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Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures

Authors

  • Dr. Deepak Koirala,

    1. Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44240 (USA)
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  • Prakash Shrestha,

    1. Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44240 (USA)
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  • Tomoko Emura,

    1. Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
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  • Kumi Hidaka,

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

    1. Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44240 (USA)
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  • Prof. Dr. Masayuki Endo,

    Corresponding author
    1. Institute for Integrated Cell Material Sciences (WPI-iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
    2. CREST (Japan) Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075 (Japan)
    • Masayuki Endo, Institute for Integrated Cell Material Sciences (WPI-iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)===

      Hiroshi Sugiyama, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)===

      Hanbin Mao, Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44240 (USA)===

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  • Prof. Dr. Hiroshi Sugiyama,

    Corresponding author
    1. Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
    2. Institute for Integrated Cell Material Sciences (WPI-iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
    3. CREST (Japan) Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075 (Japan)
    • Masayuki Endo, Institute for Integrated Cell Material Sciences (WPI-iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)===

      Hiroshi Sugiyama, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)===

      Hanbin Mao, Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44240 (USA)===

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  • Prof. Dr. Hanbin Mao

    Corresponding author
    1. Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44240 (USA)
    • Masayuki Endo, Institute for Integrated Cell Material Sciences (WPI-iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)===

      Hiroshi Sugiyama, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)===

      Hanbin Mao, Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44240 (USA)===

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  • This research work was partially supported by the NSF (grant number CHE-1026532 to H.M.) and JST CREST and JSPS KAKENHI (grant numbers 24310097, 24104002, 25253004 to H.S. and M.E.).

Abstract

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

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