding to a G-hairpin and a G-triplex: a new insight into anticancer drug design targeting G-rich regions 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Marie-Paule Teulade-Fichou, Jean-Louis Mergny, Hiroshi Sugiyama

    CHEMICAL COMMUNICATIONS   51 ( 44 )   9181 - 9184   2015年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    To gain new insights into G-quadruplex-drug interactions, we captured the solution-state structures of the complexes between a drug-like small molecule and a G-hairpin/G-triplex. Our results indicated that the ligand initially binds to the intermediates and induces step-wise folding into a quadruplex.

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  • Preparation of Chemically Modified RNA Origami Nanostructures 査読

    Masayuki Endo, Yosuke Takeuchi, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama

    CHEMISTRY-A EUROPEAN JOURNAL   20 ( 47 )   15330 - 15333   2014年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    In nucleic acid nanotechnology, designed RNA molecules are widely explored because of their usability originating from RNA's structural and functional diversity. Herein, a method to design and prepare RNA nanostructures by employing DNA origami strategy was developed. A single-stranded RNA scaffold and staple RNA strands were used for the formation of RNA nanostructures. After the annealing of the mixtures, 7-helix bundled RNA tile and 6-helix bundled RNA tube structures were observed as predesigned shapes. These nanostructures were easily functionalized by introducing chemical modification to the RNA scaffolds. The DNA origami method is extended and utilized to construct RNA nanostructures.

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  • Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials 査読

    Tomohiro Takenaka, Masayuki Endo, Yuki Suzuki, Yangyang Yang, Tomoko Emura, Kumi Hidaka, Takayuki Kato, Tomoko Miyata, Keiichi Namba, Hiroshi Sugiyama

    CHEMISTRY-A EUROPEAN JOURNAL   20 ( 46 )   14951 - 14954   2014年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high-speed AFM. The encapsulation of the DNA-modified AuNP within the NC was carried out by hybridization of a specific DNA strand (capture strand), and the release of the AuNP was examined by addition of toehold-containing complementary DNA strand (release strand). The release of the AuNP from the NC was achieved by the opening of the NC and subsequent strand displacement.

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  • Engineering RNA-Protein Complexes with Different Shapes for Imaging and Therapeutic Applications 査読

    Eriko Osada, Yuki Suzuki, Kumi Hidaka, Hirohisa Ohno, Hiroshi Sugiyama, Masayuki Endo, Hirohide Saito

    ACS NANO   8 ( 8 )   8130 - 8140   2014年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Molecular machines composed of RNA-protein (RNP) complexes may expand the fields of molecular robotics, nanomedicine, and synthetic biology. However, constructing and directly visualizing a functional RNP nanostructure to detect and control living cell function remains a challenge. Here we show that RNP nanostructures with modular functions can be designed and visualized at single-RNP resolution in real time The RNP structural images collected in solution through high-speed atomic force microscopy showed that a single RNP interaction induces a conformational change in the RNA scaffold, which supports the nanostructure formation designed. The specific RNP interaction also improved RNA nanostructure stability in a serum containing buffer. We developed and visualized functional RNPs (e g., to detect human cancer cells or knockdown target genes) by attaching a protein or RNA module to the same RNA scaffold of an optimal size. The synthetic RNP architecture may provide alternative materials to detect and control functions in target mammalian cells.

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  • A lock-and-key mechanism for the controllable fabrication of DNA origami structures 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Naohiko Shimada, Atsushi Maruyama, Hiroshi Sugiyama

    CHEMICAL COMMUNICATIONS   50 ( 63 )   8743 - 8746   2014年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Controllable fabrication of DNA origami structures was achieved using cationic comb-type copolymers (CCCs) as locks and polyvinyl sulphonic acid (PVS) as a key. A CCC binds to the phosphate backbone of either M13mp18/staples alone or both together and restricts origami folding, while PVS unlocks the CCC, restoring the formation of origami structures.

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  • Helical DNA Origami Tubular Structures with Various Sizes and Arrangements 査読

    Masayuki Endo, Seigi Yamamoto, Tomoko Emura, Kumi Hidaka, Nobuhiro Morone, John E. Heuser, Hiroshi Sugiyama

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   53 ( 29 )   7484 - 7490   2014年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    We developed a novel method to design various helical tubular structures using the DNA origami method. The size-controlled tubular structures which have 192, 256, and 320 base pairs for one turn of the tube were designed and prepared. We observed the formation of the expected short tubes and unexpected long ones. Detailed analyses of the surface patterns of the tubes showed that the short tubes had mainly a left-handed helical structure. The long tubes mainly formed a right-handed helical structure and extended to the directions of the double helical axes as structural isomers of the short tubes. The folding pathways of the tubes were estimated by analyzing the proportions of short and long tubes obtained at different annealing conditions. Depending on the number of base pairs involved in one turn of the tube, the population of left-/right-handed and short/long tubes changed. The bending stress caused by the stiffness of the bundled double helices and the non-natural helical pitch determine the structural variety of the tubes.

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  • Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures 査読

    Deepak Koirala, Prakash Shrestha, Tomoko Emura, Kumi Hidaka, Shankar Mandal, Masayuki Endo, Hiroshi Sugiyama, Hanbin Mao

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   53 ( 31 )   8137 - 8141   2014年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    While single-molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single-molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7-tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pm platelet-derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single-molecule sensing with improved throughput.

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  • Single-Molecule Imaging of Dynamic Motions of Biomolecules in DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy 査読

    Masayuki Endo, Hiroshi Sugiyama

    ACCOUNTS OF CHEMICAL RESEARCH   47 ( 6 )   1645 - 1653   2014年6月

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    記述言語:英語   出版者・発行元:AMER CHEMICAL SOC  

    CONSPECTUS: Direct imaging of molecular motions is one of the most fundamental issues for elucidating the physical properties of individual molecules and their reaction mechanisms. Atomic force microscopy (AFM) enables direct molecular imaging, especially for biomolecules in the physiological environment. Because AFM can visualize the molecules at nanometer-scale spatial resolution, a versatile observation scaffold is needed for the precise imaging of molecule interactions in the reactions.
    The emergence of DNA origami technology allows the precise placement of desired molecules in the designed nanostructures and enables molecules to be detected at the single-molecule level. In our study, the DNA origami system was applied to visualize the detailed motions of target molecules in reactions using high-speed AFM (HS-AFM), which enables the analysis of dynamic motions of biomolecules in a subsecond time resolution. In this system, biochemical properties such as the placement of various double-stranded DNAs (dsDNAs) containing unrestricted DNA sequences, modified nucleosides, and chemical functions can be incorporated. From a physical point of view, the tension and rotation of dsDNAs can be controlled by placement into the DNA nanostructures. From a topological point of view, the orientations of dsDNAs and various shapes of dsDNAs including Holliday junctions can be incorporated for studies on reaction mechanisms.
    In this Account, we describe the combination of the DNA origami system and HS-AFM for imaging various biochemical reactions including enzymatic reactions and DNA structural changes. To observe the behaviors and reactions of DNA methyltransferase and DNA repair enzymes, the substrate dsDNAs were incorporated into the cavity of the DNA frame, and the enzymes that bound to the target dsDNA were observed using HS-AFM. DNA recombination was also observed using the recombination substrates and Holliday junction intermediates placed in the DNA frame, and the direction of the reactions was controlled by introducing structural stress to the substrates. In addition, the movement of RNA polymerase and its reaction were visualized using a template dsDNA attached to the origami structure. To observe DNA structural changes, G-quadruplex formation and disruption, the switching behaviors of photoresponsive oligonucleotides, and B-Z transition were visualized using the DNA frame observation system. For the formation and disruption of G-quadruplex and double-helix DNA, the-two dsDNA(-) chains incorporated into the DNA frame could amplify the small structural change to the global structural change, which enabled the visualization of their association and dissociation by HS-AFM. The dynamic motion of the helical rotation induced by the B-Z transition was also directly imaged in the DNA frame. Furthermore, the stepwise motions of mobile DNA along the DNA track were visualized on the DNA origami surface. These target-orientated observation systems should contribute to the detailed analysis of biomolecule motions in real time and at molecular resolution.

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  • Single Molecule Visualization and Characterization of Sox2-Pax6 Complex Formation on a Regulatory DNA Element Using a DNA Origami Frame 査読

    Seigi Yamamoto, Debojyoti De, Kumi Hidaka, Kyeong Kyu Kim, Masayuki Endo, Hiroshi Sugiyama

    NANO LETTERS   14 ( 5 )   2286 - 2292   2014年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    We report the use of atomic force microscopy (AFM) to study Sox2-Pax6 complex formation on the regulatory DNA element at a single molecule level. Using an origami DNA scaffold containing two DNA strands with different levels of tensile force, we confirmed that DNA bending is necessary for Sox2 binding. We also demonstrated that two transcription factors bind cooperatively by observing the increased occupancy of Sox2-Pax6 on the DNA element compared to that of Sox2 alone.

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  • Direct and Single-Molecule Visualization of the Solution-State Structures of G-Hairpin and G-Triplex Intermediates 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   53 ( 16 )   4107 - 4112   2014年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    We present the direct and single-molecule visualization of the in-pathway intermediates of the G-quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high-speed atomic force microscopy (HS-AFM) for direct visualization, we captured images of the unprecedented solution-state structures of a tetramolecular antiparallel and (3+1)-type G-quadruplex intermediates, such as G-hairpin and G-triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid-state, single-molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G-quadruplexes.

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  • Dynamic Assembly/Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface 査読

    Yuki Suzuki, Masayuki Endo, Yangyang Yang, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   136 ( 5 )   1714 - 1717   2014年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Here, we report the direct visualization of the assembly/disassembly processes of photoresponsive DNA origami nanostructures which can be placed on a lipid bilayer surface. The observation relies on controlled interactions between the bilayer components and cholesterol moieties introduced to the hexagonal origami structures, one of whose outer edges carries Azo-ODNs. The bilayer-placed hexagonal dimer was disassembled into monomer units by UV irradiation, and reversibly assembled again during visible light irradiation. These dynamic processes were directly monitored with highspeed atomic force microscopy. The successful application of our approach should facilitate studies of interactive and functional behaviors of various DNA nanostructures.

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  • State-of-the-Art High-Speed Atomic Force Microscopy for Investigation of Single-Molecular Dynamics of Proteins 査読

    Arivazhagan Rajendran, Masayuki Endo, Hiroshi Sugiyama

    CHEMICAL REVIEWS   114 ( 2 )   1493 - 1520   2014年1月

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    記述言語:英語   出版者・発行元:AMER CHEMICAL SOC  

    DOI: 10.1021/cr300253x

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  • DNA Origami Based Visualization System for Studying Site-Specific Recombination Events 査読

    Yuki Suzuki, Masayuki Endo, Yousuke Katsuda, Keiyu Ou, Kumi Hidaka, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   136 ( 1 )   211 - 218   2014年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Site-specific recombination involves reciprocal exchange between defined DNA sites. The reaction initiates from the formation of a recombinase-DNA synaptic complex, in which two recombination sites arrange in an appropriate configuration. However, there is incomplete information about how the topological state of the substrate influences the synapsis and outcome of the reaction. Here, we show that Cremediated recombination can be regulated by controlling the orientation and topology of the loxP substrate in a DNA frame nanoscaffold. High-speed atomic force microscopy analyses revealed that the loxP-containing substrate strands in the antiparallel orientation can be recombined only through formation of synaptic complexes. By tethering Holliday junction (HJ) intermediates to DNA frames in different connection patterns and using them as a starting substrate, we found that the topological state of the HJ intermediates dictates the outcome of the resolution. Our approach should provide a new platform for structural-functional studies of various DNA targeting enzymes, especially which require formation of synaptic complexes.

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  • DNAオリガミによる生体分子の動的な観察システム 査読

    遠藤 政幸, 杉山 弘

    現代化学   ( 508 )   26 - 31   2014年

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  • G-quadruplex-binding ligand-induced DNA synapsis inside a DNA origami frame 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Phong Lan Thao Tran, Marie-Paule Teulade-Fichou, Jean-Louis Mergny, Hiroshi Sugiyama

    RSC ADVANCES   4 ( 12 )   6346 - 6355   2014年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Among the approaches for DNA-based drug targeting, G-quadruplex-binding ligands are of particular interest because of the high abundance of G-rich sequences in regions such as human chromosomal telomeres and promoters of several proto-oncogenes. A number of quadruplex-ligands have been reported, but their functions at single-molecule level have not been explored using direct and real-time methods. Here, we report on the direct observation of the formation of a four-stranded G-quadruplex induced by bisquinolinium pyridine dicarboxamide with a linker containing biotin at one end. We fabricated a DNA origami frame with incorporated duplex DNAs that contained 3-6 G-G mismatches in the middle. In the absence of ligand, the duplex DNAs of interest had no interaction, as visualized by their parallel-shape in high-speed atomic force microscopy (HS-AFM) images. Presence of ligand induced the formation of G-quadruplex structure, which was characterized by an X-shape. Addition of streptavidin to the ligand-induced quadruplex caused the protein to localize in the middle of the X-shape, indicating that the ligand is bound to the quadruplex. A sequence of real-time images of the ligand-induced formation of a quadruplex and its reverse conformational switching by removing the ligand was captured by HS-AFM. Unprecedented intermediate-like states were recorded in our real-time analysis.

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  • Direct observation of the dual-switching behaviors corresponding to the state transition in a DNA nanoframe 査読

    Yangyang Yang, Masayuki Endo, Yuki Suzuki, Kumi Hidaka, Hiroshi Sugiyama

    CHEMICAL COMMUNICATIONS   50 ( 32 )   4211 - 4213   2014年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    To create a nanoscale dual switch, two responsive DNA motifs, azobenzene-modified DNAs and G-telomeric repeat sequences, were introduced together into the nanoframe system. The dual-switching behaviors controlled by photoirradiation and K+ were successfully visualized in real time by high-speed atomic force microscopy.

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  • AFM analysis of changes in nucleosome wrapping induced by DNA epigenetic modification 査読

    Seiichiro Kizaki, Yuki Suzuki, Tomohiro Takenaka, Masayuki Endo, Hiroshi Sugiyama

    BIOMATERIALS SCIENCE   2 ( 10 )   1399 - 1403   2014年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    The wrapping and unwrapping of the nucleosome, which is a fundamental packing unit of chromatin, are tied to the regulation of gene expression. The accessibility of DNA within nucleosomes is controlled not only by chromatin-remodeling molecules, but also by chemical modifications of histones and DNA. Understanding the structural changes of a nucleosome during epigenetic modifications is a key to unravel the mechanisms of gene regulation. Here, we reconstituted nucleosomes using methylcytosine- or hydroxymethylcytosine-substituted DNA, and analyzed their morphological features by atomic force microscopy (AFM). Our results indicate that cytosine methylation induces overwrapping of the DNA around the histone octamer, whereas cytosine hydroxymethylation has a lesser effect on the overwrapping of the DNA. These results suggest that two types of DNA modification yield different wrapping states of nucleosomes, which may contribute to the compaction and relaxation of the chromatin structure.

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  • DNA オリガミ構造体を利用した1分子イメージングシステムの開発 査読

    遠藤 政幸, 杉山 弘

    新材料・新素材シリーズ『超分子材料の設計と応用展開』、シーエムシー出版   101 - 113   2014年

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  • DNA ナノ構造体を利用したDNA 構造変化の1分子イメージング 査読

    遠藤 政幸, 杉山 弘

    DOJIN BIOSCIENCE SERIES『1分子生物学』、化学同人   274 - 276   2014年

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  • Direct analysis of Holliday junction resolving enzyme in a DNA origami nanostructure 査読

    Yuki Suzuki, Masayuki Endo, Cristina Canas, Silvia Ayora, Juan C. Alonso, Hiroshi Sugiyama, Kunio Takeyasu

    NUCLEIC ACIDS RESEARCH   42 ( 11 )   7421 - 7428   2014年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    Holliday junction (HJ) resolution is a fundamental step for completion of homologous recombination. HJ resolving enzymes (resolvases) distort the junction structure upon binding and prior cleavage, raising the possibility that the reactivity of the enzyme can be affected by a particular geometry and topology at the junction. Here, we employed a DNA origami nano-scaffold in which each arm of a HJ was tethered through the base-pair hybridization, allowing us to make the junction core either flexible or inflexible by adjusting the length of the DNA arms. Both flexible and inflexible junctions bound to Bacillus subtilis RecU HJ resolvase, while only the flexible junction was efficiently resolved into two duplexes by this enzyme. This result indicates the importance of the structural malleability of the junction core for the reaction to proceed. Moreover, cleavage preferences of RecU-mediated reaction were addressed by analyzing morphology of the reaction products.

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  • Regulation of B-Z Conformational Transition and Complex Formation with a Z-Form Binding Protein by Introduction of Constraint to Double-Stranded DNA by using a DNA Nanoscaffold 査読

    Masayuki Endo, Masahiro Inoue, Yuki Suzuki, Chigusa Masui, Hironobu Morinaga, Kumi Hidaka, Hiroshi Sugiyama

    CHEMISTRY-A EUROPEAN JOURNAL   19 ( 50 )   16887 - 16890   2013年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    DOI: 10.1002/chem.201303830

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  • HIV-1 Nucleocapsid Proteins as Molecular Chaperones for Tetramolecular Antiparallel G-Quadruplex Formation 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Phong Lan Thao Tran, Jean-Louis Mergny, Robert J. Gorelick, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   135 ( 49 )   18575 - 18585   2013年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    HIV-1 nucleocapsid proteins (NCps) facilitate remodeling of nucleic acids to fold thermodynamically stable conformations, and thus called nucleic acid chaperones. To date only little is known on the stoichiometry, NCp-NCp interactions, chaperone activity on G-quadruplex formation, and so on. We report here the direct and real-time analysis on such properties of proteolytic intermediate NCp15 and mature NCp7 using DNA origami. The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. We anticipate that this pioneering study will strengthen our understanding on the chaperone activity of HIV-1 proteins which in turn will be helpful for the drug design based on G-quadruplex and also for the development of drugs against AIDS.

