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Elucidation of DNA higher order conformation by development of a novel tweezer controlling force and torque independently

Research Project

Project/Area Number 26400426
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionTokyo University of Agriculture and Technology

Principal Investigator

Murayama Yoshihiro  東京農工大学, 工学(系)研究科(研究院), 准教授 (60334249)

Research Collaborator ANDO Daisuke  
YOSHIDA Kotaro  
KURODA Masafumi  
ABE Hiroki  
MASUDA Shinichiro  
TANOGUCHI Masaya  
SAGA Sayuka  
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2016: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
KeywordsDNA / 高次構造 / 構造変化 / 捩じれ / 張力 / トルク / 磁気ピンセット
Outline of Final Research Achievements

Complicated conformations of DNA appear when strain is accumulated by stretching and twisting DNA. In living cells, gene expression is regulated by regulating the higher order conformation of DNA. In this study, we have developed a novel tweezer which enables us to stretch and twist a single DNA independently, and succeeded to observe the conformational change in low force regime that is hard to access by traditional method. Our results indicate that not only a protein design but also conformational design can be coded in DNA base sequence.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (19 results)

All 2017 2016 2015 2014 Other

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Acknowledgement Compliant: 1 results) Presentation (16 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Remarks (2 results)

  • [Journal Article] Simple method to measure and analyze the fluctuations of a small particle in biopolymer solutions2015

    • Author(s)
      Masafumi Kuroda and Yoshihiro Murayama
    • Journal Title

      Review of Scientific Instruments

      Volume: 86 Issue: 12

    • DOI

      10.1063/1.4936879

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] 捩じれ応答に現れるDNA高次構造の記憶2017

    • Author(s)
      吉田浩太郎,村山能宏
    • Organizer
      日本物理学会第72回年次大会
    • Place of Presentation
      大阪大学豊中キャンパス
    • Related Report
      2016 Annual Research Report
  • [Presentation] ポリリジンによるDNAの凝縮転移2017

    • Author(s)
      嵯峨早友佳,村山能宏
    • Organizer
      日本物理学会第72回年次大会
    • Place of Presentation
      大阪大学豊中キャンパス
    • Related Report
      2016 Annual Research Report
  • [Presentation] DNA溶液中における微粒子の束縛された拡散運動2016

    • Author(s)
      増田心一郎,黒田真史,村山能宏
    • Organizer
      日本物理学会第71回年次大会
    • Place of Presentation
      東北学院大学泉キャンパス(宮城県仙台市泉区)
    • Year and Date
      2016-03-22
    • Related Report
      2015 Research-status Report
  • [Presentation] 熱的に揺らぐDNA上における微粒子のブラウン運動2016

    • Author(s)
      安倍弘喜,村山能宏
    • Organizer
      日本物理学会第71回年次大会
    • Place of Presentation
      東北学院大学泉キャンパス(宮城県仙台市泉区)
    • Year and Date
      2016-03-22
    • Related Report
      2015 Research-status Report
  • [Presentation] DNAの網目構造が微粒子の拡散に及ぼす影響2016

    • Author(s)
      田之口将也,村山能宏
    • Organizer
      第15回関東ソフトマター研究会
    • Place of Presentation
      首都大学東京
    • Related Report
      2016 Annual Research Report
  • [Presentation] 微粒子が感じるDNAの揺らぎ,粘性,弾性2016

    • Author(s)
      村山能宏
    • Organizer
      異常拡散をめぐる最近の進展
    • Place of Presentation
      慶應大学 日吉キャンパス
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Dependence of twisting velocity on higher order structure of DNA2016

    • Author(s)
      Kotaro Yoshida and Yoshihiro Murayama
    • Organizer
      日本生物物理学会第54回年会
    • Place of Presentation
      つくば国際会議場
    • Related Report
      2016 Annual Research Report
  • [Presentation] Effect of a mesh structure of DNA on diffusion of a small particle2016

