Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

Naturally occurring ribozymes with a modular architecture are promising platforms for construction of RNA nanostructures because modular redesign enables their oligomerization. The resulting RNA nanostructures can exhibit the catalytic function of the parent ribozyme in an assembly dependent manner. In this study, we designed and constructed open-form oligomers of a bimolecular form of an RNase P ribozyme. The ribozyme oligomers were analyzed biochemically and by atomic force microscopy (AFM).

DOI： 10.3390/molecules27238298

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpclett.2c02253

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.jbiosc.2022.06.008

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Language：English  

DOI： 10.3390/molecules27134224

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acsami.2c03265

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/cbic.202100446

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/cbic.202100573

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Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/anie.202105425

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/cbic.202100109

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Part of collection (book)   Publisher：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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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/cbic.202000332

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/chem.202003071

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.0c01978

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.0c03972

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/cbic.201900481

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Authorship：Lead author,　Last author,　Corresponding author  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Publishing type：Part of collection (book)   Publisher：Elsevier  

DOI： 10.1016/bs.mie.2020.04.045

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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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/asia.201901193

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/anie.201908392

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.jbiosc.2019.04.003

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.ymeth.2019.04.007

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.bioconjchem.9b00040

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/anie.201900610

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Optical Society  

DOI： 10.1364/ol.44.002831

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Other Link： https://www.osapublishing.org/viewmedia.cfm?URI=ol-44-11-2831&seq=0

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/chem.201900221

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/chem.201805394

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Part of collection (book)   Publisher：Springer New York  

DOI： 10.1007/978-1-4939-9666-7_17

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Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Other Link： http://www.nature.com/articles/s41565-018-0202-3.pdf

Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/admi.201800437

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

DOI： 10.1093/nar/gkx1267

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acsnano.7b06208

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Part of collection (book)   Publisher：Springer New York  

DOI： 10.1007/978-1-4939-8591-3_13

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Other Link： http://www.nature.com/articles/nnano.2017.29

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

Various DNA-based nanodevices have been developed on the nanometer scale using light as regulation input. However, the programmed controllability is still a major challenge for these artificial nanodevices. Herein, we demonstrate a rotary DNA nanostructure in which the rotations are controlled by light. A bar-shaped DNA rotor, fabricated as a stiff double-crossover molecule, was placed on the top of a rectangular DNA tile. The photoresponsive oligonucleotides modified with azobenzenes were employed as switching motifs to release/trap the rotor at specific angular position on DNA tile by switching photoirradiations between ultraviolet and visible light. As a result, two reconfigurable states (perpendicular and parallel) of rotor were obtained, in which the angular changes were characterized by AFM and fluorescence quenching assays. Moreover, the reversible rotary motions during the photoirradiation were directly visualized on the DNA tile surface in a nanometer-scale precision using a second-scale scanning of the high-speed AFM.

DOI： 10.1002/chem.201605616

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (bulletin of university, research institution)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Other Link： http://www.nature.com/articles/ncomms9052

Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE  

The most fundamental step in gene expression is transcription, during which DNA is transcribed to a corresponding RNA strand by the action of RNA polymerases (RNAPs). Over the past two decades, atomic force microscopy (AFM) has been used as one of the key tools in the investigation of transcriptional events at the single-molecule level. AFM studies have provided significant insights into the structure-function relationships of RNAP-DNA complexes in different stages of transcription. Here, we begin by illustrating the basic setup of AFM, followed by an introduction of the applications of AFM techniques, including high-speed AFM (HS-AFM) imaging, to investigate RNAP-DNA interactions with a special focus on promoter-search processes and open promoter formations. The combination of AFM with a newly developed experimental technique, DNA origami nanotechnology, will also be described. (C) 2015 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.ymeth.2015.05.018

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/anie.201504656

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publisher：NATURE PUBLISHING GROUP  

DOI： 10.1038/nnano.2015.142

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/bm501731f

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/acsnano.5b01723

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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 nano-objects 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： 10.1007/978-1-4939-2730-2_14

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1039/c5cc01678a

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/chem.201404084

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/chem.201404757

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/nn502253c

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1039/c4cc02244k

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/anie.201402973

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/anie.201404043

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Language：English   Publisher：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.

DOI： 10.1021/ar400299m

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/nl4044949

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/anie.201308903

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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.

DOI： 10.1021/ja4109819

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Language：English   Publisher：AMER CHEMICAL SOC  

DOI： 10.1021/cr300253x

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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.

DOI： 10.1021/ja408656y

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1039/c3ra45676e

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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.

DOI： 10.1039/c4cc00489b

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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.

DOI： 10.1039/c4bm00113c

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

DOI： 10.1002/chem.201303830

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/ja409085j

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1093/nar/gkt592

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Language：Japanese   Publishing type：Research paper (scientific journal)  

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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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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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.

DOI： 10.1039/c2cc37257f

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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.

DOI： 10.1039/c2bm00154c

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DOI： 10.1039/9781849736954-00073

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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.

DOI： 10.1039/c3cc38804b

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/ja307785r

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DOI： 10.1002/anie.201201890

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/nn300727j

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DOI： 10.1002/anie.201108199

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1038/NNANO.2011.253

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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.

DOI： 10.1021/ja209023u

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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.

DOI： 10.1021/ja2074856

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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.

DOI： 10.1002/anie.201102113

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Language：Japanese   Publisher：化学同人  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/0471142700.nc1209s48

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Language：English   Publishing type：Part of collection (book)   Publisher：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.