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  • Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Phong Lan Thao Tran, Jean-Louis Mergny, Hiroshi Sugiyama

    NUCLEIC ACIDS RESEARCH   41 ( 18 )   8738 - 8747   2013年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    Guanine-rich oligonucleotides often show a strong tendency to form supramolecular architecture, the so-called G-quadruplex structure. Because of the biological significance, it is now considered to be one of the most important conformations of DNA. Here, we describe the direct visualization and single-molecule analysis of the formation of a tetramolecular G-quadruplex in KCl solution. The conformational changes were carried out by incorporating two duplex DNAs, with G-G mismatch repeats in the middle, inside a DNA origami frame and monitoring the topology change of the strands. In the absence of KCl, incorporated duplexes had no interaction and laid parallel to each other. Addition of KCl induced the formation of a G-quadruplex structure by stably binding the duplexes to each other in the middle. Such a quadruplex formation allowed the DNA synapsis without disturbing the duplex regions of the participating sequences, and resulted in an X-shaped structure that was monitored by atomic force microscopy. Further, the G-quadruplex formation in KCl solution and its disruption in KCl-free buffer were analyzed in real-time. The orientation of the G-quadruplex is often difficult to control and investigate using traditional biochemical methods. However, our method using DNA origami could successfully control the strand orientations, topology and stoichiometry of the G-quadruplex.

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  • DNA nanomachines that move on the DNA origami structures

    Masayuki Endo, Hiroshi Sugiyama

    Kobunshi   62 ( 3 )   129 - 131   2013年3月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DNA is one of the most promising bio macromolecules for the design and construction of molecular machines. Various dynamic motions of DNA molecules can be operated by the strand displacement using the sequence programmability and the precise self-assembly. In this article, we give an overview of the recent DNA nanomachines that are working on the DNA origami structure. We describe the details of three types of DNA nanomachines including DNA walker, DNA spider, and DNA motor. The construction, operation, and analysis of the movements of the DNA nanomachines are also described. Copyright ©2013 The Society of Polymer Science, Japan.

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  • Direct and Real-Time Observation of Rotary Movement of a DNA Nanomechanical Device 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama

    Journal of the American Chemical Society   135 ( 3 )   1117 - 1123   2013年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    Analogous to the biologically abundant protein-based linear molecular machines that translocate along their target surface, we have recently constructed the DNA-based synthetic molecular motors that effect linear movement or navigate a network of tracks on a DNA origami substrate. However, a DNA-based molecular machine with rotary function, analogous to rotary proteins, is still unexplored. Here, we report the construction of a rotary motor based on the B-Z conformational transition of DNA and the direct and real-time observation of its function within a frame-shaped DNA origami. The motor can be switched off by introducing conditions that stabilize B-DNA, while it can be fueled by adding Z-DNA-promoting high-saline buffer. When MgCl2 was used as external stimulus, 70% of the motors rotated, while 76% of the stators/controls exhibited no rotation. Such a motor system could be successfully applied to perform multiple actions aimed for our benefit. Moreover, for the first time we have directly observed the B-Z conformational transition of DNA in real-time, which shed light on the fundamental understanding of DNA conformations. © 2012 American Chemical Society.

    DOI: 10.1021/ja310454k

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  • Control of the two-dimensional crystallization of DNA origami with various loop arrangements 査読

    Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama

    CHEMICAL COMMUNICATIONS   49 ( 7 )   686 - 688   2013年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    We have developed a new strategy to control the two-dimensional (2D) crystallization of DNA origami by introducing loops on the surface and aligning them in various orientations. Among the orientations tested, vertically connected loops successfully produced the 2D crystal lattice on a micrometer scale, while all other orientations failed.

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  • DNAオリガミ構造体と高速原子間力顕微鏡を用いた1分子観察系の構築 査読

    遠藤 政幸, 杉山 弘

    生物物理   53 ( 3 )   153 - 157   2013年

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  • DNAナノ構造上を動くDNA分子マシーン 査読

    遠藤 政幸, 杉山 弘

    高分子   62 ( 3 )   129 - 131   2013年

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  • DNAオリガミ法を用いた次世代ナノシステム 査読

    遠藤 政幸, 杉山 弘

    化学工業   65 ( 1 )   42 - 48   2013年

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  • DNA origami technology for biomaterials applications 査読

    Masayuki Endo, Yangyang Yang, Hiroshi Sugiyama

    BIOMATERIALS SCIENCE   1 ( 4 )   347 - 360   2013年

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    記述言語:英語   出版者・発行元:ROYAL SOC CHEMISTRY  

    DNA origami is an emerging technology for designing and constructing defined multidimensional nanostructures. This technology is now expanding to materials science. This article introduces the basics of DNA origami, the design of various two-dimensional and three-dimensional DNA origami structures, and the programmed assembly of origami structures. DNA origami has unique properties, such as an addressable surface, which enables selective functionalization with biomolecules and nanomaterials. The origami can also be combined with top-down nanotechnology, such as placement on a fabricated substrate. The technology is also applied to single-molecule imaging and analysis systems constructed on designed DNA origami structures. Furthermore, DNA mechanical nanodevices working on DNA origami have been realized, and cell-oriented applications are now in progress. DNA origami technology has practical potential in various research fields.

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  • G-quadruplex nanostructures probed at the single molecular level by force-based methods 査読

    S. Dhakal, H. Mao, A. Rajendran, M. Endo, H. Sugiyama

    Guanine quartets: Structure and application, Royal Society of Chemistry   73 - 85   2013年

  • RNA-templated DNA origami structures 査読

    Masayuki Endo, Seigi Yamamoto, Koichi Tatsumi, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama

    CHEMICAL COMMUNICATIONS   49 ( 28 )   2879 - 2881   2013年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Using the RNA transcript as a template, RNA-templated DNA origami structures were constructed by annealing with designed DNA staple strands. RNA-templated DNA origami structures were folded to form seven-helix bundled rectangular structures and six-helix bundled tubular structures. The chemically modified RNA-DNA hybrid origami structures were prepared by using RNA templates containing modified uracils.

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  • Photo-Controllable DNA Origami Nanostructures Assembling into Predesigned Multiorientational Patterns 査読

    Yangyang Yang, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   134 ( 51 )   20645 - 20653   2012年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    We demonstrate a novel strategy for constructing multidirectional programmed 2D DNA nanostructures in various unique patterns by introducing photoresponsive oligonucleotides (Azo-ODNs) into hexagonal DNA origami structures. We examined regulation of assembly and disassembly of DNA nanostructures reversibly by different photoirradiation conditions in a programmed manner. Azo-ODNs were incorporated to the hexagonal DNA origami structures, which were then employed as self-assembly units for building up nanosized architectures in regulated arrangements. By adjusting the numbers and the positions of Azo-ODNs in the hexagonal units, the specific nanostructures with face controlling can be achieved, resulting in construction of ring-shaped nanostructures. By combining DNA origami strategy with photoregulating system, remote controlling of assembly and disassembly of DNA nanostructures has been accomplished simply by photo irradiation.

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  • Direct Visualization of the Movement of a Single T7 RNA Polymerase and Transcription on a DNA Nanostructure 査読

    Masayuki Endo, Koichi Tatsumi, Kosuke Terushima, Yousuke Katsuda, Kumi Hidaka, Yoshie Harada, Hiroshi Sugiyama

    Angewandte Chemie International Edition   51 ( 35 )   8778 - 8782   2012年8月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/anie.201201890

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  • Design and Development of Nanosized DNA Assemblies in Polypod-like Structures as Efficient Vehicles for Immunostimulatory CpG Motifs to Immune Cells 査読

    Kohta Mohri, Makiya Nishikawa, Natsuki Takahashi, Tomoki Shiomi, Nao Matsuoka, Kohei Ogawa, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama, Yuki Takahashi, Yoshinobu Takakura

    ACS NANO   6 ( 7 )   5931 - 5940   2012年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    The immunostimulatory activity of phosphodiester DNA containing unmethylated cytosine-phosphate-guanine (CpG) dinucleotides, or CpG motifs, was significantly increased by the formation of Y-, X-, or dendrimer-like multibranched shape. These results suggest the possibility that the activity of CpG DNA is a function of the structural properties of branched DNA assemblies. To elucidate the relationship between them, we have designed and developed nanosized DNA assemblies in polypod-like structures (polypod-like structured DNA, or polypodna for short) using oligodeoxynudeotides (ODNs) containing CpG motifs and investigated their structural and immunological properties. Those assemblies consisting of three (tripodna) to eight (odapodna) ODNs were successfully obtained, but one consisting of 12 ODNs was not when 36-mer ODNs were annealed under physiological sodium chloride concentration. High-speed atomic force microscopy revealed that these assemblies were in polypod-like structures. The apparent size of the products was about 10 nm in diameter, and there was an increasing trend with an increase in ODN length or with the pod number. Circular dichroism spectral data showed that DNA in polypodna preparations were in the B-form. The melting temperature of polypodna decreased with increasing pod number. Each polypodna induced the secretion of tumor necrosis factor-alpha and interleukin-6 from macrophage-like RAW264.7 cells, with the greatest induction by those with hexa- and octapodna. Increasing the pod number increased the uptake by RAW264.7 cells but reduced the stability in serum. These results indicate that CpG DNA-containing polypodna preparations with six or more pods are a promising nanosized device with biodegradability and high immunostimulatory activity.

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  • Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures 査読

    Eiji Nakata, Fong Fong Liew, Chisana Uwatoko, Shigeki Kiyonaka, Yasuo Mori, Yousuke Katsuda, Masayuki Endo, Hiroshi Sugiyama, Takashi Morii

    Angewandte Chemie International Edition   51 ( 10 )   2421 - 2424   2012年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/anie.201108199

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  • A DNA-based molecular motor that can navigate a network of tracks 査読

    Shelley F. J. Wickham, Jonathan Bath, Yousuke Katsuda, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama, Andrew J. Turberfield

    NATURE NANOTECHNOLOGY   7 ( 3 )   169 - 173   2012年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    Synthetic molecular motors can be fuelled by the hydrolysis(1-4) or hybridization(5-11) of DNA. Such motors can move autonomously(1-4,7,11) and programmably(12), and long-range transport has been observed on linear tracks(13,14). It has also been shown that DNA systems can compute(8,15-18). Here, we report a synthetic DNA-based system that integrates long-range transport and information processing. We show that the path of a motor through a network of tracks containing four possible routes can be programmed using instructions that are added externally or carried by the motor itself. When external control is used we find that 87% of the motors follow the correct path, and when internal control is used 71% of the motors follow the correct path. Programmable motion will allow the development of computing networks, molecular systems that can sort and process cargoes according to instructions that they carry, and assembly lines(19,20) that can be reconfigured dynamically in response to changing demands.

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  • Sequence-Selective Single-Molecule Alkylation with a Pyrrole-Imidazole Polyamide Visualized in a DNA Nanoscaffold 査読

    Tomofumi Yoshidome, Masayuki Endo, Gengo Kashiwazaki, Kumi Hidaka, Toshikazu Bando, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   134 ( 10 )   4654 - 4660   2012年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    We demonstrate a novel strategy for visualizing sequence-selective alkylation of target double-stranded DNA (dsDNA) using a synthetic pyrrole imidazole (PI) polyamide in a designed DNA origami scaffold. Doubly functionalized PI polyamide was designed by introduction of an alkylating agent 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz [e] indole (seco-CBI) and biotin for sequence-selective alkylation at the target sequence and subsequent streptavidin labeling, respectively. Selective alkylation of the target site in the substrate DNA was observed by analysis using sequencing gel electrophoresis. For the single-molecule observation of the alkylation by functionalized PI polyamide using atomic force microscopy (AFM), the target position in the dsDNA (similar to 200 base pairs) was alkylated and then visualized by labeling with streptavidin. Newly designed DNA origami scaffold named "five-well DNA frame" carrying five different dsDNA sequences in its cavities was used for the detailed analysis of the sequence-selectivity and alkylation. The 64-mer dsDNAs were introduced to five individual wells, in which target sequence AGTXCCA/TGGYACT (XY = AT, TA, GC, CG) was employed as fully matched (X = G) and one-base mismatched (X = A, T, C) sequences. The fully matched sequence was alkylated with 88% selectivity over other mismatched sequences. In addition, the PI polyamide failed to attach to the target sequence lacking the alkylation site after washing and streptavidin treatment. Therefore, the PI polyamide discriminated the one mismatched nucleotide at the single-molecule level, and alkylation anchored the PI polyamide to the target dsDNA.

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  • Transcription Regulation System Mediated by Mechanical Operation of a DNA Nanostructure 査読

    Masayuki Endo, Ryoji Miyazaki, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   134 ( 6 )   2852 - 2855   2012年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    A transcription regulation system initiated by DNA nanostructure changes was designed and constructed. Using the toehold system, specific DNA strands induced the opening of the tubular structure. A transcription product from the purified tube-attached dsDNA template was observed by addition of DNA strands that were specific for opening the tubular structure.

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  • Single-Molecule Analysis Using DNA Origami 査読

    Arivazhagan Rajendran, Masayuki Endo, Hiroshi Sugiyama

    Angewandte Chemie International Edition   51 ( 4 )   874 - 890   2012年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    During the last two decades, scientists have developed various methods that allow the detection and manipulation of single molecules, which have also been called "in singulo" approaches. Fundamental understanding of biochemical reactions, folding of biomolecules, and the screening of drugs were achieved by using these methods. Single-molecule analysis was also performed in the field of DNA nanotechnology, mainly by using atomic force microscopy. However, until recently, the approaches used commonly in nanotechnology adopted structures with a dimension of 10-20 nm, which is not suitable for many applications. The recent development of scaffolded DNA origami by Rothemund made it possible for the construction of larger defined assemblies. One of the most salient features of the origami method is the precise addressability of the structures formed: Each staple can serve as an attachment point for different kinds of nanoobjects. Thus, the method is suitable for the precise positioning of various functionalities and for the single-molecule analysis of many chemical and biochemical processes. Here we summarize recent progress in the area of single-molecule analysis using DNA origami and discuss the future directions of this research. Origami for singles: Concurrent to the development of single-molecule analytical techniques has been rapid progress in nanobiotechnology and efforts at building lab-on-a-chip systems for high-throughput analytical biochemistry. The scaffolded DNA origami method is suitable for the construction of defined larger assemblies that can act as a platform for the positioning of various functionalities and their single-molecule analysis (see picture). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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  • ナノ空間でDNA 1 分子の動作を捉える ―極小の分子システムで操るナノマシン 査読

    遠藤 政幸, 杉山 弘

    化学   67 ( 5 )   32 - 37   2012年

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    記述言語:日本語   出版者・発行元:化学同人  

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  • Dna origami: Synthesis and self-assembly 査読

    Arivazhagan Rajendran, Masayuki Endo, Hiroshi Sugiyama

    Current Protocols in Nucleic Acid Chemistry   1 ( 48 )   12.9.18   2012年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Blackwell Publishing Inc.  

    DNA origami is an emerging technology for designing defined two- and threedimensional (2D and 3D) DNA nanostructures. Here, we report an introductory practical guide with step-by-step experimental details for the design and synthesis of origami structures, and their size expansion in 1D and 2D space by means of self-assembly. © 2012 by John Wiley &amp
    Sons, Inc.

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  • STRUCTURAL AND FUNCTIONAL ANALYSIS OF PROTEINS BY HIGH-SPEED ATOMIC FORCE MICROSCOPY 査読

    Arivazhagan Rajendran, Masayuki Endo, Hiroshi Sugiyama

    STRUCTURAL AND MECHANISTIC ENZYMOLOGY: BRINGING TOGETHER EXPERIMENTS AND COMPUTING   87   5 - 55   2012年

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    記述言語:英語   掲載種別:論文集(書籍)内論文   出版者・発行元:ELSEVIER ACADEMIC PRESS INC  

    Proteins are dynamic in nature, work at the single-molecule level, and facilitate several biological functions. The structure of a protein is closely associated with its function; thus, a large number of structural analyses of proteins were performed using techniques such as X-ray crystallography and NMR. Although these methods provide structural information, they often fail because of difficulties in crystallizing the proteins that are complexed with other biomolecules. Moreover, these techniques do not allow the observation of structural changes in the active form of the molecule. Single-molecule fluorescence techniques have been used for the direct observation of protein functions; however, they only reveal the dynamics of individual fluorescent spots, rather than the structural changes that occur over the entire protein. The recent development of high-speed atomic force microscopy (HS-AFM) overcame this problem and allowed the observation of the structural dynamics of proteins and other biomacromolecules directly and in real time. In this chapter, we describe the HS-AFM analysis of the dynamic molecular processes in photoactivated bacteriorhodopsin, membrane-mediated protein-protein interactions, ATP-induced conformational changes in purinergic receptors, the two-dimensional crystal structure of streptavidin, the nature of FtsZ polymers, the role of ClpX in the regulation of FtsZ polymer dynamics, the function of restriction enzymes, the action of motor proteins, the movement of TiCel7A on crystalline cellulose substrates, and the antimicrobial peptide activity on individual bacterial cells.

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  • ChemInform Abstract: Single-Molecule Analysis Using DNA Origami 査読

    Rajendran Arivazhagan, Endo Masayuki, Sugiyama Hiroshi

    ChemInform   43 ( 19 )   no - no   2012年

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    出版者・発行元:Wiley Blackwell (John Wiley &amp; Sons)  

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  • DNAオリガミ構造体と1分子観察への応用 査読

    遠藤 政幸, 杉山 弘

    化学工業   63 ( 2 )   36 - 41   2012年

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  • Single-Molecule Visualization of the Hybridization and Dissociation of Photoresponsive Oligonucleotides and Their Reversible Switching Behavior in a DNA Nanostructure 査読

    Masayuki Endo, Yangyang Yang, Yuki Suzuki, Kumi Hidaka, Hiroshi Sugiyama

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   51 ( 42 )   10518 - 10522   2012年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

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  • DNAオリガミによる1分子観察系の構築 査読

    遠藤 政幸, 杉山 弘

    『疾患克服を目指したケミカルバイオロジー』実験医学2012年増刊号   30 ( 7 )   180 - 186   2012年

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  • DNAオリガミによるメゾスケール多次元構造の構築とナノ空間での機能発現 査読

    遠藤 政幸, 杉山 弘

    有機合成化学協会誌   69 ( 12 )   1352 - 1362   2011年12月

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  • Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-Assembly 査読

    Arivazhagan Rajendran, Masayuki Endo, Yousuke Katsuda, Kumi Hidaka, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   133 ( 37 )   14488 - 14491   2011年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Heat tolerance of DNA origami structures has been improved about 30 degrees C by photo-cross-linking of 8-methoxypsoralen. To demonstrate one of its applications, the cross-linked origami were used for higher-temperature self-assembly, which markedly increased the yield of the assembled product when compared to the self-assembly of non-cross-linked origami at lower-temperature. By contrast, at higher-temperature annealing, native non-cross-linked tiles did not self-assemble to yield the desired product; however, they formed a nonspecific broken structure.

