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

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Modified Nucleic Acids in Biology and Medicine

Part of the book series: RNA Technologies ((RNATECHN))

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Abstract

Visualization of biomolecules is one of the straightforward ways to elucidate the physical properties of individual molecules and their reaction processes. Atomic force microscopy (AFM) enables direct imaging of biomolecules in the physiological environment. Because AFM visualizes the molecules at nanometer-scale spatial resolution, a versatile observation scaffold should be required for the precise imaging of molecules in the reactions. The emergence of DNA origami technology allows the precise placement of target molecules in the designed nanostructures and enables molecules to be detected at the single-molecule level. The DNA origami is applied for visualizing the detailed motions of target molecules in the reaction using high-speed AFM (HS-AFM), which enables the analysis of dynamic motions of biomolecules in a subsecond time resolution.

In this review article, I describe the combination of the DNA origami system and HS-AFM for imaging various biochemical reactions including enzyme reactions and DNA structural changes. For observation of the enzyme reactions including the DNA methylation, base-excision repair, recombination, and transcription, the substrate DNA strands were placed in DNA nanostructures and their reactions were observed by HS-AFM. In addition, DNA structural changes including G-quadruplex formation and disruption, the hybridization and dehybridization of photoresponsive oligonucleotides, B–Z transition, and G-quadruplex/i-motif formation were visualized using this observation system. The stepwise movement of mobile DNA molecule along the DNA track was visualized on the DNA origami surface. Furthermore, the dynamic assembly/disassembly of photoresponsive DNA origami structures and formation of micrometer-sized DNA origami assemblies were directly visualized on the lipid bilayer. Catalytic reactions and RNA interactions were imaged by HS-AFM. These target-orientated observation systems should contribute to the detailed analysis of biomolecule motions in real time and at molecular resolution.

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Authors and Affiliations

  1. Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan

    Masayuki Endo

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  1. Masayuki Endo
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Correspondence to Masayuki Endo .

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Editors and Affiliations

  1. Nanobiomedical Center, Adam Mickiewicz University, Poznań, Poland

    Stefan Jurga

  2. Formerly at Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany

    Volker A. Erdmann (Deceased)

  3. Institute of the Bioorganic Chemistry of the Polish Academy of Sciences, Poznań, Poland

    Jan Barciszewski

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Endo, M. (2016). Single-Molecule Visualization of Biomolecules in the Designed DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy. In: Jurga, S., Erdmann (Deceased), V., Barciszewski, J. (eds) Modified Nucleic Acids in Biology and Medicine. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-319-34175-0_17

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