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Optical detection of single DNA molecules using a silicon nanopore for readout of sequence information

Research Project

Project/Area Number 26600055
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Nanobioscience
Research InstitutionKeio University

Principal Investigator

Saiki Toshiharu  慶應義塾大学, 理工学部, 教授 (70261196)

Co-Investigator(Renkei-kenkyūsha) IWASAKI Wataru  東京大学, 大学院理学系研究科, 准教授 (50545019)
Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2014: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywordsナノポアセンシング / DNA / 蛍光計測 / プラズモン / 1分子計測 / ナノ光学 / ナノ流体工学 / ナノデバイス / 生体生命情報学 / バイオセンシング / ナノオプティクス
Outline of Final Research Achievements

The challenge in highly accurate identification of each nucleotide is slowing and stabilizing DNA translocation velocity. For this purpose, DNA conformation and drift-diffusion motion immediately before and after translocation should be investigated. In this study, an optical microscopic method with 100-nm and 0.1-ms resolution is developed to observe DNA coiling immediately after translocation and its motion. Characteristic DNA translocation dynamics caused by the electric field in the vicinity of nanopore exit is obtained and the mechanism is discussed in detail. To achieve higher spatial resolution aiming to single-molecule sequencing, the possibility of combination with STED and plasmonic nanopore is also demonstrated.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • Research Products

    (12 results)

All 2016 2015 2014

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Acknowledgement Compliant: 3 results,  Open Access: 1 results) Presentation (8 results) (of which Int'l Joint Research: 3 results,  Invited: 2 results)

  • [Journal Article] Optical observation of DNA motion during and immediately after nanopore translocation2016

    • Author(s)
      H. Yamazaki, S. Ito, K. Esashika, and T. Saiki
    • Journal Title

      Applied Physics Express

      Volume: 9 Issue: 1 Pages: 017001-017001

    • DOI

      10.7567/apex.9.017001

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Optical observation of DNA translocation through Al2O3 sputtered silicon nanopores in porous membrane2016

    • Author(s)
      H. Yamazaki, S. Ito, K. Esashika, Y. Taguchi, and T. Saiki
    • Journal Title

      Applied Physics A

      Volume: 122 Issue: 3

    • DOI

      10.1007/s00339-016-9764-9

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Salt dependence of DNA translocation dynamics through silicon nanopores detected by ultraviolet excitation2016

    • Author(s)
      S. Ito, H. Yamazaki, M. Tsukahara, K. Esashika, and T. Saiki
    • Journal Title

      Applied Physics A

      Volume: 122 Issue: 4

    • DOI

      10.1007/s00339-016-9762-y

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Robust discrimination between single gold nanoparticles and their dimers in aqueous solution for ultrasensitive homogeneous bioassays2015

    • Author(s)
      J. Kobayashi, Y. Takeshita, N. Mizuno, K. Esashika, and T. Saiki
    • Journal Title

      Advances in Optical Technologies

      Volume: 2015 Pages: 1-5

    • DOI

      10.1155/2015/581381

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] シリコンナノポアへのDNA捕捉過程の光学的観察2015

    • Author(s)
      山崎洋人, 伊藤晋太郎, アマルビー ユーゴ, 江刺家恵子, 斎木敏治
    • Organizer
      第76回応用物理学会秋季学術講演会
    • Place of Presentation
      名古屋国際会議場(愛知県・名古屋市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Optical Observation of DNA Translocation Dynamics through Solid-State Nanopores2015

    • Author(s)
      H. Yamazaki, M. Tsukahara, S. Ito, K. Esashika, and T. Saiki
    • Organizer
      The 11th Conference on Laers and Electro-Optics Pacific-Rim
    • Place of Presentation
      Busan, Korea
    • Year and Date
      2015-08-24 – 2015-08-28
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Optical Observation of DNA Translocation Dynamics through Solid-State Nanopores2015

    • Author(s)
      H. Yamazaki, S. Itoh, K. Esashika, and T. Saiki
    • Organizer
      The 11th Conference on Lasers and Electro-Optics Pacific Rim
    • Place of Presentation
      Busan (Korea)
    • Year and Date
      2015-08-24
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Salt Dependence of DNA Translocation Dynamics through Silicon Nanopores Detected by Ultraviolet Excitation2015

    • Author(s)
      S. Ito, H. Yamazaki, M. Tsukahara, K. Esashika, and T. Saiki
    • Organizer
      The 10th Asia-Pacific Conference on Near-field Optics
    • Place of Presentation
      函館市国際水産・海洋総合研究センター(北海道・函館市)
    • Year and Date
      2015-07-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Optical observation of DNA dynamics near nanopores at sub-millisecond and sub-micrometer levels2015

    • Author(s)
      H. Yamazaki, S. Ito, H. Amalvy, K. Esashika and T. Saiki
    • Organizer
      The 10th Asia-Pacific Conference on Near-field Optics
    • Place of Presentation
      函館市国際水産・海洋総合研究センター(北海道・函館市)
    • Year and Date
      2015-07-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNA dynamics near nanopores at submillisecond and sub-micrometer levels by ultraviolet light spot2015

    • Author(s)
      H. Yamazaki, M. Tsukahara, S. Ito, K. Esashika, and T. Saiki
    • Organizer
      Biophysical Society 59th Annual Meeting
    • Place of Presentation
      Baltimore, USA
    • Year and Date
      2015-02-07 – 2015-02-11
    • Related Report
      2014 Research-status Report
  • [Presentation] Measurement of salt dependence of single DNA translocation through Si nanopores with ultraviolet excitation2015

    • Author(s)
      S. Ito, H. Yamazaki, M. Tsukahara, K. Esashika, and T. Saiki
    • Organizer
      Biophysical Society 59th Annual Meeting
    • Place of Presentation
      Baltimore, USA
    • Year and Date
      2015-02-07 – 2015-02-11
    • Related Report
      2014 Research-status Report
  • [Presentation] Fabrication and evaluation of plasmonic nanopore towards single molecule DNA sequencing2014

    • Author(s)
      M. Tsukahara, S. Itoh, H. Yamazaki, K. Esashika, T. Narsushima, H. Okamoto, and T. Saiki
    • Organizer
      The 13th international conference of Near-field Optics and Nanophotonics
    • Place of Presentation
      Salt Lake City, USA
    • Year and Date
      2014-08-31 – 2014-09-04
    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2017-05-10  

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