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  • Direct observation of stepwise movement of a synthetic molecular transporter 査読

    Shelley F. J. Wickham, Masayuki Endo, Yousuke Katsuda, Kumi Hidaka, Jonathan Bath, Hiroshi Sugiyama, Andrew J. Turberfield

    NATURE NANOTECHNOLOGY   6 ( 3 )   166 - 169   2011年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    Controlled motion at the nanoscale can be achieved by using Watson-Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor(1-12) and fuel(13-15), all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold(16), and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor. Real-time atomic force microscopy allows direct observation of individual steps of a single motor, revealing mechanistic details of its operation. This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.

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  • Programmed Two-Dimensional Self-Assembly of Multiple DNA Origami Jigsaw Pieces 査読

    Arivazhagan Rajendran, Masayuki Endo, Yousuke Katsuda, Kumi Hidaka, Hiroshi Sugiyama

    ACS NANO   5 ( 1 )   665 - 671   2011年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    We demonstrate a novel strategy of self-assembly to scale up origami structures in two- dimensional (2D) space using multiple origami structures, named "2D DNA jigsaw pieces", with a specially designed shape. For execution of 2D self-assembly along the helical axis (horizontal direction), sequence-programmed tenon and mortise were introduced to promote selective connections via pi-stacking interaction, sequence-complementarity, and shape-complementarity. For 2D self-assembly along the helical side (vertical direction), the jigsaw shape-complementarity in the top and bottom edges and the sequence-complementarity Of single?: stranded overhangs were used. We designed and prepared nine different jigsaw pieces and tried to,obtain a 3 X. 3 assembly. The proof of concept was obtained by performing the assembly in four different ways. Among them, the stepwise self assembly from the three vertical trimer assemblies gave the target 2D assembly with similar to 35% yield. Finally, the surfaces of jigsaw pieces were decorated with hairpin DNAs to display the letters of the alphabet;, and the self-assembled 2D structure displayed the word "DNA JIG SAW" in nanoscale. The method can be expanded to create self-assembled modules carrying various functional molecules for practical applications.

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  • Programmed placement of gold nanoparticles onto a slit-type DNA origami scaffold 査読

    Masayuki Endo, Yangyang Yang, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama

    CHEMICAL COMMUNICATIONS   47 ( 38 )   10743 - 10745   2011年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    A novel DNA scaffold, called a DNA slit, was designed for the programmed positioning of Au nanoparticles (AuNPs), and various patterns of thiolated DNA slits were constructed. AuNPs were correctly placed at the predesigned positions in the thiolated DNA slits, indicating that the thiolated staples and the slit cavities guide the correct assembly of AuNPs.

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  • Recent progress in DNA origami unit 12.8 technology 査読

    Masayuki Endo, Hiroshi Sugiyama

    Current Protocols in Nucleic Acid Chemistry   45 ( 45 )   12.8.1 - 12.8.19   2011年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Blackwell Publishing Inc.  

    DNA origami is an emerging technology for designing defined two-dimensional DNA nanostructures. In this review, we focus on and describe several types of DNA origami-related studies, as follows: (1) programmed DNA origami assembly, (2) DNA origami-templated molecular assembly, (3) design and construction of various three-dimensional DNA origami structures, (4) programmed functionalization of DNA origami and combination with top-down nanotechnology, (5) single molecular observation on a designed DNA origami, and (6) DNA nanomachines working on a DNA origami. © 2011 John Wiley &amp
    Sons, Inc.

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  • DNAオリガミ法による多次元構造体の構築と高次機能化 査読

    遠藤 政幸, 杉山 弘

    未来材料   11 ( 5 )   2 - 10   2011年

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    記述言語:日本語   出版者・発行元:エヌ・ティー・エス  

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  • DNAナノ空間での生体分子のコントロールと直接的な観察 査読

    遠藤 政幸, 杉山 弘

    パリティ   26 ( 1 )   72 - 74   2011年

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  • Direct AFM observation of an opening event of a DNA cuboid constructed via a prism structure 査読

    Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama

    ORGANIC & BIOMOLECULAR CHEMISTRY   9 ( 7 )   2075 - 2077   2011年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    A cuboid structure was constructed using a DNA origami design based on a square prism structure. The structure was characterized by atomic force microscopy (AFM) and dynamic light scattering. The real-time opening event of the cuboid was directly observed by high-speed AFM.

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  • Two-dimensional DNA origami assemblies using a four-way connector 査読

    Masayuki Endo, Tsutomu Sugita, Arivazhagan Rajendran, Yousuke Katsuda, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama

    CHEMICAL COMMUNICATIONS   47 ( 11 )   3213 - 3215   2011年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Two-dimensional self-assembly of DNA origami structures was carried out using a connector that has connection sites at all four edges. By utilizing this four-way connector, five and eight origami monomers were assembled to form a cruciate and a hollow square structure, respectively.

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  • Visualization of Dynamic Conformational Switching of the G-Quadruplex in a DNA Nanostructure 査読

    Yuta Sannohe, Masayuki Endo, Yousuke Katsuda, Kumi Hidaka, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   132 ( 46 )   16311 - 16313   2010年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    We herein report the real-time observation of G-quadruplex formation by monitoring the G-quadruplex-induced global change of two duplexes incorporated in a DNA nanoscaffold. The introduced G-rich strands formed an interstrand (3 + 1) G-quadruplex structure in the presence of K(+), and the formed four-stranded structure was disrupted by removal of K. These conformational changes were visualized in a nanoscaffold in real-time with fast-scanning atomic force microscopy.

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  • Regulation of DNA Methylation Using Different Tensions of Double Strands Constructed in a Defined DNA Nanostructure 査読

    Masayuki Endo, Yousuke Katsuda, Kumi Hidaka, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   132 ( 5 )   1592 - 1597   2010年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    A novel strategy for regulation of an enzymatic DNA modification reaction has been developed by employing a designed nanoscale DNA scaffold. DNA modification using enzymes often requires bending of specific DNA strands to facilitate the reaction. The DNA methylation enzyme EcoRI methyltransferase (M.EcoRI) bends double helix DNA by 55 degrees-59 degrees during the reaction with flipping out of the second adenine in the GAATTC sequence as the methyl transfer reaction proceeds. In this study, two different double helical tensions, tense and relaxed states of double helices, were created to control the methyl transfer reaction of M.EcoRI and examine the structural effect on the methylation. We designed and prepared a two-dimensional (2D) DNA scaffold named the "DNA frame" using the DNA origami method that accommodates two different lengths of the double-strand DNA fragments, a tense 64mer double strand and a relaxed 74mer double strand. Fast-scanning atomic force microscope (AFM) imaging revealed the different dynamic movement of the double-strand DNAs and complexes of M.EcoRI with 64mer and 74mer double-strand DNAs. After treatment of the double strands in the DNA frame with M.EcoRI and the subsequent digestion with restriction enzyme EcoRI (R.EcoRI), AFM analysis revealed that the 74mer double-strand DNA was not effectively cleaved compared with the 64mer double-strand DNA, indicating that the methylation preferentially occurred in the relaxed 74mer double-strand DNA compared with that in the tense 64mer double strand. Biochemical analysis of the methylation and specific digestion using a real-time PCR also supported the above results. These results indicate the importance of the structural flexibility for bending of the duplex DNA during the methyl transfer reaction with M.EcoRI. Therefore, the DNA methylation can be regulated using the structurally controlled double-strand DNAs constructed in the DNA frame nanostructure.

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  • DNAとジグソーパズル 査読

    遠藤 政幸, 杉山 弘

    化学   65 ( 6 )   49 - 52   2010年1月

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  • DNAナノ構造の設計・構築とその応用 査読

    遠藤 政幸, 杉山 弘

    BIO INDUSTRY   27 ( 10 )   48 - 54   2010年

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    記述言語:日本語   出版者・発行元:シーエムシー出版  

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  • A Versatile DNA Nanochip for Direct Analysis of DNA Base-Excision Repair 査読

    Masayuki Endo, Yousuke Katsuda, Kumi Hidaka, Hiroshi Sugiyama

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   49 ( 49 )   9412 - 9416   2010年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

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  • Programmed-Assembly System Using DNA Jigsaw Pieces 査読

    Masayuki Endo, Tsutomu Sugita, Yousuke Katsuda, Kumi Hidaka, Hiroshi Sugiyama

    CHEMISTRY-A EUROPEAN JOURNAL   16 ( 18 )   5362 - 5368   2010年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    A novel method for assembling multiple DNA origami structures has been developed by using designed 2D DNA origami rectangles, so-called "DNA jigsaw pieces" that have sequence-programmed connectors. Shape and sequence complementarity were introduced to the concavity and convex connectors in the DNA rectangles for selective connection with the help of nonselective pi-stacking interactions between the side edges of the DNA jigsaw piece structures. Single DNA jigsaw piece units were assembled into unidirectional nanostructures with the correct alignment and uniform orientation. Three and five different DNA jigsaw pieces were assembled into pre-designed and ordered nanostructures in a programmed fashion. Finally, three-, four-, and five-letter words have been displayed by using this programmed DNA jigsaw piece system.

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  • DNA Prism Structures Constructed by Folding of Multiple Rectangular Arms 査読

    Masayuki Endo, Kumi Hidaka, Takayuki Kato, Keiichi Namba, Hiroshi Sugiyama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   131 ( 43 )   15570 - +   2009年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Novel multiarm DNA structures were designed using two-dimensional DNA origami scaffolds, and these structures were folded into hollow three-dimensional. (3D) structures by introducing connection strands into the arms. The opening of the prism structures was examined by high-speed AFM imaging, which showed the dissociation of the connecting arms in the 3D structures.

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  • Chemical Approaches to DNA Nanotechnology 査読

    Masayuki Endo, Hiroshi Sugiyama

    CHEMBIOCHEM   10 ( 15 )   2420 - 2443   2009年10月

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    記述言語:英語   出版者・発行元:WILEY-V C H VERLAG GMBH  

    Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built up by self-assembly of the designed DNA strands. DNA nanotechnology has already reached the stage at which the organization of desired functional molecules and nanomaterials can be programmed on a defined DNA scaffold. In this review, we will focus on DNA nanotechnology and describe the potential of synthetic chemistry to contribute to the further development of DNA nanomaterials.

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  • Programmable conformational regulation of porphyrin dimers on geometric scaffold of duplex DNA 査読

    Masayuki Endo, Mamoru Fujitsuka, Tetsuro Majima

    TETRAHEDRON   64 ( 8 )   1839 - 1846   2008年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:PERGAMON-ELSEVIER SCIENCE LTD  

    DNA-porphyrin conjugates were designed and synthesized in which free-base and Zn-coordinated porphyrins were introduced to the N(6)-position of the internal adenosine. Conformations of the porphyrin dimer in the major groove of duplex DNA were controlled by changing the orientation and the distance between the two porphyrin moieties. The porphyrin dimers formed a thermally favorable face-to-face conformation on the duplex DNA. In the disadvantageous geometry for porphyrin dimer formation on the duplex, the porphyrins induced the DNA duplex structures to the Z-form conformation. These results indicate that the interaction of the two porphyrins and the conformation of duplex DNA are controlled by the program of DNA sequences. (C) 2007 Published by Elsevier Ltd.

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  • Diastereochemically controlled porphyrin dimer formation on a DNA duplex scaffold 査読

    Masayuki Endo, Mamoru Fujitsuka, Tetsuro Majima

    JOURNAL OF ORGANIC CHEMISTRY   73 ( 3 )   1106 - 1112   2008年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    [GRAPHICS]
    DNA-porphyrin conjugates were designed and synthesized for the preparation of the conformationally controlled porphyrin dimer structures constructed on a d(GCGTATACGC)(2). Porphyrin derivatives were introduced to the central TATpA sequence where p represents the phosphoramidate for the attachment of the free-base porphyrin (FbP) and zinc-coordinated porphyrin (ZnP), which allows contact of the two porphyrins in the minor groove. The porphyrin dimers were characterized using CD, UV-vis, steady-state, and time-resolved fluorescence spectroscopies, indicating that the porphyrins form face-to-face conformations. Also the co-facial conformation was confirmed by comparison with spectra of the non-self-complementary duplex containing one porphyrin moiety. Introduction of zinc into porphyrin moiety destabilized the duplex formation. Two diastereomers showed different thermal stabilities and affected the conformations of porphyrin dimers. The temperature-dependent assembly and the conformational change of the porphyrin dimer on the duplex DNA were observed in the UV-vis spectra, indicating that the dynamic movement of the porphyrin dimer occurs on the duplex. The results indicate that the porphyrin dimers of DNA-FbP conjugates are overlapped clockwise and are located in the minor groove of the usual B-form DNA backbone. The interaction and conformation of two porphyrin moieties are controlled by the following three factors: (1) temperature change during and after formation of the duplex porphyrins at lower temperature; (2) diastereochemistry of the phosphoramidates where porphyrins are connected via a linker; and (3) zinc ion coordination that destabilizes the interaction of porphyrins as well duplex formation.

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  • Porphyrin light-harvesting arrays constructed in the recombinant tobacco mosaic virus scaffold 査読

    Masayuki Endo, Mamoru Fujitsuka, Tetsuro Majima

    CHEMISTRY-A EUROPEAN JOURNAL   13 ( 31 )   8660 - 8666   2007年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    We have demonstrated the construction of multiple porphyrin arrays in the tobacco mosaic virus (TMV) supramolecular structures by self-assembly of recombinant TMV coat protein (TMVCP) monomers, in which Zn-coordinated porphyrin (ZnP) and free-base porphyrin (FbP) were site-selectively incorporated. The photophysical properties of porphyrin moieties incorporated in the TMV assemblies were also characterized. TMV-porphyrin conjugates employed as building blocks self-assembled into unique disk and rod structures under the proper conditions as similar to native TMV assemblies. The mixture of a ZnP donor and an FbP acceptor was packed in the TMV assembly and showed energy transfer and light-harvesting activity. The detailed photo-physical properties of the arrayed porphyrins in the TMV assemblies were examined by time-resolved fluorescence spectroscopy, and the energy transfer rates were determined to be 3.1-6.4 x 10(9) s(-1). The results indicate that the porphyrins are placed at the expected positions in the TMV assemblies.

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  • Monitoring of three distinct structures of restriction enzyme complexes using characteristic fluorescence from site-selectively incorporated solvatochromic probe 査読

    Koji Nakayama, Masayuki Endo, Mamoru Fujitsuka, Tetsuro Majima

    PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES   6 ( 8 )   836 - 841   2007年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    The local change in the three different structures of restriction enzyme BamHI, which include DNA-free dimer and non-specific and specific complexes with DNA, were detected by the fluorescence from a site-selectively introduced solvatochromic fluorophore N-beta-L-alanyl-5-(N,N-dimethylamino)naphthalene-1-sulfonamide (DanAla). According to the crystal structure, alpha-helices of the non-specific complex containing Ile82, Glu86 and Trp206 residues are converted into random coil by the formation of specific complex with a substrate. To understand the microenvironmental change caused by the structural transition around these positions, the DanAla probe was site-specifically introduced into the positions, and steady-state and time-resolved fluorescence was observed. The steady-state fluorescence gave us information that the rigidity of the polypeptide chains would be enhanced by the formation of the specific complex. The time-resolved fluorescence supported that the change in a water molecule-accessible space was induced by DNA-binding. We revealed that the change in rigidity and solvation around the specific positions was detected by the characteristic fluorescence using the combination of steady-state and time-resolved fluorescence techniques.

    DOI: 10.1039/b705049f

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  • Detection of the local structural changes in the dimer interface of BamHI initiated by DNA binding and dissociation using a solvatochromic fluorophore 査読

    Koji Nakayama, Masayuki Endo, Mamoru Fujitsuka, Tetsuro Majima

    JOURNAL OF PHYSICAL CHEMISTRY B   110 ( 42 )   21311 - 21318   2006年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    To detect the local structural change in an interface between proteins induced by the substrate binding and dissociation, a solvatochromic fluorescent N-beta-L-alanyl-5-(N, N-dimethylamino)-naphthalene-1-sulfonamide (DanAla) was introduced into 132 position of the dimer interface in BamHI. Before addition of the substrate, the fluorescence from the normal planer excited state of DanAla moiety was observed as a main emission, and thereby the DanAla in the dimer interface is located in the hydrophobic microenvironment. The incubation with the substrate for 20 min induced the gradual increase in fluorescence intensity around 430 nm. The fact reflects that the polarity is reduced by the slight structural change initiated by the formation of the complex with the substrate. Furthermore, the incubation for more than 20 min caused the slight decrease in fluorescence around 430 nm and an appearance of fluorescence ( 560 nm) due to twisted intramolecular charge transfer (TICT) excited state. Therefore, the DanAla is exposed to comparative polar environment after the dissociation of the substrate. The fluorescence lifetime as a minor component, which is attributed to the TICT excited state, was reduced by addition of the substrate. The results provide that the hydrophobicity in the dimer interface is increased by the substrate binding. Interestingly, we found that the structure of an initial form is different from that of a refolded form after the dissociation of the substrate using a spectral subtraction technique. We have achieved detection of the changing structure induced by the substrate binding and dissociation using a steady-state and time-resolved fluorescence.

    DOI: 10.1021/jp064031d

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  • Pyrene-stacked nanostructures constructed in the recombinant tobacco mosaic virus rod scaffold 査読

    M Endo, HX Wang, M Fujitsuka, T Majima

    CHEMISTRY-A EUROPEAN JOURNAL   12 ( 14 )   3735 - 3740   2006年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    The effect of pyrenes introduced into a tobacco mosaic virus (TMV) coat protein monomer on the formation and stability of the TMV assembly was investigated. The possible arrangement of the pyrenes in the inner cavity of the TMV rod was also estimated. The pyrene derivative was introduced to four specific amino acids in the cavity of the TMV rod structure. Rod-structure formation was examined by atomic force microscopy (AFM). Two pyrene-attached mutants (positions 99 and 100) assembled to increase the length of the rod structures by 2.5 mu m at pH 5.5. The interaction of the pyrene moieties in the TMV cavity was investigated by steady-state and time-resolved spectroscopic analysis. Strong excimer emission with significantly short wavelength (465 nm) was observed from the two mutants mentioned above. Excitation and UV-visible spectra indicate that the pyrene moieties form it-stacked structures in the TMV cavity. Details of the pyrene interaction were investigated by analyzing the fluorescence lifetime of the excimer. Results suggest that the pyrenes formed preassociated rigid structures with partially overlapped geometry in the restricted space of the TMV cavity. The pyrenes effectively stabilize the TMV rod through a it-stacking interaction in a well-ordered way, and the single pyrene moiety introduced into the monomer affects the overall formation of the TMV rod structure.

    DOI: 10.1002/chem.200501309

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  • Thermodynamic properties of branched DNA complexes with full-matched and mismatched DNA strands 査読

    Masayuki Endo, Tetsuro Majima

    CHEMICAL COMMUNICATIONS   ( 22 )   2329 - 2331   2006年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Complexes consisting of a branched DNA with full-matched and mismatched DNA strands were prepared, and the cross-linking of the DNA strands and their diastereochemistry affected the stability of the complexes and the thermodynamics of the complex formation.