    • Author(s)
      Masaya Tanoguchi and Yoshihiro Murayama
    • Organizer
      日本生物物理学会第54回年会
    • Place of Presentation
      つくば国際会議場
    • Related Report
      2016 Annual Research Report
  • [Presentation] 捩じれ速度に依存したDNAの超螺旋形成・崩壊過程2015

    • Author(s)
      吉田浩太郎,安藤大輔,村山能宏
    • Organizer
      日本物理学会2015年秋季大会
    • Place of Presentation
      関西大学千里山キャンパス(大阪府吹田市)
    • Year and Date
      2015-09-19
    • Related Report
      2015 Research-status Report
  • [Presentation] Probability Distribution of the Position of a DNA Binding Protein on a Thermally Fluctuating DNA2015

    • Author(s)
      Hiroki Abe and Yoshihiro Murayama
    • Organizer
      International Symposium on Fluctuation and Structure out of Equilibrium 2015
    • Place of Presentation
      Inamori Hall, Shiran-Kaikan, Kyoto University (京都市左京区)
    • Year and Date
      2015-08-21
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Effective elasticity acting on a small particle in DNA solution2015

    • Author(s)
      Shinichiro Masuda, Masafumi Kuroda, and Yoshihiro Murayama
    • Organizer
      International Symposium on Fluctuation and Structure out of Equilibrium 2015
    • Place of Presentation
      Inamori Hall, Shiran-Kaikan, Kyoto University (京都市左京区)
    • Year and Date
      2015-08-21
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 張力・トルク独立制御型ピンセットを用いたDNAの超らせん形成の観測2015

    • Author(s)
      安藤大輔,村山能宏
    • Organizer
      日本物理学会第70回年次大会
    • Place of Presentation
      早稲田大学早稲田キャンパス
    • Year and Date
      2015-03-21 – 2015-03-24
    • Related Report
      2014 Research-status Report
  • [Presentation] Formation of DNA supercoils under independent control of tension and torque2015

    • Author(s)
      Daisuke Ando, Masahiro Makuta, and Yoshihiro Murayama
    • Organizer
      Physics of Structural and Dynamical Hierarchy in Soft Matter
    • Place of Presentation
      Institute of Industrial Science, University of Tokyo
    • Year and Date
      2015-03-16 – 2015-03-18
    • Related Report
      2014 Research-status Report
  • [Presentation] 1D diffusion of a DNA binding protein along a thermally fluctuating DNA2015

    • Author(s)
      Hiroki Abe and Yoshihiro Murayama
    • Organizer
      Physics of Structural and Dynamical Hierarchy in Soft Matter
    • Place of Presentation
      Institute of Industrial Science, University of Tokyo
    • Year and Date
      2015-03-16 – 2015-03-18
    • Related Report
      2014 Research-status Report
  • [Presentation] 非一様な溶液中における微粒子の運動観測2014

    • Author(s)
      増田心一郎,村山能宏
    • Organizer
      日本物理学会2014年秋季大会
    • Place of Presentation
      中部大学春日井キャンパス
    • Year and Date
      2014-09-07 – 2014-09-10
    • Related Report
      2014 Research-status Report
  • [Presentation] DNA結合蛋白質によるDNAの力学特性変化2014

    • Author(s)
      安倍弘喜,村山能宏
    • Organizer
      日本物理学会2014年秋季大会
    • Place of Presentation
      中部大学春日井キャンパス
    • Year and Date
      2014-09-07 – 2014-09-10
    • Related Report
      2014 Research-status Report
  • [Remarks] 国立大学法人東京農工大学/研究者紹介

    • URL

      http://kenkyu-web.tuat.ac.jp/Profiles/27/0002621/profile.html

    • Related Report
      2016 Annual Research Report 2015 Research-status Report
  • [Remarks] 村山研究室ホームページ

    • URL

      http://web.tuat.ac.jp/~ymura/publications.html

    • Related Report
      2016 Annual Research Report 2015 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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