DOI： 10.1016/B978-0-12-398312-1.00002-0

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Publisher：Wiley Blackwell (John Wiley &amp; Sons)  

DOI： 10.1002/chin.201219276

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DOI： 10.1002/anie.201205247

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Because of the defined double-helical structure and programmed nature, DNA is an excellent molecule for the creation of various multidimensional nanostructures and the programmed placement of functional molecules and materials. DNA origami is an emerging strategy in the DNA nanotechnology field for designing defined two-dimensional DNA nanostructures. In this review, we focus on and describe the following DNA origami-based researches; (i) DNA origami-templated molecular assembly, (ii) programmed DNA origami assembly, (iii) design and construction of various three-dimensional DNA origami structures, (iv) programmed functionalization of DNA origami and combination with top-down nanotechnology, (v) single molecular observation on designed DNA origami, and (vi) DNA nanomachines working on DNA origami.

DOI： 10.5059/yukigoseikyokaishi.69.1352

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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.

DOI： 10.1021/ja204546h

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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.

DOI： 10.1038/NNANO.2010.284

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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.

DOI： 10.1021/nn1031627

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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.

DOI： 10.1039/c1cc13984c

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/0471142700.nc1208s45

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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.

DOI： 10.1039/c0ob01093f

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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.

DOI： 10.1039/c0cc05306f

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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.

DOI： 10.1021/ja1058907

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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.

DOI： 10.1021/ja907649w

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DOI： 10.1002/anie.201003604

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/chem.200903057

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PubMed

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1021/ja904252e

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PubMed

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Language：English   Publisher：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.

DOI： 10.1002/cbic.200900286

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PubMed

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1016/j.tet.2007.11.096

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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.

DOI： 10.1021/jo7025004

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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.

DOI： 10.1002/chem.200700895

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Photoreaction of trans-4'-benzyl-5-styrylfuran (trans-BSF) has been studied by the 355-nm laser flash photolysis (LFP) in CH2Cl2 using a Nd3+:YAG laser (30 ps, 5 mJ pulse(-1) or 5 ns, 30 mJ pulse(-1)). Transient fluorescence and absorption spectra assigned to the singlet excited trans-BSF were observed during the 30-ps LFP, whereas a transient absorption spectrum with two peaks at 400 and 510 nm, assigned to the trans-fused dihydrophenanthrene (DHP)-type intermediate (DP1), was observed during the 5-ns LFP. It is clearly suggested that a two-photon absorption process is involved in the formation of DP1. The first photoreaction is the photoisomerization of trans-BSF, which occurs to give cis-BSF. The second photoreaction process is photocyclization of cis-BSF, which occurs to give DP1 decaying with the half lifetime (tau(1/2)) of 2.8-4.0 mu s to produce another DHP-type intermediate (DP2) with an absorption peak at 400 nm in the absence of O-2, through [1,9]-hydrogen shift. DP2 decayed with tau(1/2) &gt; 500 mu s to give the product through aromatization. In O-2-saturated CH2Cl2, DP1 decayed with tau(1/2) = 250 ns to give a radical intermediate (X) with two peaks at 410 and 510 nm, through hydrogen abstraction of DP1 by O-2. X decayed with tau(1/2) = 150 mu s to give the product through successive hydrogen abstraction.

DOI： 10.1021/jo047977x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

DOI： 10.1002/anie.200501034

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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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

DOI： 10.1021/ja049007x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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 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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

DOI： 10.1002/anie.200460889

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

DOI： 10.1021/ja0367521

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

Novel photo responsive nucleosides, 1-N-(2'-deoxyribofuranosyl) 2-phenylazoimidazole and 1-N-ribofuranosyl 2-phenylazoimidazole have been designed and synthesized. trans-cis Photoisomerizations of the nucleosides with irradiation at a specific wavelength have been observed and the isomerizations are perfectly reversible. (C) 2003 Elsevier Ltd. All rights reserved.

DOI： 10.1016/S0040-4039(03)01697-6

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

DOI： 10.1002/anie.200352546

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jo9611780

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jo951621r

Scopus

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/ja960009u

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Language：English   Publishing type：Research paper (scientific journal)  

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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Language：English   Publishing type：Research paper (scientific journal)  

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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Language：English   Publisher：NATURE PUBLISHING GROUP  

DOI： 10.1038/srep17249

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Language：Japanese   Publisher：(公社)日本生化学会  

J-GLOBAL

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Language：English   Publisher：Future Medicine Ltd.  

DOI： 10.4155/fseb12013.14.37

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CiNii Books

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Language：English   Publisher：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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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

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

CiNii Books

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：TAYLOR & FRANCIS INC  

DOI： 10.1080/07391102.2013.786387

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Language：Japanese   Publisher：化学工業社  

CiNii Books

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Language：English  

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Language：English  

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Language：Japanese   Publisher：丸善  

CiNii Books

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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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J-GLOBAL

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DOI： 10.1093/nass/nrp041

PubMed

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER CHEMICAL SOC  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER CHEMICAL SOC  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER CHEMICAL SOC  

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Language：Japanese   Publisher：学会出版センタ-  

CiNii Books

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Language：Japanese   Publisher：化学同人  

CiNii Books

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Presentation type：Oral presentation (invited, special)  

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Language：English   Presentation type：Oral presentation (invited, special)  

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