    DOI: 10.1039/b601372d

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  • Site-specific fluorescent labeling of RNA molecules by specific transcription using unnatural base pairs 査読

    R Kawai, M Kimoto, S Ikeda, T Mitsui, M Endo, S Yokoyama, L Hirao

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   127 ( 49 )   17286 - 17295   2005年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Site-specific fluorescent labeling of RNA molecules was achieved by specific transcription using an unnatural base pair system. The unnatural base pairs between 2-amino-6-(2-thienyl)purine (s) and 2-oxo-(1H)pyridine (y), and 2-amino-6-(2-thiazolyl)purine (v) and y function in transcription, and the substrates of y and 5-modified y bases can be site-specifically incorporated into RNA, opposite s or v in DNA templates, by T7 RNA polymerase. Ribonucleoside 5'-triphosphates of 5-fluorophore-linked y bases were chemically synthesized from the nucleoside of y. These fluorescent substrates were site-specifically incorporated into RNA by transcription mediated by the s-y and v-y pairs. By using this fluorescent labeling method, specific positions of Raf-binding and theophylline-binding RNA aptamers were fluorescently labeled, and the specific binding to their target molecules was detected by their fluorescent intensities. This site-specific labeling method using an unnatural base pair system will be useful for analyzing conformational changes of RNA molecules and for detecting interactions between RNA and its binding species.

    DOI: 10.1021/ja0542946

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  • A hydrophilic azobenzene-bearing amino acid for photochemical control of a restriction enzyme BamHI 査読

    K Nakayama, M Endo, T Majima

    BIOCONJUGATE CHEMISTRY   16 ( 6 )   1360 - 1366   2005年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    A novel hydrophilic and negatively charged azobenzene-bearing amino acid, 4'-carboxyphenylazophenylalanine (azoAla 1), has been designed and synthesized for investigation of the photochemical regulation of the enzyme activity. The properties of photoisomerization and thermal stability of the cis-isomer were similar to those of a commonly used phenylazophenylalanine (azoAla 2). For photochemical control of the enzyme, these two azobenzene-bearing amino acids were incorporated into the specific position at the dimer interface of a restriction enzyme BamHI. These trans-azobenzene derivatives in the BamHI suppressed the enzymatic activity, and the following photoirradiation at 366 nm induced the recovery of its activity. Although the activities of both azoAla-BamHI mutants were same level after a long time irradiation, the recovery of the activity of azoAla 1-BamHI was faster than that of azoAla 2-BamHI with a short time irradiation. This result suggests that the negatively charged carboxylate group introduced into an azobenzene moiety affects the behavior of azoAla in the protein scaffold during the trans-cis photoisomerization.

    DOI: 10.1021/bc04972g

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  • Four-way-branched DNA-porphyrin conjugates for construction of four double-helix-DNA assembled structures 査読

    M Endo, T Shiroyama, M Fujitsuka, T Majima

    JOURNAL OF ORGANIC CHEMISTRY   70 ( 19 )   7468 - 7472   2005年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    DNA-porphyrin conjugates having four DNA strands were designed and synthesized. Four double helices were assembled using two DNA-porphyrin conjugates and their complementary strands, and the formation of the four double-helix assembled structures with the two DNA-porphyrin units was examined by gel electrophoresis and spectroscopic analysis. The interaction between two porphyrin chromophores in the complex was investigated by measurement of fluorescence lifetimes, and the singlet energy transfer between the two different phorphyrin units (Zn-porphyrin and H-2-porphyrin) was observed. These results indicate that multiple and different porphyrin chromophores can be integrated into the DNA structures by programming the sequences of the DNA strands.

    DOI: 10.1021/jo0503781

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  • Stepwise photocleavage of C-O bonds of bis(substituted-methyl)naphthalenes with stepwise excitation by two-color two-laser and three-color three-laser irradiations 査読

    XC Cai, M Sakamoto, M Hara, S Tojo, A Ouchi, A Sugimoto, K Kawai, M Endo, M Fujitsuka, T Majima

    JOURNAL OF PHYSICAL CHEMISTRY A   109 ( 17 )   3797 - 3802   2005年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Stepwise photocleavage of naphthylmethyl-oxygen (C-O) bonds of mono(substituted-methyl)naphthalenes [1- and 2-ROCH2Np, R = 4-benzoylphenyl (BP), phenyl (Ph), and methyl (CH3)] and bis(substituted-methyl)naphthalenes [1,8-(ROCH2)(2)Np and 1,4-(ROCH2)(2)Np, R = BP and Ph] was observed to give the naphthylmethyl radicals (NpCH2center dot or ROCH2NpCH2center dot) in almost 100 % yield with two-step or three-step excitation by the two-color two-laser or three-color three-laser irradiation, respectively, at room temperature. The C-O bond cleavage quantum yields of 1-PhOCH2Np, 2-PhOCH2Np, 1,8-(PhOCH2)(2)Np, and 1,4-(PhOCH2)(2)Np were higher than those of 1-BPOCH2Np, 2-BPOCH2Np, 1,8-(BPOCH2)(2)Np, and 1,4-(BPOCH2)(2)Np. No C-O bond cleavage occurred from 1,8-(HOCH2)(2)Np and 2-CH3OCH2Np in the higher triplet excited state (T-n). The experimental results show that the C-O bond cleavage was determined not only by the position of the substituents on Np but also by the type of the substituents. The C-O bond cleavage of 1-ROCH2Np was more efficient than that of 2-ROCH2Np. In the case of 1,8-(ROCH2)(2)Np and 1,4-(ROCH2)(2)Np. (R = BP and Ph), the first C-O bond cleavage from the T-n states occurred to give ROCH2-substituted naphthylmethyl radicals (1,8- and 1,4-ROCH2-NpCH2center dot) when the T-1 states, generated with the 308-nm first laser irradiation, were excited using the 430-nm second laser. The second C-O bond cleavage occurred when 1,8- and 1,4-ROCH2NpCH2center dot in the ground state [1,8- and 1,4-ROCH2NpCH2center dot(D-n)] were excited to the excited states [1,8- and 1,4-ROCH2NpCH2center dot(D-n)] using the third 355-nm laser during the three-color three-laser flash photolysis at room temperature. It was revealed that acenaphthene was produced as the final product during the stepwise C-O bond cleavages of 18-(BPOCH2)(2)Np and 1,8-(PhOCH2)(2)Np. This is a successful example of stepwise cleavage of two equivalent C-O bonds in a molecule using the three-color three-laser photolysis method.

    DOI: 10.1021/jp050232q

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  • Hornolytic cleavage of C-Si bond of p-trimethylsilylmethylacetophenone upon stepwise two-photon excitation using two-color two-laser flash photolysis 査読

    XC Cai, M Sakamoto, M Hara, S Inomata, M Yamaji, S Tojo, K Kawai, M Endo, M Fujitsuka, T Majima

    CHEMICAL PHYSICS LETTERS   407 ( 4-6 )   402 - 406   2005年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    C-Si bond cleavage of p-trimethylsilylmethylacetophenone(1) occurred in a higher triplet excited state (T-n), giving mainly p-acetylbenzyl radical with the transient absorption in the region of 295-360 nm, with a quantum yield of 0.046 +/- 0.008 using the two-color two-laser photolysis techniques. In contrast, the C-Si bond cleavage of p-trimethylsilylmethylbenzophenone(2) was absent in the T-n state whose energy is larger than the C-Si bond cleavage energy. The results can explain existence of a bond cleavage crossing between potential surfaces of the T-n state and a dissociative state of the C-Si bond for 1, but not for 2. (c) 2005 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cplett.2005.03.127

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  • Dihydrophenanthrene-type intermediates during photoreaction of trans-4′-benzyl-5-styrylfuran 査読

    S. Samori, M. Hara, T.-I. Ho, S. Tojo, K. Kawai, M. Endo, M. Fujitsuka, T. Majima

    Journal of Organic Chemistry   70 ( 7 )   2708 - 2712   2005年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/jo047977x

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  • Inhibition of the formation and decay of stilbene core radical cations by the dendron during the photoinduced electron transfer 査読

    M Hara, S Samori, XC Cai, S Tojo, T Arai, A Momotake, J Hayakawa, M Uda, K Kawai, M Endo, M Fujitsuka, T Majima

    JOURNAL OF PHYSICAL CHEMISTRY B   109 ( 2 )   973 - 976   2005年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Formation and decay processes of stilbene core radical cation (ST./) during the photoinduced electron transfer have been studied for a series of stilbene bearing benzyl ether-type dendrons (D). ST./ and the radical cation of peripheral dendron (D-./) were generated by intermolecular hole transfer from biphenyl radical cation. which was venerated from photoinduced electron transfer from biphenyl to the singlet-excited 9, 10-dicyanoanthracene in a mixture of acetonitrile and 1.2-dichloroethane (3:1). An intramolecular dimer radical cation of benzyl groups at the terminal of stilbene dendrimer was indicated as a hole trapping site. Subsequent hole transfer from the trapping site to the core ST generated ST./. The shielding effects of D depending on the dendrimer generation on the growth and decay of ST./ were observed. It was revealed for the first time that D acts as the hole trapping site and the hole conductor on the way of the exothermic hole transfer from the terminal of D to the central core ST. We also found that D inhibits the charge recombination with 9, 10-dicyanoanthracene radical anion because of the steric hindrance.

    DOI: 10.1021/jp045777j

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  • DNA tube structures controlled by a four-way-branched DNA connector 査読

    M Endo, NC Seeman, T Majima

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   44 ( 37 )   6074 - 6077   2005年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    DOI: 10.1002/anie.200501034

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  • Programmable DNA translation system using cross-linked DNA mediators 査読

    M Endo, S Uegaki, T Majima

    CHEMICAL COMMUNICATIONS   ( 25 )   3153 - 3155   2005年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    The information of template DNA strands was converted into the specific sequences in a programmable way by following the mediation of cross-linked DNAs.

    DOI: 10.1039/b503247d

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  • Structural arrangement of DNA constrained by a cross-linker 査読

    M Endo, T Majima

    ORGANIC & BIOMOLECULAR CHEMISTRY   3 ( 19 )   3476 - 3478   2005年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Self-complementary cross-linked oligonucleotides with a disulfide linkage were designed and synthesized. Double helix and hairpin structures were controlled using the different diastereochemistry of phosphoramidate where the cross-linker was introduced. The structures of the strained cross- linked DNAs were estimated by gel mobility, circular dichroism spectra, and melting profiles.

    DOI: 10.1039/b507126g

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  • Photocatalytic oxidation reactivity of holes in the sulfur- and carbon-doped TiO2 powders studied by time-resolved diffuse reflectance spectroscopy 査読

    T Tachikawa, S Tojo, K Kawai, M Endo, M Fujitsuka, T Ohno, K Nishijima, Z Miyamoto, T Majima

    JOURNAL OF PHYSICAL CHEMISTRY B   108 ( 50 )   19299 - 19306   2004年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    The photocatalytic oxidation reactivities of the photogenerated holes (h(+)) during ultraviolet or visible laser flash photolysis of pure anatase and sulfur- and carbon-doped TiO2 powders were investigated using time-resolved diffuse reflectance (TDR) spectroscopy. The one-electron oxidation processes of substrates such as methanol and 4-(methylthio)phenyl methanol (MTPM) by h(+) at the TiO2 surface were examined. The TDR spectra and time traces observed for charge carriers and the MTPM radical cation (MTPM.+) revealed that the oxidation reactions of substrates by h(+) generated during the 355-nm laser photolysis of TiO2 powders increased in the order of pure TiO2 &gt; S-doped TiO2 &gt; C-doped TiO2. On the other hand, no one-electron oxidation reactions of the substrates were observed during the 430-nm laser photolysis of the S- and C-doped TiO2 powders, although the charge carriers were sufficiently generated upon excitation. The effects of the trapping and detrapping processes of h(+) at the doping sites on the oxidation reactions during the laser flash photolyses of the TiO2 powders are discussed.

    DOI: 10.1021/jp0470593

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  • Effects of benzyl ether type dendrons as hole-harvesting antennas, and shielding for the neutralization of stilbene core radical cations with chloride ion during two-photon ionization of stilbene dendrimers having stilbene core and benzyl ether type dendrons 査読

    M Hara, S Samori, XC Cai, S Tojo, T Arai, A Momotake, J Hayakawa, M Uda, K Kawai, M Endo, M Fujitsuka, T Majima

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   126 ( 43 )   14217 - 14223   2004年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    The two-photon ionization (TPI) process (308 and 266 nm) of stilbene dendrimers having a stilbene core and benzyl ether type dendrons has been investigated in an acetonitrile and 1,2-dichloroethane mixture (3:1) in order to elucidate the dendrimer effects. The quantum yield of the formation of stilbene core radical cation during the 308-nm TPI was independent of the dendron generation of the dendrimers, whereas a generation dependence of the quantum yield of the radical cation was observed during the 266-nm TPI, where both the stilbene core and benzyl ether type dendron were ionized, suggesting that the subsequent hole transfer occurs from the dendron to the stilbene core, and that the dendron acts as a hole-harvesting antenna. The neutralization rate of the stilbene core radical cation with the chloride ion, generated from the dissociative electron capture by 1,2-dichloroethane, decreased with the increase in the dendrimer generation, suggesting that the dendron is an effective shield of the stilbene core radical cation against the chloride ion.

    DOI: 10.1021/ja046650a

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  • Transient phenomena of polyphenyls in the higher triplet excited state 査読

    XC Cai, M Sakamoto, M Hara, S Tojo, K Kawai, M Endo, M Fujitsuka, T Majima

    JOURNAL OF PHYSICAL CHEMISTRY A   108 ( 43 )   9361 - 9364   2004年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    Transient phenomena of polyphenyls (PP), such as biphenyl (BP), p-terphenyl (TP), and 1,3,5-triphenylbenzene (TPB) in the higher triplet excited states (T-n, n greater than or equal to 2), were investigated with the nanosecond-nanosecond (ns-ns) two-color two-laser excitation method. PP(T-n) was generated by the excitation of PP in the lowest triplet excited state (PP(T-1)) at the wavelength tuned to the absorption of PP(T-1). Bleaching of the transient absorption of BP(T-1) and TP(T-1) was observed during the second laser irradiation in the presence of chloroalkanes (RCl) such as carbon tetrachloride (CCl4), dichloromethane (CH2Cl2), or 1,2-dichloroethane (DCE). In the case of TPB, clear bleaching of TPB(T-1) was observed in the presence of CCl4, while no bleaching was observed in the presence of CH2Cl2 and DCE. No formation of PP.+ was detected during the quenching of PP(T-n) by RCl. Therefore, the bleaching of PP(T-1) is attributed to triplet energy transfer quenching of PP(T-n) by RCl followed by the C-Cl bond cleavage. The lifetimes (tau(Tn)) of PP(T-n) were estimated from the dependence of the quenching efficiency on the RCl concentration. It was found that the tau(Tn) value decreased with the increasing number of benzene rings, BP(T-n) (950 ps) &gt; TP(T-n) (620 ps) &gt; TPB(T-n) (360 ps). The quenching mechanism of PP(T-n) by RCl was discussed.

    DOI: 10.1021/jp047184e

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  • Rate constant of bimolecular triplet energy transfer from chrysene in the higher triplet excited states 査読

    XC Cai, M Sakamoto, M Hara, S Tojo, K Kawai, M Endo, M Fujitsuka, T Majima

    JOURNAL OF PHYSICAL CHEMISTRY A   108 ( 35 )   7147 - 7150   2004年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    The rate constant of the bimolecular triplet energy transfer from chrysene in the second higher triplet excited state (T-2) to triplet quenchers (Q) such as biphenyl, naphthalene, and carbon tetrachloride was determined based on the lifetime of chrysene(T-2) (45 +/- 7 ps) measured directly with ns-ps two-color two-laser flash photolysis method. The rate constant was found to be larger than the diffusion-controlled rate constant in the solvents. The occurrence of the fast bimolecular triplet energy transfer is considered clear evidence of the Ware theoretical model on the energy transfer quenching of the excited species with short lifetimes by the quencher.

    DOI: 10.1021/jp0479771

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  • Structural arrangement of two DNA double helices using cross-linked oligonucleotide connectors 査読

    M Endo, T Majima

    CHEMICAL COMMUNICATIONS   10 ( 11 )   1308 - 1309   2004年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Disulfide cross-linked oligonucleotides, which connect two different sequences of DNA strands, have been synthesized and characterized. Two double helices connected by two different cross-linked oligonucleotides can be arranged in both parallel and antiparallel orientations by addition of the specific complementary strands.

    DOI: 10.1039/b402783c

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  • Design and synthesis of photochemically controllable restriction endonuclease BamHI by manipulating the salt-bridge network in the dimer interface 査読

    M Endo, K Nakayama, T Majima

    JOURNAL OF ORGANIC CHEMISTRY   69 ( 13 )   4292 - 4298   2004年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    The strategy for the design of photochemically controllable enzymes by manipulating the dimer interface is described. Employing a restriction endonuclease BamHI, the selective incorporation of amino acids having a photoremovable 6-nitroveratryl group into the specific position (Lys132) in the dimer interface of the BamHI mutant (H133A) was performed. The activity of the photofunctionalized BamHI mutant was significantly suppressed, and the following photoirradiation induced the recovery of the activity. In addition, uncaging of the 6-nitroveratryl group introduced to Lys132 did not seriously reduce the catalytic activity and affinity for the substrate. These results indicate that the activity of the enzyme can be effectively regulated by caging and uncaging of the specific amino acid in the dimer interface using the photoremovable group.

