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

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Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto 606-8502, Japan
Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
§ CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
Cite this: Chem. Rev. 2014, 114, 2, 1493–1520
Publication Date (Web):November 12, 2013
https://doi.org/10.1021/cr300253x
Copyright © 2013 American Chemical Society
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  2. Ariane Nunes-Alves and Guilherme Menegon Arantes . Mechanical Unfolding of Macromolecules Coupled to Bond Dissociation. Journal of Chemical Theory and Computation 2018, 14 (1) , 282-290. https://doi.org/10.1021/acs.jctc.7b00805
  3. Na Wu and Itamar Willner . pH-Stimulated Reconfiguration and Structural Isomerization of Origami Dimer and Trimer Systems. Nano Letters 2016, 16 (10) , 6650-6655. https://doi.org/10.1021/acs.nanolett.6b03418
  4. Na Wu and Itamar Willner . DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles. Nano Letters 2016, 16 (4) , 2867-2872. https://doi.org/10.1021/acs.nanolett.6b00789
  5. Masayuki Endo, Xiwen Xing, Xiang Zhou, Tomoko Emura, Kumi Hidaka, Bodin Tuesuwan, and Hiroshi Sugiyama . Single-Molecule Manipulation of the Duplex Formation and Dissociation at the G-Quadruplex/i-Motif Site in the DNA Nanostructure. ACS Nano 2015, 9 (10) , 9922-9929. https://doi.org/10.1021/acsnano.5b03413
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  10. Toshio Ando, Takayuki Uchihashi, and Simon Scheuring . Filming Biomolecular Processes by High-Speed Atomic Force Microscopy. Chemical Reviews 2014, 114 (6) , 3120-3188. https://doi.org/10.1021/cr4003837
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  15. Giulio Fittolani, Peter H. Seeberger, Martina Delbianco. Helical polysaccharides. Peptide Science 2020, 112 (1) https://doi.org/10.1002/pep2.24124
  16. Ryu Tashiro, Hiroaki Taguchi, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama. Effects of Physical Damage in the Intermediate Phase on the Progression of Amyloid β Fibrillization. Chemistry – An Asian Journal 2019, 14 (23) , 4140-4145. https://doi.org/10.1002/asia.201901193
  17. Saminathan Ramakrishnan, Boxuan Shen, Mauri A. Kostiainen, Guido Grundmeier, Adrian Keller, Veikko Linko. Real‐Time Observation of Superstructure‐Dependent DNA Origami Digestion by DNase I Using High‐Speed Atomic Force Microscopy. ChemBioChem 2019, 20 (22) , 2818-2823. https://doi.org/10.1002/cbic.201900369
  18. Masayuki Endo. AFM-based single-molecule observation of the conformational changes of DNA structures. Methods 2019, 169 , 3-10. https://doi.org/10.1016/j.ymeth.2019.04.007
  19. Yangyang Yang, Shiwei Zhang, Shengtao Yao, Rizhao Pan, Kumi Hidaka, Tomoko Emura, Chunhai Fan, Hiroshi Sugiyama, Yufang Xu, Masayuki Endo, Xuhong Qian. Programming Rotary Motions with a Hexagonal DNA Nanomachine. Chemistry – A European Journal 2019, 25 (20) , 5158-5162. https://doi.org/10.1002/chem.201900221
  20. Akinori Kuzuya. Manipulation of Molecular Architecture with DNA. 2019,,, 25-41. https://doi.org/10.1002/9783527823987.vol2_c2
  21. , . Molecular Technology. 2018,,https://doi.org/10.1002/9783527823987
  22. Charlotte Kielar, Francesco V. Reddavide, Stefan Tubbenhauer, Meiying Cui, Xiaodan Xu, Guido Grundmeier, Yixin Zhang, Adrian Keller. Pharmacophore Nanoarrays on DNA Origami Substrates as a Single-Molecule Assay for Fragment-Based Drug Discovery. Angewandte Chemie 2018, 130 (45) , 15089-15093. https://doi.org/10.1002/ange.201806778
