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Investigation of intramolecular collision dynamics of RNA

Research Project

Project/Area Number 23750202
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Chemistry related to living body
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

UZAWA Takanori  独立行政法人理化学研究所, 伊藤ナノ医工学研究室, 研究員 (60554376)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2011: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords核酸 / 両末端の衝突速度 / ダイナミクス / ルテニウム錯体 / 両末端衝突速度 / 発光寿命
Research Abstract

Formation of three dimensional structures of a protein and an oligonucleotide require stepwise formation of intramolecular interactions, indicating that intramolecular collision is the most essential process of 3D structure formation. Although the intraolecular collision dynamics of unstructured polypeptides have seen extensively studied, those of oligonucleotides are limited. Thus motivated, in this study I aimed to investigate the base-composition, chain-length and temperature dependences of the end-to-end collision rates for both oligonucleotides of DNA and RNA. I measured the intramolecular collision dynamics using lifetime of a luminophore modified at the end of a oligonucleotide whose the other terminal was modified with a quencher. For a DNA over 20 bases in length, conformational change of polyadenine contributes on the end-to-end collision dynamics at lower temperature. At high temperature, however, this contribution disappears and the dynamics of polyadenine corresponds to the dynamics of polythymine. A similar experiment on RNA did not exhibit clear difference of the luminophore lifetimes between with presence of the quencher and absence of the quencher.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (5 results)

All 2013 2012 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results) Presentation (2 results) Remarks (1 results)

  • [Journal Article] Electrostatic and Base Stacking Effects Define the End-to-end Collision Dynamics of Single-stranded DNA2013

    • Author(s)
      Takanori Uzawa, Takashi Isoshima, Yoshihiro Ito, Koichiro Ishimori, Dmitrii E. Makarov, and Kevin W Plaxco
    • Journal Title

      Biophys.J.

      Volume: (in press)

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA2013

    • Author(s)
      T. Uzawa
    • Journal Title

      Biophysical journal

      Volume: -

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] ルテニウム錯体に結合するRNA アプタマーの選出2012

    • Author(s)
      鵜澤 尊規、Thoa TRAN、伊藤 嘉浩
    • Organizer
      光合成領域会議
    • Place of Presentation
      東京工業大学
    • Year and Date
      2012-12-17
    • Related Report
      2012 Final Research Report
  • [Presentation] ルテニウム錯体に結合するRNAアプタマーの選出2012

    • Author(s)
      鵜澤尊規
    • Organizer
      新学術領域 人工光合成 第1回公開シンポジウム
    • Place of Presentation
      東京工業大学大岡山キャンパス
    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.riken.jp/nano-med.eng.lab/home.html

    • Related Report
      2012 Final Research Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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