    DOI: 10.1021/jo035774n

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  • Stepwise photocleavage of two C-O bonds of ′1,8-Bis [(4,-benzoylphenoxy)-methyl]naphthalene with three-step excitation using three-color, three-laser flash photolysis 査読

    X. Cai, M. Sakamoto, M. Hara, S. Tojo, A. Ouchi, K. Kawai, M. Endo, M. Fujitsuka, T. Majima

    Journal of the American Chemical Society   126 ( 24 )   7432 - 7433   2004年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/ja049007x

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  • Unnatural base pairs mediate the site-specific incorporation of an unnatural hydrophobic component into RNA transcripts 査読

    M Endo, T Mitsui, T Okuni, A Kimoto, Hirao, I, S Yokoyama

    BIOORGANIC & MEDICINAL CHEMISTRY LETTERS   14 ( 10 )   2593 - 2596   2004年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:PERGAMON-ELSEVIER SCIENCE LTD  

    Site-specific incorporation of a hydrophobic nucleotide analog into RNA, by T7 transcription mediated by unnatural base pairs, was developed. The nucleotide analog, 5-phenylethynyl-3-(beta-D-ribofuranosyl)pyridin-2-one 5-triphosphate (denoted by Ph-yTP), was chemically synthesized and then site-specifically incorporated by T7 RNA polymerase into RNA opposite the pairing partner, 2-amino-6-(2-thienyl)purine (denoted by s) in DNA templates. The introduction of Ph-y into a theophylline-binding RNA aptamer, in which a uridine in the internal loop was replaced by Ph-y, raised the thermal stability of the aptamer. Thus, this unnatural nucleotide analog would be useful for stabilizing RNA tertiary structures and complexes between RNA and other molecules. (C) 2004 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.bmcl.2004.02.072

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  • Quenching processes of aromatic hydrocarbons in the higher triplet excited states-energy transfer vs. electron transfer 査読

    XC Cai, M Sakamoto, M Hara, S Tojo, K Kawai, M Endo, M Fujitsuka, T Majima

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   6 ( 8 )   1735 - 1741   2004年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Quenching processes of several aromatic hydrocarbons (AH) such as naphthalene (NAP), dibenz[a,h]anthracene (DBA), and chrysene (CHR) in the higher triplet excited states (T-2) by different quenchers (Q) such as p-dichlorobenzene, o-dicyanobenzene aromatic compounds, and chloroalkanes (RCl), have been investigated by the two-color two-laser excitation method. AH in the higher triplet excited states (AH(T-n, n greater than or equal to 2)) initially generated by the excitation of AH(T-1) at the wavelength tuned to the absorption of AH(T-1). AH(T-n) decays to a AH(T-2) with the longest lifetime among AH(T-n) through the fast internal conversion. In the presence of Q, the competition of triplet energy transfer (TENT) and electron transfer (ELT) reactions between AH(T-2) and Q are expected. However, no AH radical cation was observed, especially when the quenchers were chloroalkanes such as carbon tetrachloride (CCl4), methylene dichloride (CH2Cl2), 1,2-dichloroethane, which are good electron acceptors. It is suggested that the TENT is important during the quenching of AH(T-2) by Q. The lifetimes of NAP(T-2) DBA(T-2), and CHR(T-2) were calculated from the TENT quenching experiments. It was found that the lifetimes of AH(T-2) increase in the order of NAP(T-2) (4.5 ps) &lt; DBA(T-2) (16 ps) &lt; CHR(T-2) (60 ps), which is consistent very well with the energy gap law for the transition from AH(T-2) to AH(T-1).

    DOI: 10.1039/b400128a

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  • Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs 査読

    M Kimoto, M Endo, T Mitsui, T Okuni, Hirao, I, S Yokoyama

    CHEMISTRY & BIOLOGY   11 ( 1 )   47 - 55   2004年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:CELL PRESS  

    A photo-sensitive ribonucleotide of 5-iodo-2-oxo(1H) pyridine (ly) capable of site-specific incorporation into transcripts was developed. The site-specific ly incorporation into RNA was achieved by T7 transcription mediated by unnatural base pairing between ly and its partner, 2-amino-6-(2-thienyl)purine (s). By this specific transcription, ly was incorporated into an anti(Raf-1) RNA aptamer, which binds to human Raf-1 and inhibits the interaction between Raf-1 and Ras. Protein-dependent photo-dimerization of the aptamer was observed when ly was located at specific positions in the aptamer, showing that the site-specific incorporation of the photo-sensitive component into RNA achieves highly specific crosslinking. This specific transcription mediated by the unnatural base pair would be a powerful tool for generating high-affinity RNA ligands and for analyzing RNA-RNA and RNA-protein interactions, as well as for constructing RNA-based nanostructures.

    DOI: 10.1016/j.chembiol.2003.12.016

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  • Photochemical regulation of the activity of an endonuclease BamHI using an azobenzene moiety incorporated site-selectively into the dimer interface 査読

    K Nakayama, M Endo, T Majima

    CHEMICAL COMMUNICATIONS   10 ( 21 )   2386 - 2387   2004年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Endonuclease BamHI mutants having an azophenylalanine residue in the dimer interface (azoAla-BamHI) were synthesized; while the activity was almost suppressed using trans-azoAla-BamHI, the cis-isomer generated with photoirradiation recovered its intrinsic activity.

    DOI: 10.1039/b409844g

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  • Design and synthesis of photochemically controllable caspase-3 査読

    M Endo, K Nakayama, Y Kaida, T Majima

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   43 ( 42 )   5643 - 5645   2004年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    DOI: 10.1002/anie.200460889

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  • Control of a double helix DNA assembly by use of cross-linked oligonucleotides 査読

    M Endo, T Majima

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   125 ( 45 )   13654 - 13655   2003年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    DOI: 10.1021/ja0367521

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  • Photoisomerization of 2′-deoxyribofuranosyl and ribofuranosyl 2-phenylazoimidazole 査読

    M. Endo, K. Nakayama, Y. Kaida, T. Majima

    Tetrahedron Letters   44 ( 36 )   6903 - 6906   2003年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/S0040-4039(03)01697-6

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  • Benzophenones in the higher triplet excited states 査読

    XC Cai, M Sakamoto, M Hara, A Sugimoto, S Tojo, K Kawai, M Endo, M Fujitsuka, T Majima

    PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES   2 ( 11 )   1209 - 1214   2003年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Transient phenomena of benzophenone ( BP) in the higher triplet excited state ( T-n) have been investigated by the two- colour two- laser excitation method. Triplet energy transfer from BP( T-n) to quenchers ( Q) occurred within the duration of a laser pulse ( 5 ns) to give Q( T-1) with higher triplet energy than that of BP( T-1). The quantum yield of the triplet energy- transfer quenching of BP( T-n) by CCl4 was found to be 0.0023 +/- 0.0002 from the bleaching of the transient absorption of BP( T-1) and the absorbed photon number. It appears that internal conversion from BP( Tn) to BP( T-1) is the predominant process. The lifetimes ( tau(Tn)) of BP( T-n) and several substituted benzophenones ( BPs) in the higher triplet excited state [ BPs( T-n)] were estimated from the dependence of the Q concentration on the efficiency of the triplet energy- transfer quenching of BP( T-n) by Q, and found to be 110 - 450 ps, depending on the nature of the substituents on the BPs. The effect of the substituents on tau(Tn) may be explained by the energy gap between the T-n and T-1 states, because the main deactivation pathway for BPs( T-n) is the internal conversion process. In contrast, the substituent effect on the lifetimes of BPs( T-1) cannot be explained by the energy gap law. The transient behaviour of Q( T-1) depends on the properties of the quencher. Sequential triplet energy transfer from Q( T-1) to BP occurred for p- dichlorobenzene and tert- butylbenzene as quenchers, while Q( T-1) reacted partly with Q to form triplet excimers ( (3)Q(2)*) for benzene, chlorobenzene, and o- dichlorobenzene as quenchers. When CCl4 was used as the quencher, the homolytic cleavage of a C - Cl bond of CCl4( T-1) occurred to give Cl-. and Cl3C. radicals.

    DOI: 10.1039/b307443a

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  • Parallel, double-helix DNA nanostructures using interstrand cross-linked oligonucleotides with bismaleimide linkers 査読

    M Endo, T Majima

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   42 ( 46 )   5744 - 5747   2003年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

    DOI: 10.1002/anie.200352546

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  • Molecular Design for a Pinpoint RNA Scission. Interposition of Oligoamines between Two DNA Oligomers1 査読

    Masayuki Endo, Yasushi Azuma, Yoshitaka Saga, Akinori Kuzuya, Gota Kawai, Makoto Komiyama

    The Journal of Organic Chemistry   62 ( 4 )   846 - 852   1997年2月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jo9611780

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  • Novel Phosphoramidite Monomer for the Site-Selective Incorporation of a Diastereochemically Pure Phosphoramidate to Oligonucleotide 査読

    Masayuki Endo, Makoto Komiyama

    The Journal of Organic Chemistry   61 ( 6 )   1994 - 2000   1996年1月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/jo951621r

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  • RNA Hydrolysis by the Cooperation of Carboxylate Ion and Ammonium Ion 査読

    Masayuki Endo, Kouichiro Hirata, Toshihiro Ihara, Shinji Sueda, Makoto Takagi, Makoto Komiyama

    Journal of the American Chemical Society   118 ( 23 )   5478 - 5479   1996年1月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/ja960009u

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  • A novel phosphoramidite for the site-selective introduction of functional groups into oligonucleotides via versatile tethers 査読

    Masayuki Endo, Yoshitaka Saga, Makoto Komiyama

    Tetrahedron Letters   35 ( 32 )   5879 - 5882   1994年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    A phosphoramidite monomer, which has a benzyl ester moiety in the side chain and is useful for the site-selective introduction of functional groups into oligonucleotides via various tethers, has been synthesized. © 1994.

    DOI: 10.1016/S0040-4039(00)78208-6

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  • Lanthanide complex-oligo-DNA hybrid for sequence-selective hydrolysis of RNA 査読

    Kazunari Matsumura, Masayuki Endo, Makoto Komiyama

    Journal of the Chemical Society, Chemical Communications   ( 17 )   2019 - 2020   1994年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Iminodiacetate complexes of lanthanide(III) ions (lutetium, europium, thulium and lanthanum), attached to the 5′-end of a 15-mer DNA, hydrolyse a 39-mer RNA selectively at the 3′-side of its 15-mer sequence, which is complementary with the DNA.

    DOI: 10.1039/C39940002019

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書籍等出版物

  • DNA オリガミによる分子デリバリー

    遠藤 政幸( 担当: 分担執筆 範囲: 核酸医薬と神経疾患)

    中外医薬社、CLINICAL NEUROSCIENCE vol.41, no.5 , pp668-670  2023年 

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  • DNA Origami: Structures, Technology, and Applications

    Masayuki Endo( 担当: 編纂)

    Wiley  2022年5月  ( ISBN:9781119682547

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  • DNAオリガミを用いた分子デリバリーシステム

    遠藤 政幸( 担当: 分担執筆 範囲: 実験医学増刊号『核酸医薬 本領を発揮する創薬モダリティ 』)

    羊土社  2021年10月 

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  • DNA nanotechnology to disclose molecular events at the nanoscale and mesoscale levels.

    Masayuki Endo( 担当: 分担執筆 範囲: Cell-Inspired Materials and Engineering (Dan O. Wang, Daniel Packwood Eds.), pages 65-122)

    Springer Nature  2021年 

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  • DNAナノテクノロジーと1分子科学 ~1分子で捉えるユニークな生体分子反応~

    遠藤 政幸( 担当: 分担執筆 範囲: 日本化学会編『CSJカレントレビュー 進化を続ける核酸化学』)

    化学同人  2021年 

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  • DNAオリガミを利用した1分子可視化と計測

    遠藤 政幸( 担当: 分担執筆 範囲: 講談社サイエンティフィック『核酸科学ハンドブック』pp 193-200)

    講談社  2021年 

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  • DNA分子マシン

    遠藤 政幸, 杉山 弘( 担当: 分担執筆 範囲: 日本化学会編『CSJカレントレビュー 分子マシンの科学』 pp 140-148)

    化学同人  2017年 

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  • Single-Molecule Visualization of Biomolecules in the designed DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy

    Masayuki Endo( 担当: 分担執筆 範囲: RNA Technologies (V. A. Erdmann, S. Jurga, J. Barciszewski Eds.) Modified Nucleic Acids in Biology and Medicine, Volume 7, pages 403-427)

    Springer Nature  2016年 

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  • Folding RNA–Protein Complex into Designed Nanostructures

    T. Shibata, Y. Suzuki, H. Sugiyama, M. Endo, H. Saito( 担当: 分担執筆 範囲: Methods in Molecular Biology (Luc Ponchon Ed.), RNA Scaffolds: Methods and Protocols, vol. 1316, pages 169-179)

    Springer Nature  2015年 

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  • Direct Observation of G-Quadruplexes and their Folding Intermediates

    A. Rajendran, Y. Li, M. Endo, H. Sugiyama( 担当: 分担執筆 範囲: DNA G-quadruplexes as new anticancer targets (R. De Vooght-Johnson Ed.), pages 38-54)

    Future Science Ltd, London  2015年 

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  • DNAナノ構造体を利用したDNA構造変化の1分子イメージング

    遠藤 政幸, 杉山 弘( 担当: 分担執筆 範囲: DOJIN BIOSCIENCE SERIES『1分子生物学』 pp 274-276)

    化学同人  2014年 

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  • DNAオリガミ構造体を利用した1分子イメージングシステムへの応用

    遠藤 政幸, 杉山 弘( 担当: 分担執筆 範囲: 新材料・新素材シリーズ『超分子材料の設計と応用展開』 pp 101-113)

    シーエムシー出版  2014年 

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  • G-quadruplex nanostructures probed at the single molecular level by force-based methods

    S. Dhakal, H. Mao, A. Rajendran, M. Endo, H. Sugiyama( 担当: 分担執筆 範囲: Guanine quartets: Structure and application (L. Spindler, W. Fritzsche Ed.), pages 73−85)

    Royal Society of Chemistry  2013年 

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  • DNAオリガミによる1分子観察系の構築

    遠藤 政幸, 杉山 弘( 担当: 分担執筆 範囲: 実験医学『疾患克服をめざしたケミカルバイオロジー』2012年増刊号、Vol. 30, No. 7, pp180-186)

    羊土社  2012年 

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  • DNA Supramolecular Structures and Nanostructures for the Creation of Functional Nanomaterials

    M. Endo, T. Majima( 担当: 分担執筆 範囲: Soft Nanomaterials (H. S. Nalwa Ed.), volume 2, pages 151-179)

    American Scientific Publishers  2009年 

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  • DNAナノテクノロジー

    遠藤 政幸( 担当: 分担執筆 範囲: 化学フロンティア『ゲノム化学』 18巻、169-177)

    化学同人  2007年 

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▼全件表示

MISC

  • Direct observation of nucleosome in DNA frame using high-speed AFM

    Y. Feng, K. Hidaka, F. Hashiya, H. Sugiyama, M. Endo

    日本化学会第99春季年会(2019)   2019年3月

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  • Surface Observation of Self-Assembled 3D DNA Crystals by Atomic Force Microscopy

    H. Eki, H. Sugiyama, M. Endo

    The 45th International Symposium on Nucleic Acid Chemistry   2018年11月

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  • 自己集合性3次元DNA結晶のAFMによる結晶表面観察

    浴 晴彦, 杉山 弘, 遠藤 政幸

    日本化学会第98春季年会(2018)   2018年3月

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  • Direct observation of photoresponsive DNA nanodevice and its self-assembly

    Y. Kamada, E. Willner, Y. Suzuki, T. Emura, K. Hidaka, H. Dietz, H. Sugiyama, M. Endo

    The 44th International Symposium on Nucleic Acid Chemistry   2017年11月

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    記述言語:英語  

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  • Biophysical property of G-quadruplex caged in a confined DNA nanospace 査読

    M. Endo, P. Shrestha, S. Jonchhe, T. Emura, K. Hidaka, H. Sugiyama, H. Mao

    DNA23: The 23rd International Meeting on DNA Computing and Molecular Programming   2017年9月

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    記述言語:英語  

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  • 光応答性を持つDNA分子デバイスの構築とその自己集積化

    鎌田 佑, Elena Willner, 鈴木 勇輝, 江村 智子, 日高 久美, Hendrik Dietz, 杉山 弘, 遠藤 政幸

    日本ケミカルバイオロジー学会 第12回年会   2017年6月

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  • Observation of single biomolecule properties in a DNA nanospace

    M. Endo, P. Shrestha, S. Jonchhe, T. Emura, K. Hidaka, H. Sugiyama, H. Mao

    14th Conference on the Foundations of Nanoscience 2017, Snowbird, UT, USA   2017年4月

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    記述言語:英語  

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  • コンフォメーション変換により化学反応を誘導するDNAナノ構造体の構築

    鎌田 佑, 竹内 洋祐, 竹中 友洋, 江村 智子, 杉山 弘, 遠藤 政幸

    日本化学会第97春季年会(2017)   2017年3月

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  • DNA鎖の拘束によるCas9切断への影響

    Michael H. Räz, 日高 久美, Shana J. Sturla, 杉山 弘, 遠藤 政幸

    日本化学会第97春季年会(2017)   2017年3月

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  • Direct observation of the duplex formation and dissociation in the G-quadruplex-/i-motif-forming site

    M. Endo, X. Xing, X. Zhou, T. Emura, K. Hidaka, B. Tuesuwa, H. Sugiyama

    The 43rd International Symposium on Nucleic Acid Chemistry, Kumamoto   2016年9月

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    記述言語:英語  

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  • Photoregulated DNA-based rotary nanomachine and direct visualization of the rotational movement 査読

    Y. Yang, R. Tashiro, Y. Suzuki, T. Emura, K. Hidaka, H. Sugiyama, M. Endo

    DNA22: The Twentieth International Meeting on DNA Computing and Molecular Programming, Ludwig-Maximilians-Universität München, Germany   2016年9月

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    記述言語:英語  

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  • Filling cavities of lipid-bilayer-supported two-dimensional DNA origami arrays 査読

    Y. Suzuki, H. Sugiyama, M. Endo

    DNA22: The Twentieth International Meeting on DNA Computing and Molecular Programming, Ludwig-Maximilians-Universität München, Germany   2016年9月

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    記述言語:英語  

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  • Efficient amplification of self-gelling polypod-like structured DNA by rolling circle amplification and enzymatic digestion (vol 5, 14979, 2015)

    Tomoya Yata, Yuki Takahashi, Mengmeng Tan, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Yoshinobu Takakura, Makiya Nishikawa

    SCIENTIFIC REPORTS   6   2016年1月

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    記述言語:英語   出版者・発行元:NATURE PUBLISHING GROUP  

    DOI: 10.1038/srep17249

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  • Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures

    Y. Suzuki, M. Endo, H. Sugiyama

    2015 International Chemical Congress of Pacific Basin Societies (PacifiChem 2015), Honolulu, HI   2015年12月

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    記述言語:英語  

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  • DNA origamiを用いたイオンチャネル集積化法の開発

    黒川 竜紀, 清中 茂樹, 中田 栄司, 遠藤 政幸, 小山 祥平, 森 恵美子, 矢野 将太郎, 鈴木 勇輝, 日高 久美, 川田 正晃, 佐藤 主税, 杉山 弘, 森井 孝, 森 泰生

    日本生化学会大会・日本分子生物学会年会合同大会講演要旨集   88回・38回   [1P0164] - [1P0164]   2015年12月

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    記述言語:日本語   出版者・発行元:(公社)日本生化学会  

    J-GLOBAL

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  • Single-molecule manipulation and visualization of multiple DNA structural changes in the DNA nanostructures using high-speed AFM

    M. Endo, H. Sugiyama

    2015 International Chemical Congress of Pacific Basin Societies (PacifiChem 2015), Honolulu, HI   2015年12月

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    記述言語:英語  

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  • 脂質膜‒溶液界面におけるDNA オリガミナノテクノロジー

    鈴木 勇輝, 遠藤 政幸, 杉山 弘

    「細胞を創る」研究会 8.0   2015年11月

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  • DNA ナノ構造体上での光駆動型DNA モーターの歩行運動の1 分子観察

    遠藤 政幸, 楊 泱泱, Marisa A. Goetzfried, 日高 久美, Mingxu You, Weihong Tan, 杉山 弘

    「細胞を創る」研究会8.0   2015年11月

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  • Single-molecule observation of a photo-controlled DNA walker on the DNA origami tile

    Y. Yang, M. A. Goetzfried, K. Hidaka, M. You, W. Tan, H. Sugiyama, M. Endo

    The 42nd International Symposium on Nucleic Acid Chemistry, Himeji   2015年9月

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    記述言語:英語  

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  • Direct visualization of a photo-controlled DNA walker on the DNA nanostructure 査読

    M. Endo, Y. Yang, M. Goetzfried, K. Hidaka, M. You, W. Tan, H. Sugiyama

    DNA21: The Twentieth International Meeting on DNA Computing and Molecular Programming, Harvard University, Cambridge, MA   2015年8月

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  • Direct observation of G-quadruplexes using DNA origami nanoscafiold

    Arivazhagan Rajendran, Yue Li, Masayuki Endo, Hiroshi Sugiyama

    Biological Relevance and Therapeutic Applications of DNA and RNA Quadruplexes   39 - 54   2015年7月

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    記述言語:英語   出版者・発行元:Future Medicine Ltd.  