  23. Charlotte Kielar, Francesco V. Reddavide, Stefan Tubbenhauer, Meiying Cui, Xiaodan Xu, Guido Grundmeier, Yixin Zhang, Adrian Keller. Pharmacophore Nanoarrays on DNA Origami Substrates as a Single-Molecule Assay for Fragment-Based Drug Discovery. Angewandte Chemie International Edition 2018, 57 (45) , 14873-14877. https://doi.org/10.1002/anie.201806778
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  27. Q Li, J P Froning, M Pykal, S Zhang, Z Wang, M Vondrák, P Banáš, K Čépe, P Jurečka, J Šponer, R Zbořil, M Dong, M Otyepka. RNA nanopatterning on graphene. 2D Materials 2018, 5 (3) , 031006. https://doi.org/10.1088/2053-1583/aabdf7
  28. Masayuki Endo, Hiroshi Sugiyama. DNA Origami Nanomachines. Molecules 2018, 23 (7) , 1766. https://doi.org/10.3390/molecules23071766
  29. Pranjal Nautiyal, Fahad Alam, Kantesh Balani, Arvind Agarwal. The Role of Nanomechanics in Healthcare. Advanced Healthcare Materials 2018, 7 (3) , 1700793. https://doi.org/10.1002/adhm.201700793
  30. Masayuki Endo, Hiroshi Sugiyama. Direct Observation of Dynamic Movement of DNA Molecules in DNA Origami Imaged Using High-Speed AFM. 2018,,, 213-224. https://doi.org/10.1007/978-1-4939-8591-3_13
  31. . Nanoscale Imaging. 2018,,https://doi.org/10.1007/978-1-4939-8591-3
  32. Elena M. Willner, Yuu Kamada, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hendrik Dietz, Hiroshi Sugiyama, Masayuki Endo. Single-Molecule Observation of the Photoregulated Conformational Dynamics of DNA Origami Nanoscissors. Angewandte Chemie 2017, 129 (48) , 15526-15530. https://doi.org/10.1002/ange.201708722
  33. Elena M. Willner, Yuu Kamada, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hendrik Dietz, Hiroshi Sugiyama, Masayuki Endo. Single-Molecule Observation of the Photoregulated Conformational Dynamics of DNA Origami Nanoscissors. Angewandte Chemie International Edition 2017, 56 (48) , 15324-15328. https://doi.org/10.1002/anie.201708722
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  35. Arivazhagan Rajendran, Eiji Nakata, Shun Nakano, Takashi Morii. Nucleic-Acid-Templated Enzyme Cascades. ChemBioChem 2017, 18 (8) , 696-716. https://doi.org/10.1002/cbic.201600703
  36. Na Wu, Itamar Willner. Programmed dissociation of dimer and trimer origami structures by aptamer–ligand complexes. Nanoscale 2017, 9 (4) , 1416-1422. https://doi.org/10.1039/C6NR08209B
  37. Uroš Maver, Tomaž Velnar, Miran Gaberšček, Odon Planinšek, Matjaž Finšgar. Recent progressive use of atomic force microscopy in biomedical applications. TrAC Trends in Analytical Chemistry 2016, 80 , 96-111. https://doi.org/10.1016/j.trac.2016.03.014
  38. Yutaro Yamagata, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo. Triple Helix Formation in a Topologically Controlled DNA Nanosystem. Chemistry - A European Journal 2016, 22 (16) , 5494-5498. https://doi.org/10.1002/chem.201505030
  39. Masayuki Endo. Single-Molecule Visualization of Biomolecules in the Designed DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy. 2016,,, 403-427. https://doi.org/10.1007/978-3-319-34175-0_17
  40. , , . Modified Nucleic Acids in Biology and Medicine. 2016,,https://doi.org/10.1007/978-3-319-34175-0
  41. Hisashi Tadakuma, Takeya Masubuchi, Takuya Ueda. RNA Study Using DNA Nanotechnology. 2016,,, 121-163. https://doi.org/10.1016/bs.pmbts.2015.11.004
  42. . Nanotechnology Tools for the Study of RNA. 2016,,https://doi.org/
  43. Yosuke Takeuchi, Masayuki Endo, Yuki Suzuki, Kumi Hidaka, Guillaume Durand, Eric Dausse, Jean-Jacques Toulmé, Hiroshi Sugiyama. Single-molecule observations of RNA–RNA kissing interactions in a DNA nanostructure. Biomaterials Science 2016, 4 (1) , 130-135. https://doi.org/10.1039/C5BM00274E
