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Efficient polymerase chain reaction from single DNA molecules

Research Project

Project/Area Number 18K14260
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 34020:Analytical chemistry-related
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

Zhang Yi  国立研究開発法人海洋研究開発機構, 超先鋭研究開発部門(超先鋭研究プログラム), 研究員 (40795358)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2020: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
KeywordsHigh throughput / Microfabrication / Single molecule / Enzyme / Sensitivity / Poisson statistics / Image processing / Screening / Restriction enzyme / Electrophoresis / Digital counting / Droplet / Biosensor / Cell-free / Directed evolution / Synthetic biology / PCR / Protein synthesis / Micromanipulation / DNA / Bioreactor / Microdevice
Outline of Final Research Achievements

We cannot study what we cannot measure. This simple philosophy is the basic driving force for analytical chemistry to move forward. This Early-Career Scientists study was also planned and implemented based on this general interest. My research platform features high throughput and deals with a massive number of single DNA molecules, which enabled: (1) cell-free protein synthesis from every single DNA molecule; (2) genotype-phenotype linkage at the single DNA molecule; (3) sorting and amplification for single DNA molecules; and (4) amplification-free single DNA molecule detection. During the period of this research, I succeeded in obtaining the world's most active enzyme capable of hydrolyzing phosphate esters, establishing the novel digital high-throughput screening theory, and developing the world's most sensitive method capable of evaluating the performance of any DNA-cleaving enzymes.

Academic Significance and Societal Importance of the Research Achievements

The massively parallel, highly uniform, and individually addressable femtoliter droplet array technology offered a high-end standard and new possibilities for future diverse bioanalytical applications. The integrated system also stressed the significance of the multidisciplinary approach.

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (17 results)

All 2020 2019 Other

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Open Access: 3 results) Presentation (10 results) (of which Int'l Joint Research: 2 results,  Invited: 5 results) Remarks (2 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] A single-molecule counting approach for convenient and ultrasensitive measurement of restriction digest efficiencies2020

    • Author(s)
      Zhang Yi、Nunoura Takuro、Nishiura Daisuke、Hirai Miho、Shimamura Shigeru、Kurosawa Kanako、Ishiwata Chieko、Deguchi Shigeru
    • Journal Title

      PLOS ONE

      Volume: 15 Issue: 12 Pages: e0244464-e0244464

    • DOI

      10.1371/journal.pone.0244464

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Femtoliter Droplet Array for Massively Parallel Protein Synthesis from Single DNA Molecules2020

    • Author(s)
      Zhang Yi、Kurosawa Kanako、Nishiura Daisuke、Tei Mika、Tsudome Mikiko
    • Journal Title

      Journal of Visualized Experiments

      Volume: (160) Issue: 160

    • DOI

      10.3791/60945

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multiplexed single-molecule enzyme activity analysis for counting disease-related proteins in biological samples2020

    • Author(s)
      Shingo Sakamoto, Toru Komatsu, Rikiya Watanabe, Yi Zhang, Taiki Inoue, Mitsuyasu Kawaguchi, Hidehiko Nakagawa, Takaaki Ueno, Takuji Okusaka, Kazufumi Honda, Hiroyuki Noji, Yasuteru Urano
    • Journal Title

      Science Advances

      Volume: 6 Issue: 11

    • DOI

      10.1126/sciadv.aay0888

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Accurate high-throughput screening based on digital protein synthesis in a massively parallel femtoliter droplet array2019

    • Author(s)
      Yi Zhang, Yoshihiro Minagawa, Hiroto Kizoe, Kentaro Miyazaki, Ryota Iino, Hiroshi Ueno, Kazuhito V Tabata, Yasuhiro Shimane, Hiroyuki Noji
    • Journal Title

      Science Advances

      Volume: 5 Issue: 8 Pages: 1-11

    • DOI

      10.1126/sciadv.aav8185

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] A cell culture-independent approach for treasure hunting of marine microbial proteins2020

    • Author(s)
      Yi Zhang
    • Organizer
      JAMSTEC International Day
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Large-scale femtoliter droplet array for ultrahigh-throughput protein screening2020

    • Author(s)
      Yi Zhang
    • Organizer
      CAS KLSMN Forum No. 234
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] A SINGLE-MOLECULE VIEW OF RESTRICTION DIGESTS2019

    • Author(s)
      Yi Zhang, Takuro Nunoura, Daisuke Nishiura, Miho Hirai, Shigeru Shimamura, Shigeru Deguchi
    • Organizer
      第6回新学術領域「ネオウイルス学」領域班会議
    • Related Report
      2019 Research-status Report
  • [Presentation] Development of Novel Disease Diagnosis Platform based on Enzyme Activity Detection at Single Protein Level2019

    • Author(s)
      Shingo Sakamoto, Toru Komatsu, Rikiya Watanabe, Yi Zhang, Hiroyuki Noji, Yasuteru Urano
    • Organizer
      The 56th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2019 Research-status Report
  • [Presentation] マイクロデバイスを用いた単一酵素活性検出による病態診断法の開発2019

    • Author(s)
      坂本眞伍、小松徹、渡邉力也、張翼、野地博行、浦野泰照
    • Organizer
      第19回日本蛋白質科学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] 1分子酵素活性プロファイリングによる疾患関連酵素の超高感度検出2019

    • Author(s)
      坂本眞伍, 小松徹, 渡邉力也, 張翼, 井上大輝, 川口充康, 中川秀彦, 植野高章, 奥坂拓志, 本田一文, 野地博行, 浦野泰照
    • Organizer
      第92回日本生化学会大会
    • Related Report
      2019 Research-status Report
  • [Presentation] 異分野融合によるタンパク質探索ツールの開発と応用2019

    • Author(s)
      張翼
    • Organizer
      第97回生命科学若手セミナー
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Development of enzymomics approach to search for disease-related alternation of enzymatic functions2019

    • Author(s)
      Toru Komatsu, Jun Onagi, Yuki Ichihashi, Shingo Sakamoto, Rikiya Watanabe, Yi Zhang, Hiroyuki Noji, Tetsuo Nagano, Yasuteru Urano
    • Organizer
      The 56th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2019 Research-status Report
  • [Presentation] Accurate high-throughput screening based on digital protein synthesis in a massively parallel femtoliter droplet array2019

    • Author(s)
      Yi Zhang
    • Organizer
      Fourth Microbial Single Cell Genomics Workshop
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Digital protein screening2019

    • Author(s)
      Yi Zhang
    • Organizer
      第4回 岡崎発動分子科学セミナー
    • Related Report
      2019 Research-status Report
    • Invited
  • [Remarks] 特集 こんな技術が欲しかった

    • URL

      http://www.jamstec.go.jp/j/pr/wp-content/uploads/2020/12/BE165all.pdf

    • Related Report
      2020 Annual Research Report
  • [Remarks] 「大海撈針にも楽な道がある デジタル・タンパク質スクリーニング・システム」

    • URL

      https://www.jamstec.go.jp/sugar/j/research/20191003/

    • Related Report
      2019 Research-status Report
  • [Patent(Industrial Property Rights)] 核酸分解酵素の核酸分解効率を求める方法2019

    • Inventor(s)
      張翼, 布浦拓郎
    • Industrial Property Rights Holder
      国立研究開発法人海洋研究開発機構
    • Industrial Property Rights Type
      特許
    • Filing Date
      2019
    • Related Report
      2019 Research-status Report

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Published: 2018-04-23   Modified: 2022-01-27  

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