    DOI: 10.4155/fseb12013.14.37

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  • Direct visualization of the dynamic process of DNA origami assembly on the lipid bilayer surface 査読

    M. Endo, Y, Suzuki, H. Sugiyama

    12th Conference on the Foundations of Nanoscience 2015, Snowbird, UT, USA   2015年4月

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  • 細胞応答の制御を目指した機能性DNAナノ構造体の構築

    遠藤 政幸

    旭硝子財団助成研究成果報告 Reports of research assisted by the Asahi Glass Foundation   1 - 5   2015年

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    記述言語:日本語   出版者・発行元:旭硝子財団  

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  • Lipid Bilayer-assisted 2D Crystallization of DNA Origami Nanostructures

    Y. Suzuki, M. Endo, H. Sugiyama

    The 8th International Symposium on NanoBiotechnology, National Center for Nanoscience and Technology, Beijing   2014年10月

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  • Dynamic Assembly and Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface 査読

    Y. Suzuki, M. Endo, Y. Yang, H. Sugiyama

    11th Conference on the Foundations of Nanoscience 2014, Snowbird, UT   2014年4月

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  • Direct analysis of Holliday junction resolving enzyme in a DNA origami nanostructure 査読

    Yuki Suzuki, Masayuki Endo, Cristina Canas, Silvia Ayora, Juan C. Alonso, Hiroshi Sugiyama, Kunio Takeyasu

    NUCLEIC ACIDS RESEARCH   42 ( 11 )   7421 - 7428   2014年

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    記述言語:英語   出版者・発行元:OXFORD UNIV PRESS  

    Holliday junction (HJ) resolution is a fundamental step for completion of homologous recombination. HJ resolving enzymes (resolvases) distort the junction structure upon binding and prior cleavage, raising the possibility that the reactivity of the enzyme can be affected by a particular geometry and topology at the junction. Here, we employed a DNA origami nano-scaffold in which each arm of a HJ was tethered through the base-pair hybridization, allowing us to make the junction core either flexible or inflexible by adjusting the length of the DNA arms. Both flexible and inflexible junctions bound to Bacillus subtilis RecU HJ resolvase, while only the flexible junction was efficiently resolved into two duplexes by this enzyme. This result indicates the importance of the structural malleability of the junction core for the reaction to proceed. Moreover, cleavage preferences of RecU-mediated reaction were addressed by analyzing morphology of the reaction products.

    DOI: 10.1093/nar/gku320

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  • Rational design of orthogonal gene transcription nano device on DNA origami

    Masubuchi Takeya, Tadakuma Hisashi, Endo Masayuki, Sugiyama Hiroshi, Harada Yoshie, Ueda Takuya

    生物物理   54 ( 1 )   S193   2014年

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  • Programmed DNA nanostructures: photocontrollable assembly to construct pre-designed multidirectional patterns 査読

    Y. Yang, M. Endo, Y. Suzuki, K. Hidaka, H. Sugiyama

    The 40th International Symposium on Nucleic Acid Chemistry, Yokohama   2013年11月

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  • Novel DNA origami tubular structures with variable arrangements 査読

    S. Yamamoto, M. Endo, K. Hidaka, H. Sugiyama

    The 40th International Symposium on Nucleic Acid Chemistry, Yokohama   2013年11月

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  • Dynamic assembly/disassembly processes of photoresponsive DNA origami nanostructures captured by high-speed atomic force microscopy 査読

    Y. Suzuki, M. Endo, Y. Yang, H. Sugiyama

    The 40th International Symposium on Nucleic Acid Chemistry, Yokohama   2013年11月

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  • DNAオリガミを使った1分子解析

    遠藤 政幸, 杉山 弘

    生物物理   53 ( 3 )   153 - 157   2013年5月

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    記述言語:日本語   出版者・発行元:一般社団法人 日本生物物理学会  

    The dynamic behaviors of the enzymes and DNA structural changes were visualized using the designed DNA origami structures and high-speed AFM. The movement and the reactions of DNA methyltransferase, DNA repair enzymes, and RNA polymerase were observed by introducing the substrate double-stranded DNAs (dsDNA) to the DNA nanostructures. For the formation and disruption of G-quadruplex and double-stranded DNA, the two dsDNA incorporated in the DNA frame can amplify the small structural change to the global structural change, which enable the visualization of the reactions. The stepwise strand migration of a DNA nanomachine was visualized and analyzed on the DNA track constructed on the DNA origami surface.&lt;br&gt;

    DOI: 10.2142/biophys.53.153

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  • Photo-functionalization of DNA origami: photo-responsible behavior observation and reversible multi-orientational assembling 査読

    Y. Yang, M. Endo, Y. Suzuki, K. Hidaka, H. Sugiyama

    10th Conference on the Foundations of Nanoscience 2013, Snowbird, UT   2013年4月

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  • Direct visualization of Cre-loxP site specific recombination using DNA origami scaffold

    Y. Suzuki, Y. Katsuda, K. Ou, K. Hidaka, M. Endo, H. Sugiyama

    10th Conference on the Foundations of Nanoscience 2013, Snowbird, UT   2013年4月

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  • 連載”DDS研究のための最新機器” 高速原子間力顕微鏡

    遠藤政幸, 西川元也

    Drug Delivery System   28   150 - 152   2013年1月

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    記述言語:日本語  

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  • Single-molecule observation of enzymes and DNA structural changes in the DNA nanostructures

    Hiroshi Sugiyama, Masayuki Endo

    JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS   31   93 - 94   2013年1月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:TAYLOR & FRANCIS INC  

    DOI: 10.1080/07391102.2013.786387

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  • DNAナノ構造上での分子運動の直接観察

    遠藤 政幸

    日本生物物理学会第51回年会(2013年度)) 生物物理   53 ( 1 )   S92   2013年

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  • Dynamic assembly and disassembly processes of photoresponsive DNA origami nanostructures captured by high-speed atomic force microscopy

    Y. Suzuki, M. Endo, Y. Yang, H. Sugiyama

    7th Annual Symposium on Nanobiotechnology, Bristol, UK   2012年11月

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  • Direct observation of reversible mechanical behaviors of photoresponsive oligonucleotides in DNA nanostructure

    Y. Yang, M. Endo, Y. Suzuki, K. Hidaka, H. Sugiyama

    The 39th International Symposium on Nucleic Acid Chemistry, Nagoya   2012年11月

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  • Two-Dimensional Self-Assembly and Photo-Cross-Linking Induced Thermal-Stabilization of DNA Origami Structures

    A. Rajendran, M. Endo, K. Hidaka, H. Sugiyama

    9th Conference on the Foundations of Nanoscience 2012, Snowbird, UT   2012年4月

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  • DNAオリガミ構造体と1分子観察への応用 (特集 高機能ナノ構造体の創出)

    遠藤 政幸, 杉山 弘

    化学工業   63 ( 2 )   124 - 129   2012年2月

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    記述言語:日本語   出版者・発行元:化学工業社  

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  • Programmed Self-Assembly and Thermal-Stabilization of DNA Origami Nanostructure

    A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama

    The 38th International Symposium on Nucleic Acid Chemistry, Sapporo   2011年11月

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  • Direct observation of the movement of DNA modifying enzymes in the DNA nanostructure 査読

    Y. Katsuda, M. Endo, K. Hidaka, H. Sugiyama

    8th Conference on the Foundations of Nanoscience 2011, Snowbird, UT,   2011年4月

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  • DNAオリガミでの生体分子の制御と直接観察 (2010年の成果の総まとめ 特集 物理科学,この1年) -- (生物物理)

    遠藤 政幸, 杉山 弘

    パリティ   26 ( 1 )   72 - 74   2011年1月

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    記述言語:日本語   出版者・発行元:丸善  

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  • Development of the immobilization technology of functional proteins on DNA origami 査読

    E. Nakata, C. Uwatoko, F.F. Liew, S. Kiyonaka, Y. Mori, Y. Katsuta, M. Endo, H. Sugiyama, T. Morii

    The 38th International Symposium on Nucleic Acid Chemistry,Hokkaido,2011.11.9-11   2011年

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  • Configurable assembly of DNA origami on MEMS by microfluidic device 査読

    Chunmei Huang, Takahiro Saeki, Masayuki Endo, Hiroshi Sugiyama, Chen-Hsun Weng, Gwo-Bin Lee, Koji Sugano, Toshiyuki Tsuchiya, Osamu Tabata

    NEMS 2011 - 6th IEEE International Conference on Nano/Micro Engineered and Molecular Systems   197 - 200   2011年

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    記述言語:英語  

    Configurable assembly technique of a DNA origami tile on Micro Electromechanical Systems (MEMS) using a microfluidic device to realize a Nanosystem was proposed. In this newly proposed approach, multiple DNA origami tiles fabricated by DNA origami technique are utilized as a sub-micro-scale functional building block on which nano-materials such as nano-particles and SWCNTs are assembled by DNA hybridization. This paper presents the proposed methodology and preliminary experimental results. © 2011 IEEE.

    DOI: 10.1109/NEMS.2011.6017328

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  • DNA origami上への機能性タンパク質固定化技術の開発 査読

    中田栄司, 上床知佐奈, 劉芳芳, 清中茂樹, 森泰生, 勝田陽介, 遠藤政幸, 杉山弘, 森井孝

    第5回バイオ関連化学シンポジウム,つくば国際会議場「エポカルつくば」,2011.9.12-14   2011年

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  • Direct Observation of Single Molecular Behavior of T7 RNA Polymerase on the Defined DNA Nanostructure 査読

    M. Endo, K. Tatsumi, K. Terushima, Y. Katsuda, K. Hidaka, H. Sugiyama

    Pacific Basin Societies (PACIFICHEM), Hawaii   2010年12月

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  • Programmed Self-Assembly of Pre-Designed DNA Nanoconstrcts for the preparation of suitable Platform for Nano-Bio Application 査読

    A. Rajendran, M. Endo, T. Sugita, Y. Katsuda, K. Hidaka, H. Sugiyama

    Pacific Basin Societies (PACIFICHEM), Hawaii   2010年12月

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  • Direct Analysis of DNA Modifying and Repair Enzymes Using High-Speed Atomic Force Microscopy 査読

    Y. Katsuda, M. Endo, K. Hidaka, H. Sugiyama

    The International Chemical Congress of Pacific Basin Societies (PACIFICHEM), Hawaii   2010年12月

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  • Dynamic Conformational Switching via G-Quadruplex Formation Observed in the DNA Nanostructure 査読

    Y. Sannohe, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama

    The 37th International Symposium on Nucleic Acids Chemistry 2010, Yokohama   2010年11月

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  • Observation and Control of Enzymatic Reaction in DNA Frame 査読

    M. Endo, H. Sugiyama

    7th Conference on the Foundations of Nanoscience 2010 (FNANO10), Snowbird, UT   2010年4月

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  • Three-dimensional DNA nanostructures constructed by folding of multiple rectangles. 査読

    M. Endo, H. Sugiyama

    Nucleic acids symposium series   ( 53 )   81 - 82   2009年

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    記述言語:英語  

    DOI: 10.1093/nass/nrp041

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  • Photochemical regulation of the activity of a restriction enzyme BamHI using an azobenzene moiety incorporated into the dimer interface.

    K Nakayama, M Endo, T Majima

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   229   U399 - U400   2005年3月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:AMER CHEMICAL SOC  

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  • Photochemical control of caspase-3 activity for induction of apoptosis.

    K Nakayama, M Endo, Y Kaida, T Majima

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   229   U400 - U400   2005年3月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:AMER CHEMICAL SOC  

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  • Manipulation of the dimer interface for photochemical regulation of the activity of an endonuclease BamHI.

    K Nakayama, M Endo, T Majima

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   227   U154 - U154   2004年3月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:AMER CHEMICAL SOC  

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  • 核酸による超分子形成と人工制限酵素の構築 (超分子をめざす化学) -- (高次構造と超分子化学)

    小宮山 真, 遠藤 政幸

    季刊化学総説   ( 31 )   196 - 205   1997年4月

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    記述言語:日本語   出版者・発行元:学会出版センタ-  

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  • 人工制限酵素の分子設計 (1993年の化学-9-)

    小宮山 真, 遠藤 政幸

    化学   48 ( 9 )   p654 - 655   1993年9月

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    記述言語:日本語   出版者・発行元:化学同人  

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▼全件表示

講演・口頭発表等

  • DNA origami-based integrated molecular systems and functional nanomachines 招待

    Masayuki Endo

    国際生物物理学会議(IUPAB 2024) 京都国際会館  2024年6月 

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    会議種別:口頭発表(招待・特別)  

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  • Molecular Nanomachines Using DNA Origami Nanostructures 招待

    Masayuki Endo

    国際生物物理学会議(IUPAB 2024) Hands-on 'DNA Nanomachine Tutrial' 関西大学  2024年6月 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • DNA origami nanotechnology for imaging, analytical and biomaterial applications 招待

    Masayuki Endo

    Indian Institute of Technology (IIT) Bombay, Munbai, India  2024年4月 

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    会議種別:口頭発表(招待・特別)  

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  • DNA origami nanotechnology for imaging, analytical and biomaterial applications 招待

    Masayuki Endo

    Indian Institute of Technology (IIT) Roorkee, Roorkee, India  2024年4月 

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  • New Molecular Technologies Emerging from DNA Origami Nanotechnology 招待

    Masayuki Endo

    DNA Origami workshop 京都大学理学部  2024年3月 

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    会議種別:口頭発表(招待・特別)  

    開催地:京都大学理学部  

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  • DNA ナノテクノロジーから生まれる新たな分子技術 招待

    遠藤 政幸

    電子情報通信学会研究会 生物・自然に学ぶ DNA システムの工学への活用 情報通信研究機構 小金井  2023年7月 

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    会議種別:口頭発表(招待・特別)  

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  • DNAオリガミを使った生体分子デバイスの開発 招待

    遠藤 政幸

    第4回 発動分子科学サロン 発動分子と核酸 東京工業大学  2023年1月 

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    会議種別:口頭発表(招待・特別)  

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  • Creation of DNA origami nanostructures for imaging, analysis, and material applications 招待

    Masayuki Endo

    暨南大学生命科学技術学院  2022年12月 

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    会議種別:口頭発表(招待・特別)  

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  • DNA origami for nanosystem and nanodevice applications 招待

    Masayuki Endo

    PacifiChem2021  2021年12月 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • DNAをノリシロとした世界最小のオリガミに挑戦! DNAオリガミを使った生体分子デバイスの開発 招待

    遠藤 政幸

    化学フェスタ  2021年10月 

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    会議種別:口頭発表(招待・特別)  

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  • DNA origami nanostructures: imaging, analysis, and material applications 招待

    Masayuki Endo

    College of Chemistry and Molecular Sciences, Wuhan University  2019年12月 

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  • Designed DNA origami nanostructures for imaging, analysis, and material applications 招待

    Masayuki Endo

    School of Chemistry, Sun Yat-sen University  2019年12月 

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  • DNA origami nanostructures: design and their applications" 招待

    Masayuki Endo

    College of Life Science and Technology, Jinan University  2019年12月 

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  • Single-Molecule Observation and Analysis of the Dynamics of the Photoresponsive Transcription Factor

    G. Raghavan, K. Hidaka, H. Sugiyama, M. Endo

    The 46th International Symposium on Nucleic Acid Chemistry  2019年10月 

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  • Investigation of physical properties of a confined nanospace using G-quadruplex and i-motif as a molecular probes 招待

    Masayuki Endo

    日本生物物理学会 第57回年会  2019年9月 

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  • Characterization of DNA origami nanospace using G-quadruplex and i-motif structure

    M. Endo, S. Jonchhe, S. Pandey, T. Emura, K. Hidaka, H. Sugiyama, H. Mao

    CISNAC 2019, Kobe  2019年7月 

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  • Designed DNA origami nanostructures for imaging, analysis, and material applications 招待

    Masayuki Endo

    Department of Physics, Kent State University  2019年7月 

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  • DNAオリガミで構築する分子マシン 招待

    遠藤 政幸

    分子モーター討論会, 国立遺伝学研究所  2019年6月 

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  • Designed DNA origami nanostructures for analysis and material applications 招待

    Masayuki Endo

    10th International Conference on Materials for Advanced Technologies (ICMAT2019), Singapore  2019年6月 

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  • Characterization of DNA origami nanospace using G-quadruplex and i-motif structure as a molecular probe

    Masayuki Endo

    NANTECH 2019, Aalto Unoversity  2019年5月 

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    記述言語:英語  

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  • Investigation of physical properties of G-quadruplex and i-motif in a confined nanospace 招待

    Masayuki Endo

    16th Conference on the Foundations of Nanoscience 2019  2019年4月 

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    記述言語:英語  

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  • 光応答性転写因子GAL4のDNAナノ構造内での1分子観察