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  45. Masayuki Endo, Yosuke Takeuchi, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Fuan Wang, Itamar Willner, Hiroshi Sugiyama. Single-Molecule Visualization of the Activity of a Zn 2+ -Dependent DNAzyme. Angewandte Chemie International Edition 2015, 54 (36) , 10550-10554. https://doi.org/10.1002/anie.201504656
  46. Ryu Tashiro, Masahiro Iwamoto, Hironobu Morinaga, Tomoko Emura, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama. Linking two DNA duplexes with a rigid linker for DNA nanotechnology. Nucleic Acids Research 2015, 43 (14) , 6692-6700. https://doi.org/10.1093/nar/gkv662
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  48. Fuan Wang, Xiaoqing Liu, Itamar Willner. DNA-Schalter: Grundlagen und Anwendungen. Angewandte Chemie 2015, 127 (4) , 1112-1144. https://doi.org/10.1002/ange.201404652
  49. Fuan Wang, Xiaoqing Liu, Itamar Willner. DNA Switches: From Principles to Applications. Angewandte Chemie International Edition 2015, 54 (4) , 1098-1129. https://doi.org/10.1002/anie.201404652
  50. Tomonori Shibata, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, Hirohide Saito. Folding RNA–Protein Complex into Designed Nanostructures. 2015,,, 169-179. https://doi.org/10.1007/978-1-4939-2730-2_14
  51. . RNA Scaffolds. 2015,,https://doi.org/10.1007/978-1-4939-2730-2
  52. Laura Nevola, Ernest Giralt. Modulating protein–protein interactions: the potential of peptides. Chemical Communications 2015, 51 (16) , 3302-3315. https://doi.org/10.1039/C4CC08565E
  53. Fabio Variola. Atomic force microscopy in biomaterials surface science. Physical Chemistry Chemical Physics 2015, 17 (5) , 2950-2959. https://doi.org/10.1039/C4CP04427D
  54. Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Marie-Paule Teulade-Fichou, Jean-Louis Mergny, Hiroshi Sugiyama. Small molecule binding to a G-hairpin and a G-triplex: a new insight into anticancer drug design targeting G-rich regions. Chemical Communications 2015, 51 (44) , 9181-9184. https://doi.org/10.1039/C5CC01678A
  55. Tomohiro Takenaka, Masayuki Endo, Yuki Suzuki, Yangyang Yang, Tomoko Emura, Kumi Hidaka, Takayuki Kato, Tomoko Miyata, Keiichi Namba, Hiroshi Sugiyama. Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials. Chemistry - A European Journal 2014, 20 (46) , 14951-14954. https://doi.org/10.1002/chem.201404757
  56. Ilko Bald, Adrian Keller. Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy. Molecules 2014, 19 (9) , 13803-13823. https://doi.org/10.3390/molecules190913803
  57. Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama. Direct and Single-Molecule Visualization of the Solution-State Structures of G-Hairpin and G-Triplex Intermediates. Angewandte Chemie 2014, 126 (16) , 4191-4196. https://doi.org/10.1002/ange.201308903
  58. Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama. Direct and Single-Molecule Visualization of the Solution-State Structures of G-Hairpin and G-Triplex Intermediates. Angewandte Chemie International Edition 2014, 53 (16) , 4107-4112. https://doi.org/10.1002/anie.201308903
  59. Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Naohiko Shimada, Atsushi Maruyama, Hiroshi Sugiyama. A lock-and-key mechanism for the controllable fabrication of DNA origami structures. Chemical Communications 2014, 50 (63) , 8743. https://doi.org/10.1039/C4CC02244K
  60. Arivazhagan Rajendran, Masayuki Endo, Kumi Hidaka, Phong Lan Thao Tran, Marie-Paule Teulade-Fichou, Jean-Louis Mergny, Hiroshi Sugiyama. G-quadruplex-binding ligand-induced DNA synapsis inside a DNA origami frame. RSC Advances 2014, 4 (12) , 6346. https://doi.org/10.1039/c3ra45676e

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