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Molecular Design of RNA aptamers

Research Project

Project/Area Number 16H06692
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Biomolecular chemistry
Research InstitutionThe University of Tokyo

Principal Investigator

Imashimizu Masahiko  東京大学, 医科学研究所, 特任講師 (90465930)

Project Period (FY) 2016-08-26 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords熱ゆらぎ / RNAアプタマー / 核酸ータンパク質相互作用 / 結合アフィニティー / 構造不均一性 / ハイスループット法 / RNA アプタマー / ハイスループットDNAシーケンシング / ハイスループットシーケンス / 熱揺らぎ / 核酸創薬 / 核酸 / 医薬 / ナノバイオ
Outline of Final Research Achievements

Aptamers are oligonucleotide ligands with specific binding affinity to target molecules. Here we develop a non-repeated, primer-less and target immobilization-free isolation method for generating RNA aptamers, which is robust to experimental noise. Uniquely, this method focuses on finding and removal of non-aptamer sequences from the RNA pool by RNase digestion leaving target-bound aptamer molecules, and thus is independent of aptamer types. The undigested RNA sequences remaining are so few in number that they must be mixed with a large excess of a known sequence for further manipulations and this sequence is then removed by restriction digestion followed by high-throughput sequencing analysis to identify aptamers. Using this method, we generated multiple RNA aptamers targeting thrombin and TGF-beta1 proteins, independently. This method also enables us to predict a common average structural property of these aptamers that is different from input RNA.

Report

(3 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • Research Products

    (7 results)

All 2018 2017 2016

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

  • [Journal Article] Transcription pausing: biological significance of thermal fluctuations biased by repetitive genomic sequences2018

    • Author(s)
      Imashimizu Masahiko、Lukatsky David B.
    • Journal Title

      Transcription

      Volume: Vol. 9, No 3 Issue: 3 Pages: 196-203

    • DOI

      10.1080/21541264.2017.1393492

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single-round isolation of diverse RNA aptamers from a random sequence pool2018

    • Author(s)
      Imashimizu Masahiko, Takahashi Masaki, Amano Ryo and Nakamura Yoshikazu
    • Journal Title

      Biology Methods and Protocols

      Volume: ー Issue: 1

    • DOI

      10.1093/biomethods/bpy004

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences2016

    • Author(s)
      Masahiko Imashimizu, Ariel Afek, Hiroki Takahashi, Lucyna Lubkowska, and David B. Lukatsky
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 113(47) Issue: 47

    • DOI

      10.1073/pnas.1607760113

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences2017

    • Author(s)
      Masahiko Imashimizu
    • Organizer
      The 1934thBiological Symposium on NIG
    • Place of Presentation
      国立遺伝学研究所
    • Year and Date
      2017-04-20
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences2017

    • Author(s)
      今清水 正彦
    • Organizer
      The 1934thBiological Symposium on NIG
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 転写調節機構:熱揺らぎ、反復配列、転写pausingの繋がり2017

    • Author(s)
      今清水 正彦
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences2016

    • Author(s)
      Masahiko Imashimizu, Ariel Afek, Hiroki Takahashi, and David B. Lukatsky
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report

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Published: 2016-09-02   Modified: 2019-03-29  

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