    G. Raghavan, 日高 久美, 杉山 弘, 遠藤 政幸

    日本化学会第99春季年会(2019)  2019年3月 

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  • DNAナノ空間の分子環境と生体分子の振る舞い

    遠藤 政幸

    第2回分子ロボティクス年次大会  2019年3月 

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  • 制限された空間でのグアニン四重鎖とi-モチーフ構造の物性の解明

    遠藤 政幸, S. Jonchhe, S. Pandey, 江村 智子, 日高 久美, H. Mohammad, P. Shrestha, 杉山 弘, H. Mao

    第12回バイオ関連化学シンポジウム, 大阪大学  2018年9月 

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  • 狭小空間での分子の振る舞い

    遠藤 政幸

    第1回分子ロボティクス年次大会、東北大学  2018年3月 

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  • DNAオリガミを使った1分子の観察 招待

    遠藤 政幸

    静岡ライフサイエンスシンポジウム、静岡大学  2018年3月 

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  • High-speed AFM imaging of synthetic nanomachines and nanostructures 招待

    Masayuki Endo

    The SPIRITS International Symposium 2018 Multidiciplinary Approach for Cell Control, Kyoto University  2018年2月 

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    記述言語:英語  

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  • Observation of biophysical property of G-quadruplex in a confined nanospace

    M. Endo, P. Shrestha, S. Jonchhe, T. Emura, K. Hidaka, H. Sugiyama, H. Mao

    The 44th International Symposium on Nucleic Acid Chemistry  2017年11月 

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    記述言語:英語  

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  • 制限された空間でのグアニン四重鎖の物性

    遠藤 政幸, Prakash Shrestha, Sagun Jonchhe, 江村 智子, 日高 久美, 杉山 弘, Hanbin Mao

    第11回バイオ関連化学シンポジウム  2017年9月 

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  • High-speed AFM imaging of synthetic nanomachines and nanostructures 招待

    Masayuki Endo

    Unconventional Computation and Natural Computation 2017, University of Arkansas  2017年6月 

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    記述言語:英語  

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  • Observation of single-molecule behavior in the DNA nanospace 招待

    Masayuki Endo

    The 3rd SPIRIT international symposium, Light Opening up Frontier of DNA and Nanocrystal Superstructures  2017年2月 

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    記述言語:英語  

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  • ナノ空間での1分子の振る舞い 招待

    遠藤 政幸

    ケミカルバイオロジー Mini-sumposium at KIT、京都工芸繊維大学  2017年1月 

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  • Chemically controllable nanosystems constructed in the nanostructures 招待

    Masayuki Endo

    日本生物物理学会 第54回年会  2016年11月 

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    記述言語:英語  

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  • AFM-based single-molecule imaging of biomolecules and synthetic molecules in the DNA origami nanostructures 招待

    Masayuki Endo

    Department of Health Sciences and Technology, ETH Zürich, Swizerland  2016年9月 

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    記述言語:英語  

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  • High-speed AFM imaging of biomolecules and synthetic molecules in the DNA origami nanostructures 招待

    Masayuki Endo

    Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA  2016年7月 

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  • Photo-controlled mobile DNA nanosystems constructed in the DNA nanostructures 招待

    Masayuki Endo

    FNANO16, Snowbird, UT, USA  2016年4月 

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  • High-speed AFM imaging of synthetic molecules and nanostructures 招待

    Masayuki Endo

    Ten Years of DNA Origami, California Institute of Technology, Pasadena, CA, USA  2016年3月 

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  • Controllable molecular nanosystems using DNA origami nanostructures 招待

    Masayuki Endo

    The 2nd SPIRIT international symposium, Light Opening up Frontier of DNA and Nanocrystal Superstructures  2016年2月 

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  • Single-molecule nanosystems constructed in the DNA nanostructures 招待

    Masayuki Endo

    University of Bordeaux-Kyoto University Mini-Symposium on Biomolecular Science  2016年1月 

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  • AFM based imaging of single-molecule motions using DNA origami nanostructures 招待

    Masayuki Endo

    The 1st SPIRIT international symposium, Frontier of DNA and Nanocrystal Superstructure, Honolulu, HI  2015年12月 

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  • Single-molecule imaging of photoresponsive molecular system constructed in the DNA nanostructures 招待

    Masayuki Endo

    601. Wilhelm und Else Heraeus-Seminar, DNA Nanotechnology Meets Plasmonics, Physikzentrum, Bad Honnef, Germany  2015年12月 

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    記述言語:英語  

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  • 分子ロボットの感覚となるDNAレセプターの構築 招待

    遠藤 政幸

    第59回人工知能学会 分子生物情報研究会  2015年11月 

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  • AFM based imaging of single-molecule motions using DNA origami nanostructures 招待

    Masayuki Endo

    The 2nd Kobe mini-symposium on functionalized organic molecules  2015年11月 

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    記述言語:英語  

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  • 分子ロボットの感覚となるDNAオリガミ構造体と脂質二重膜との相互作用 招待

    遠藤 政幸

    情報計算化学生物(CBI)学会2015大会  2015年10月 

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  • 脂質2重膜を利用したDNAナノ構造体の自己集合化とその動的な挙動の観察 招待

    遠藤 政幸

    第64回高分子討論会  2015年9月 

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  • 脂質2重膜上でのDNAナノ構造体の自己集合過程の動的な観察

    遠藤 政幸, 鈴木 勇輝, 杉山 弘

    第9回バイオ関連化学シンポジウム  2015年9月 

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  • DNAナノ構造体を使った1分子イメージング法の開発 招待

    遠藤 政幸

    第52回薬剤学懇談会研究討論会  2015年7月 

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  • AFM based single-molecule imaging of molecular motions in the DNA origami scaffold 招待

    Masayuki Endo

    The 5th International Conference on Nucleic Acid-Protein Chemical and Structural Biology for Drug Discovery, Sichuan University, Chengdu, China  2015年5月 

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    記述言語:英語  

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  • 光ピンセットによる力測定を使ったDNAナノ構造上での1分子検出

    遠藤 政幸, D. Koirala, P. Shrestha, S. Mandal, 江村 智子, 日高 久美, H. MAO, 杉山 弘

    日本化学会第95春季年会  2015年3月 

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  • DNAナノ構造体を使った1分子イメージング法の開発 招待

    遠藤 政幸

    兵庫県立大 第8回分子ナノテクノロジーセンター講演会  2015年3月 

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  • Novel helical DNA tubular structures with defined size and arrangement

    M. Endo, S. Yamamoto, T. Emura, K. Hidaka, N. Morone, J. E. Heuser, H. Sugiyama

    The 41st International Symposium on Nucleic Acid Chemistry  2014年11月 

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  • Creation of mechanical nanodevices using DNA origami 招待

    Masayuki Endo

    The 8th International Symposium on NanoBiotechnology, National Center for Nanoscience and Technology, Beijing  2014年10月 

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    記述言語:英語  

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  • Construction of helical DNA origami tubes with various sizes and arrangements

    M. Endo, S. Yamamoto, T. Emura, K. Hidaka, N. Morone, J. E. Heuser, H. Sugiyama

    DNA20  2014年9月 

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    記述言語:英語  

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  • 新規DNAチューブ構造体の構築とその性質

    遠藤 政幸, 山本 清義, 江村 智子, 日高 久美, 杉山 弘

    第8回バイオ関連化学シンポジウム  2014年9月 

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  • DNAオリガミを利用した生体分子の動きの1分子観察 招待

    遠藤 政幸

    東京大学化学生命工学専攻談話会  2014年7月 

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  • Photoresponsive DNA nanostructures; single-molecule imaging and controlled assembly 招待

    Masayuki Endo

    FNANO14, Snowbird, UT, USA  2014年4月 

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    記述言語:英語  

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  • らせん状のDNAチューブ構造体の設計と構築

    遠藤政幸, 山本清義, 江村智子, 日高久美, 杉山 弘

    日本化学会第94春季年会(2014)  2014年3月 

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  • Single-molecule manipulation of artificial DNA nanostructures

    Masayuki Endo

    2nd Kyoto-Bristol Symposium  2014年1月 

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  • Single-molecule observation and control of DNA recombination in the DNA frames

    M. Endo, Y, Suzuki, Y. Katsuda, K. Ou, K. Hidaka, H. Sugiyama

    The 40th International Symposium on Nucleic Acid Chemistry, Yokohama  2013年11月 

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    記述言語:英語  

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  • DNAオリガミを利用した生体分子の動きの1分子観察 招待

    遠藤 政幸

    日本農芸化学会中部支部 第169回例会 若手シンポジウム『核酸科学の新潮流』  2013年11月 

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  • Single-molecule observation and control of DNA recombination in the DNA frames 招待

    Masayuki Endo

    7th Annual Symposium on Nanobiotechnology, Bristol, UK  2013年11月 

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    記述言語:英語  

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  • Visualizing molecular motions on the DNA origami 招待

    遠藤 政幸

    第10回日独先端科学シンポジウム  2013年11月 

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  • Direct observation of molecular motions on the DNA nanostructure 招待

    遠藤 政幸

    日本生物物理学会 第51回年会  2013年10月 

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    記述言語:英語  

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  • DNAナノ構造体上でのDNA組み換え反応の1分子観察と制御

    遠藤 政幸, 鈴木 勇輝, 勝田 陽介, 王 恵瑜, 日高 久美, 杉山 弘

    第7回バイオ関連化学シンポジウム  2013年9月 

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  • DNAナノ構造内でのB-Z構造転移の制御と可視化

    遠藤 政幸, A. Rajendran, 日高 久美, 杉山 弘

    日本ケミカルバイオロジー学会 第8回年会  2013年6月 

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  • Direct observation of DNA structural changes in the designed DNA nanostructures 招待

    Masayuki Endo

    FNANO13, Snowbird, UT, USA  2013年4月 

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  • DNA分子テクノロジーの1分子観察と材料への応用 招待

    遠藤 政幸

    北陸先端科学技術大学院大学 マテリアルサイエンス研究科セミナー  2013年2月 

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  • Direct observation of RNA polymerase and transcription in the designed DNA nanostructure

    M. Endo, K. Tatsumi, K. Terushima, Y. Katsuda, K. Hidaka, Y. Harada, H. Sugiyama

    The 39th International Symposium on Nucleic Acid Chemistry  2012年11月 

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  • DNA分子テクノロジーの材料化への応用 招待

    遠藤 政幸

    バイオテンプレート研究会  2012年10月 

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  • DNA Molecular Technology for Imaging and Biological Applications 招待

    Masayuki Endo

    6th Annual Symposium on Nanobiotechnology  2012年10月 

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    記述言語:英語  

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  • DNAナノ構造体上でのRNAポリメラーゼの挙動と転写の1分子観察

    遠藤 政幸, 辰巳 紘一, 照島 功祐, 勝田 陽介, 日高 久美, 原田 慶恵, 杉山 弘

    第6回バイオ関連化学シンポジウム  2012年9月 

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  • Direct observation of single enzymatic and chemical reactions in the designed DNA nanostructures 招待

    Masayuki Endo

    dnatec2012, Aahus, Denmark  2012年8月 

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    記述言語:英語  

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  • DNAナノマシーンの操作と運動の可視化 招待

    遠藤 政幸

    分子ロボティクス研究会  2012年7月 

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  • DNA分子テクノロジーのケミカルバイオロジーへの応用 招待

    遠藤 政幸

    大阪大学薬学研究科  2012年7月 

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  • DNA ナノ構造上でのDNA 組み換え反応の直接観察

    遠藤政幸, 勝田陽介, 鈴木勇輝, 王恵瑜, 日高久美, 杉山弘

    日本ケミカルバイオロジー学会  2012年6月 

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  • Direct visualization of single transcription on the designed DNA nanoscaffold 招待

    Masayuki Endo

    9th Conference on the Foundations of Nanoscience 2012  2012年4月 

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    記述言語:英語  

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  • DNAナノ構造変換を利用した転写の制御

    遠藤 政幸, 宮崎 亮次, 江村 智子, 日高 久美, 杉山 弘

    日本化学会第92春季年会  2012年3月 

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  • Direct Observation of DNA recombination in the DNA nanoscaffold

    M. Endo, Y.Katsuda, K.Ou, K.Hidaka, H.Sugiyama

    The 38th International Symposium on Nucleic Acid Chemistry  2011年11月 

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  • Designed DNA Nanostructures for Assembly, Functionalization, & Visualization 招待

    M. Endo

    POSTECH AMS Symposium on Nanotechnology  2011年11月 

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  • Visualization of the Biomolecular Behavior in the Designed DNA Nanostructures 招待

    M. Endo

    Seminar in Department of Chemistry, POSTECH  2011年11月 

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    記述言語:英語  

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  • DNAナノ構造体の生体反応への応用 招待

    遠藤 政幸

    創剤フォーラム若手研究会シンポジウム  2011年11月 

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  • AFM-based Imaging of the Movement of Biomolecules in the Designed DNA Nanostructures 招待

    M. Endo

    5th Annual Symposium on Nanobiotechnology  2011年11月 

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    記述言語:英語  

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  • DNAナノマシーンの1分子運動の可視化 招待

    第84回 日本生化学会大会 シンポジウム「分子ロボティクス」  2011年9月 

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  • DNAオリガミ上でのDNA分子の移動の精密な操作

    ケミカルバイオロジー学会 第6回年会  2011年5月 

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  • Programmed assembly of DNA nanostructures using designed DNAorigami tiles

    8th Conference on the Foundations of Nanoscience  2011年4月 

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    記述言語:英語  

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  • DNAナノ構造内の2本鎖DNAの構造変化検出を用いたグアニン4重鎖形成の1分子観察

    日本化学会弟91春季年会  2011年3月 

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  • Direct Observation of Single Molecular Behaviour of T7 RNA Polymerase on the Defined DNA Nanostructure

    Masayuki Endo

    International Chemical Congress of Pacific Basin Societies  2010年12月 

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    記述言語:英語  

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  • Visualization of single molecular movement in the designed DNA nano-space 招待

    The SSI 2010 International Symposium  2010年11月 

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  • Direct observation of stepwise movement of DNA nanomachine walking along the track constructed on a DNA origami scaffold

    The 37th Symposium on Nucleic Acids Chemistry 2010  2010年11月 

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  • DNA修復反応を観察するDNAナノチップの開発

    ケミカルバイオロジー学会 第5回年会  2010年5月 

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  • Programmed self-assembly of DNA jigsaw pieces

    7th Conference on the Foundations of Nanoscience  2010年4月 

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    記述言語:英語  

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  • 2次元DNAオリガミ構造の折りたたみによる3次元ナノ構造の構築

    日本化学会 第90春季年会  2010年3月 

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  • Preparation of DNA scaffolds for the 3D-nanostructure construction

    The 6th International Symposium on Nucleic Acids Chemistry and 36th Symposium on Nucleic Acids Chemistry  2009年10月 

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▼全件表示

産業財産権

  • MECHNOCHEMICAL PLATFORM AND SENSING METHODS USING DNA ORIGAMI NANOSTRUCTURES

    Hanbin Mao, Deepak Koirala, Hiroshi Sugiyama, Masayuki Endo

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    出願人:Kyoto University, Kent State University

    出願番号:US patent Application NO.: 62/084,687  出願日:2014年11月

    公開番号:US 2017/0108517 A1  公開日:2017年4月

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受賞

  • 長瀬研究振興賞

    2012年4月   長瀬科学技術振興財団  

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共同研究・競争的資金等の研究課題

  • 集積化DNAオリガミナノポアによるトランスクリプトームシーケンシングの開発

    研究課題/領域番号:JPMJKP23H4  2024年4月 - 2029年3月

    科学技術振興機構 (JST)  経済安全保障重要技術育成プログラム(K Program) 

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    担当区分:研究分担者 

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  • 遺伝子発現デバイスによる細胞内転写制御

    2023年 - 2025年

    科研費 挑戦的研究(萌芽) 

    遠藤 政幸

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    担当区分:研究代表者 

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  • DNAオリガミを用いたエピジェネティック遺伝子発現の1分子可視化

    2021年 - 2023年

    科研費 基盤研究B 

    遠藤 政幸

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  • 機能集積型DNAナノデバイスによる分子デリバリーシステムの開発

    2020年 - 2021年

    平和中島財団 

    遠藤 政幸

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    担当区分:研究代表者 

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  • 分子機能を集積したDNAデバイスによる細胞機能の制御

    2019年 - 2020年

    上原記念生命科学財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • ナノスケール空間内での生体分子の物性の1分子計測法の開発

    2019年 - 2020年

    中谷医工計測技術振興財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 設計したDNAナノスケール空間が生体分子の物性に与える影響とその機構の解明

    2018年 - 2021年

    科研費  国際共同研究強化B 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • ナノ空間での生体分子の1分子物性測定と空間-分子間相互作用の解明

    2018年 - 2019年

    京都大学教育研究振興財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • RNPナノ構造体による細胞内分子の空間制御

    研究課題/領域番号:16K21117  2016年4月 - 2019年3月

    日本学術振興会  科学研究費助成事業  若手研究(B)

    大野 博久, 齊藤 博英, 遠藤 政幸, 望月 めぐみ, 宮里 智博

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    配分額:3250000円 ( 直接経費:2500000円 、 間接経費:750000円 )

    細胞内においては、分子の空間的な制御がその機能発現に重要な役割を果たしている。そのような分子の分布や他分子との位置関係を規定するために生物がしばしば利用しているのが、分子足場である。本研究では、ヒト細胞内において任意の分子の空間配置を制御できる分子足場の構築を試みた。RNAとタンパク質からなる分子足場を使うことで、特定の機能性タンパク質の局在を制御することに成功し、それによって細胞運命を制御することに成功した。

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  • DNAナノ構造のマイクロ界面制御によるプログラマブルで動的な細胞型分子ロボット

    研究課題/領域番号:16K12521  2016年4月 - 2018年3月

    日本学術振興会  科学研究費助成事業  挑戦的萌芽研究

    瀧ノ上 正浩, 石川 大輔, 川野 竜司, 遠藤 政幸

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    配分額:3250000円 ( 直接経費:2500000円 、 間接経費:750000円 )

    本研究では,DNAナノ構造による分子機能制御とマイクロ流体工学による流体界面制御による細胞型分子ロボットの創製と制御を目指した研究を行った.DNAオリガミによる機能性の両親媒性DNA分子ナノデバイスをマイクロ油中水滴の界面に自己組織化させて細胞型分子ロボットを構築できた.期間全体を通じた研究により,分子センシングや自律的な運動などの機能を含めた,プログラマブルに,動的な機能をもつ細胞型分子ロボットを構築する基礎技術ができた.

