title: Single-Molecule Visualization of the Activity of a Zn(2+)-Dependent DNAzyme.
abstract: We demonstrate the single-molecule imaging of the catalytic reaction of a Zn(2+)-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.
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan). endo@kuchem.kyoto-u.ac.jp.|CREST (Japan) Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075 (Japan). endo@kuchem.kyoto-u.ac.jp.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Endo
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Takeuchi
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).
authors.forename: Yuki
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).
authors.forename: Tomoko
authors.initials: T
authors.lastname: Emura
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).
authors.forename: Kumi
authors.initials: K
authors.lastname: Hidaka
authors.affiliation: Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel).
authors.forename: Fuan
authors.initials: F
authors.lastname: Wang
authors.affiliation: Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel). willnea@vms.huji.ac.il.
authors.forename: Itamar
authors.initials: I
authors.lastname: Willner
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan). hs@kuchem.kyoto-u.ac.jp.|Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan). hs@kuchem.kyoto-u.ac.jp.|CREST (Japan) Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075 (Japan). hs@kuchem.kyoto-u.ac.jp.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D001483:Base Sequence; D055162:Biocatalysis; D021881:DNA, Catalytic / Q000737:chemistry*; D018625:Microscopy, Atomic Force; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015032:Zinc / Q000737:chemistry*
chemical_list: D021881:DNA, Catalytic; D015032:Zinc
keywords: DNA origami; DNA structures; DNAzymes; high-speed atomic force microscopy; single-molecule imaging