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  • 人工遺伝子スイッチを用いた遺伝子発現の制御と機構の解明

    2016年 - 2021年

    科研費  基盤研究S 

    杉山 弘

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    資金種別:競争的資金

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  • 外部刺激に応答するDNAオリガミ構造体による細胞機能の制御

    2016年 - 2018年

    内藤記念科学振興財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • DNAオリガミシートを使った分子デリバリーシステムの構築

    2016年 - 2017年

    科研費  挑戦的萌芽研究 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 細胞膜を貫通するDNAナノ構造体による分子デリバリーシステムの開発

    2016年 - 2017年

    ノバルティス科学振興財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 細胞機能を制御するDNAナノ構造体分子システムの開発

    2015年 - 2017年

    科研費  基盤研究B 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • DNAナノ空間を用いた生化学反応系の再構成とその1分子可視化

    2015年

    倉田記念日立科学技術財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 三次元ナノDNA構造体を基本ユニットとする疾患治療システムの開発

    研究課題/領域番号:26293008  2014年4月 - 2017年3月

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    西川 元也, 高橋 有己, 高倉 喜信, 遠藤 政幸, 渡辺 宏

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    配分額:17030000円 ( 直接経費:13100000円 、 間接経費:3930000円 )

    三次元ナノDNA構造体を基本ユニットとする疾患治療システムの開発を目的に、構造的特徴の異なる種々のDNA基本ユニットを新たにデザインし、比較検討した。その結果、4本足DNAが最も効率よく形成可能であり、免疫細胞による取り込みも高いことが示された。そこで、自己組織化によりゲル化するシステムを開発し、DNAハイドロゲルを作製した。レオロジー解析の結果、このゲルは非常に速やかにゲル-ゾル転移することで注射投与可能であり、投与後速やかに再ゲル化することも明らかとなった。抗原ペプチドを用いた検討から、カチオン化抗原を利用することで抗原内包DNAハイドロゲルの抗腫瘍効果が著しく向上することを見出した。

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  • 新規単分子蛍光観察法によるがん抑制因子p53のDNA探索機構の解明

    研究課題/領域番号:26840045  2014年4月 - 2016年3月

    日本学術振興会  科学研究費助成事業  若手研究(B)

    鎌形 清人, 杉山 弘, 遠藤 政幸

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    配分額:3900000円 ( 直接経費:3000000円 、 間接経費:900000円 )

    p53はDNAのある部位(標的配列)へ結合することで、細胞のがん化を防ぐ。本研究では、p53の標的配列への結合の仕組み、及び、p53の特定の構造を持たない変性領域の役割の解明を行った。p53がDNA上を動く過程を一分子ごと計測した結果、標的DNA配列への結合の確率が低く、p53の修飾により結合確率が制御されることが明らかとなった。さらに、変性領域が長くなると、p53がDNAの配列を識別できなくなることが明らかとなった。

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  • 外部刺激応答性DNAナノ構造体による分子デリバリーシステムの構築

    2014年 - 2015年

    科研費  挑戦的萌芽研究 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 細胞の受容体に学ぶ人工シグナル伝達システムの構築

    2014年 - 2015年

    積水化学 自然に学ぶものづくり研究助成プログラム 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 細胞応答の制御を目指した機能性DNAナノ構造体の構築

    2013年 - 2014年

    旭硝子財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 細胞応用を目指した機能性DNAナノ構造体による分子システムの構築

    2013年 - 2014年

    三菱財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 核酸ナノ構造を活用した多元分子情報変換デバイスの創成

    2012年 - 2016年

    新学術領域研究「感覚と知能を備えた分子ロボットの創成」 

    齊藤 博英

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    資金種別:競争的資金

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  • 分子科学的アプローチによる遺伝子発現の制御と機構の解明

    2012年 - 2016年

    科研費 基盤研究S 

    杉山 弘

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    資金種別:競争的資金

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  • DNA ナノテクノロジーを基盤とした動的な1分子観察系の構築と応用

    2012年 - 2014年

    科研費 基盤研究B 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 設計したナノスケール空間での酵素反応の直接観察と反応機構の解明

    2012年

    長瀬科学技術振興財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • DNAを情報分子として媒介させた集積型分子デバイスの構築

    2011年

    池谷科学技術振興財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 設計されたDNAナノ空間中での反応制御と1分子の動的な観察

    2011年

    住友財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • プログラマブル・セルフ・アセンブルを用いたMEMSとナノ構造の融合プロセス

    2010年 - 2012年

    科研費 基盤研究B 

    田畑 修

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    資金種別:競争的資金

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  • 設計されたDNAナノ空間中での反応制御と1分子の動的な観察

    2010年

    住友財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • ポリアミド-転写活性化因子融合分子による特定遺伝子活性化法の開発

    2009年 - 2011年

    科研費 基盤研究C 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 生体分子情報-構造-機能統合ナノシステムの構築

    2008年 - 2014年

    JST 戦略的基礎研究推進事業(CREST) 

    杉山 弘

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    資金種別:競争的資金

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  • 自己集合性生体超分子による分子の組織化と機能性デバイスへの応用

    2008年

    徳山科学技術振興財団 

    遠藤 政幸

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    担当区分:研究代表者  資金種別:競争的資金

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  • 光機能化タバコモザイクウィルス超分子による光電変換デバイスの創製

    研究課題/領域番号:19655049  2007年 - 2008年

    日本学術振興会  科学研究費助成事業  萌芽研究

    真嶋 哲朗, 立川 貴士, 遠藤 政幸

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    配分額:2600000円 ( 直接経費:2600000円 )

    これまで、タンパク超分子をテンプレートとして用いナノ材料を1次元的もしくは2次元的に配列させる方法や、形成された超分子上に無機物を集積させ化学的にナノワイヤやナノ粒子を作成する方法が提案されている。いずれも一定の成果が得られているものの、作成位置の選択性や均一性という点では実用的な水準に達しているとはいえない。また、複雑なプログラムに従った分子集合による高次構造化や機能性の発現と制御、さらにはナノ空間内での分子間相互作用や化学反応は、未だに達成されておらずこれからの課題である。そこで本研究では、優れた時間応答性と空間分解能を持つクリーンなエネルギーである“光"による機能の発現と制御を目指し、光機能性分子(光異性化分子や光を吸収し電子移動及びエネルギー移動を引き起こす分子)を部位特異的に結合させた光機能性タンパク超分子を創製を行った。
    紅色光合成細菌の光捕集系II(LH2)を模倣するため、すでに確立したタバコモザイクウィルス(TMV)の合成法及び精製方法、並びに光機能性分子による修飾法によって、TMVコートタンパクの内孔側にポルフィリン誘導体を導入した。これを、TMVコートタンパクの自己集合によって、ロッド状のナノ構造を形成させた。本年度は、ロッド状のナノ構造を、原子間力顕微鏡(AFM)によって解析した。また、ポルフィリンのπ-スタッキングが拡張した光機能化TMV超分子の構造と機能性は、吸収、蛍光スペクトル及びフェムト秒過渡吸収測定により調べた。これによって、TMVの超分子構造とポルフィリン間の相互作用について議論し、バイオ光ファイバー及びバイオ導電性ファイバーの開発への展開が示唆された。さらに、ヘテロなクロモフォアの導入に着目し、エネルギー移動の系では、フリーベースポルフィリンとZnの配位したポルフィリンを用い、電子移動の系では、電子供与基(亜鉛ポルフィリンなど)と電子受容基(フラーレンなど)を用い、それらの混合比を変えることによっで効率的な電荷分離の構築についての知見を得た。

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  • 癌治療を目指したアポトーシス関連タンパクの光機能化と応用

    研究課題/領域番号:18510184  2006年 - 2008年

    日本学術振興会  科学研究費助成事業  基盤研究(C)

    遠藤 政幸

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    配分額:4140000円 ( 直接経費:3600000円 、 間接経費:540000円 )

    アポトーシスの誘導による癌細胞の細胞死を誘導することでその除去を目的とし、その間連連酵素であるcaspase-3とDNA断片化因子に光応答性分子を組み込み、光照射によって活性化することで人工的なアポトーシスの誘導を検討した。光分解性の2-nitrophenylglycine4,5-dimethoxy-2-nitrophenylglycine(DMNpg)をDNA断片化因子の阻害タンパク(ICAD)の切断位置に導入し、細胞外転写翻訳反応で光機能化ICADが高収率で発現され、精製した。精製した光機能化DNA断片化因子へ光照射を行うとICADの分解が起こり、光機能化DNA断片化因子複合体への光照射によって、DNase活性の発現を行えることを見出した。さらに細胞内導入のためにHIV由来のTAT配列の導入した光機能化DNA断片化因子を合成した。これによって細胞導入と光照射によるアポトーシスの誘導を検討できる系を構築した。

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  • 光機能性DNAのナノサイエンス

    研究課題/領域番号:17105005  2005年 - 2009年

    日本学術振興会  科学研究費助成事業  基盤研究(S)

    真嶋 哲朗, 藤塚 守, 川井 清彦, 遠藤 政幸

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    配分額:107120000円 ( 直接経費:82400000円 、 間接経費:24720000円 )

    様々な光機能性クロモフォアを修飾したDNAを用いて、DNA内の光電荷分離、電荷移動機構を明らかにし、高効率・長寿命電荷分離を実現した。さらに、光機能性DNA分子ワイヤー、光エネルギー変換などの光電変換デバイスや、高効率DNA損傷法への展開を行い、DNA光ナノサイエンスの創製を試みた。

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  • 修飾タバコモザイクウイルスコートタンパクの超分子集合による光機能性

    研究課題/領域番号:17029039  2005年 - 2006年

    日本学術振興会  科学研究費助成事業  特定領域研究

    遠藤 政幸

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    配分額:4600000円 ( 直接経費:4600000円 )

    本研究では、明確な構造に組み上げることが可能な生体超分子タバコモザイクウィルス(TMV)をフレームとして、自己集合により光機能性分子の規則的な集積とその光機能性について検討した。TMV超分子に光機能性分子を集積し、らせん状にクロモフォアが集積した構造の構築とその物性の検討を行った。TMV-ピレンで得られたクロモフォアの導入位置と超分子形成時の配置の知見を基に、TMV超分子内でのエネルギー移動系の構築を行った。光合成関連の光機能分子であるポルフィリン誘導体の集積を行い、そのナノ構造の形成とエネルギー移動過程の検討を行った。porphyrin (FbP)-maleimideとZn-porphyrin (ZnP)-maleimideを合成し、TMVCPの123位をシステインに変異させ、それぞれのポルフィリン誘導体を位置選択的に導入した。これらのTMV-porphyrinモノマーをpH7.0及びpH5.5で自己集合を行い、ZnPからFbPへのエネルギー移動を検討した。ZnPとFbPのモル比を変化させたTMV超分子を作成し、それぞれの比のモノマーの発光スペクトルと比較した。その結果、TMV超分子ZnPの発光強度の減少及びFbPの発光強度の増加が見られた。FbP発光強度は多層超分子構造を形成するpH5.5では10%FbPが含まれるTMV超分子構造で4.5倍まで増加した。エネルギー移動効率は10%FbPで2層のディスク構造を形成するpH7.0では24%、pH5.5では32%であった。このことからエネルギー移動は2層間よりも多層間の超分子構造で効率的に行われ、隣接したポルフィリン間と層間のポルフィリン間でもエネルギー移動が起こることが示唆された。TMV超分子内のZnP発光の蛍光寿命測定からZnPのみの超分子では1成分であるのに対して、FbPが添加されると、短寿命成分が見られ、エネルギー移動に由来する成分であることが示唆された。その寿命から、エネルギー移動速度はpH5.5の10%FbP/ZnP-TMV超分子でk_<ET>=6.4x10^9s^<-1>であった。以上のように、TMV超分子を足場としたポルフィリンの位置選択的な導入と集積が可能となり、ZnP/FbP-TMV超分子内でZnPからFbPへのエネルギー移動を介して光捕集が行われることが明らかとなった。

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  • 光機能性生体分子によるアポトーシスの誘導と癌治療への応用

    研究課題/領域番号:15710161  2003年 - 2005年

    日本学術振興会  科学研究費助成事業  若手研究(B)

    遠藤 政幸

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    配分額:3700000円 ( 直接経費:3700000円 )

    アポトーシス(プログラムされた細胞死)の誘導による癌細胞の除去を目的とし、最終段階で働くプロテアーゼであるcaspase-3を光機能化し、その活性を光照射によって制御すること方法の確立を行った。Caspase-3はアポトーシスシグナル伝達の上流にあるプロテアーゼcaspase-8による特異的な切断(セリン176残基)により活性化されたため、この特異的な切断位置に光分解性の2-nitrophenylglycine(Npg)をペプチド主鎖に導入し光化学反応により活性の発現を試みた。
    ヒトcaspase-3のS176への位置特異的なNpg基の導入は、4塩基コドンと細胞外翻訳反応によって行った。Npgを導入したcaspase-3を用いて、光照射(366nm、0℃)を行い、基質であるDEVD(Asp-Glu-Val-Asp)の分解[(DEVD)2-rhodamine110で測定]を用いて活性を見た。光照射前(0min)では活性は見られないが、1分間の光照射で酵素活性の回復が見られた。caspase-3阻害剤(DEVD-CHO)の添加によってその活性が抑制されたことからこれらの活性がcaspase-3に由来することが確認された。次にcaspase-3の持つ自己切断と活性化の抑制について検討した。天然型では時間に依存して徐々に活性が増加するが、Npg-caspase-3では自己活性化は抑制され、光照射によって天然型と同様の自己活性化能を回復することが明らかとなった。このことから、Npgの位置選択的な導入によって、caspase-3の活性の制御が可能であることが明らかとなった。この結果、細胞内への光機能性caspase-3が導入と光照射によって、アポトーシスの誘導が可能性となると考えられる。これらの光機能化したcaspase-3を細胞に侵入可能にするため、HIV(ヒト免疫不全ウィルス)のTAT配列(YGRKKRRQRRR)をNまたはC末端に導入した光機能性caspase-3を上記と同じ方法で合成した。Npg導入によるcaspase-3活性の抑制及び光照射による活性化は、TAT配列を導入していないものと同様に制御できることが明らかとなった。これらの合成したTAT配列の導入されたNpg-caspase-3をヒトのT細胞(Jurkat T cell)内に効率よく取り込ませる実験と光照射によるアポトーシスの誘導を行うことができる環境が現在までの研究で整った。

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  • 光機能界面における有機物の反応機構の解明

    研究課題/領域番号:14050055  2001年 - 2006年

    日本学術振興会  科学研究費助成事業  特定領域研究

    真嶋 哲朗, 藤乗 幸子, 藤塚 守, 川井 清彦, 遠藤 政幸

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    配分額:83800000円 ( 直接経費:83800000円 )

    TiO_2光触媒反応における光機能界面上での種々の有機物の分解機構を解明するため、(1)有機物ラジカルイオンの反応性、(2)ヒドロキシラジカルや酸素アニオンなどの酸素活性種と有機物の友応、特に、TiO_2光触媒による有機物の分解機構、(3)ラジカルイオン中間体の動的挙動の解明などを中心に、時間分解渦渡吸収測定法、パルスラジオリシス法、高感度固体表面NMR法を使用して研究を行い、特に種々の新規TiO_2光触媒について、反応初期過程の解明と光触媒能の定量的な評価を行うことができた。また、全反射蛍光顕微鏡を用いた活性酸素種の単一分子検出法という新しい方法論を提案することができた。具体的には、時間分解拡散反射法を用いてTiO_2表面上における基質の吸着と一電子酸化反応過程を検討し、一電子酸化効率は基質の酸化電位だけでなく基質とTiO_2との電子的な相互作用の大きさに著しく依存することを明らかにした。また、可視光応答型のN-,S-,C-ドープTiO_2光触媒反応、気相中の光触媒反応、TiO_2から表面吸着したポリ酸への電子移動反応および一電子還元ポリ酸の励起状態からの電子移動反応、TiO_2表面吸着シクロデキストリンによる有機分子の一電子酸化反応などを反応機構を詳細に検討した。内径数nm程度のTiO_2ナノチューブによる有機分子の一電子酸化反応過程では、通常のナノ粒子と比べ、電荷分離状態が10倍以上長寿命化することを見出し、これは、一次元方向に伸びたTiO_2ナノチューブの形状に起因することがわかった。TiO_2光触媒反応によって生成したヒドロキシラジカルや一重項酸素(^1O_2)を蛍光プローブにより単一分子レベルで検出することに成功し、TiO_2光触媒表面からこれらの活性酸素が空気中を拡散していることを見出した。

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  • 修飾DNAの機能化による分子デバイス

    研究課題/領域番号:13305058  2001年 - 2004年

    日本学術振興会  科学研究費助成事業  基盤研究(A)

    真嶋 哲朗, 藤塚 守, 藤乗 幸子, 川井 清彦, 遠藤 政幸

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    配分額:55510000円 ( 直接経費:42700000円 、 間接経費:12810000円 )

    本研究では、種々の機能性クロモファを共有結合によって導入した修飾DNAを用いることによって、クロモファ独自の機能性を利用して修飾DNAに様々な機能性を賦与し、その機能を自由にコントロールすることによって、機能化修飾DNAの特に生体系での分子デバイスとしての可能性を明らかにすることを目指した。中でも、DNA分子ワイヤの構築の基礎となるDNA中のホール移動に関して、一つのDNA分子に一つの光機能性クロモファを配列を制御して修飾し、その光機能をDNA分子の塩基配列の影響をnmオーダーで明らかにし、さらに、一つのDNA分子に複数の機能性クロモファを配列を制御して修飾し、例えば光電子移動がどのように発現するのかをnmオーダーでかつns-ps時間分解法で解明した。ところで、機能性分子を分子集合によって正確に操作する技術はボトムアップ型のナノテクノロジーに必要不可欠であり、人為的な情報にしたがって分子から組み上げる方法の確立が必要である。DNAは、正確な分子集合を多種類の分子で実現する最も有力な分子であり、またDNAには化学修飾によってさまざまな機能性分子を導入できる利点がある。そこで、自己集合に基づき規則的でかつ剛直なDNA構造を構築するため、枝分かれ構造を持つDNAユニットを合成し、この架橋DNAを用いたDNAナノ構造の構築に成功した。「修飾DNAの機能化による分子デバイス」の実現のためには、今後さらに、一つのDNA分子に多数の機能性クロモファを修飾し、クロロフィルのような多機能性、複合機能性などの光機能を発現させること、修飾DNAの連結によって、さらに複合した機能を有する修飾DNA超分子を構築し、生体分子の機能を上回るほどの高機能性分子デバイスの可能性、修飾DNAを分子デバイスとして生体系で利用する方法、その機能の制御方法について明らかにすることが必要である。

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