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Neutron Crystallographic study of hydration structures of DNA and its fluctuation

Research Project

Project/Area Number 23770176
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionKyoto University

Principal Investigator

CHATAKE Toshiyuki  京都大学, 原子炉実験所, 准教授 (30383475)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2013: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2012: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2011: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords水和構造 / 揺らぎ / DNA / 中性子
Research Abstract

For the purpose of revealing structure of DNA hydration including structural fluctuation, neutron and X-ray crystallographic studies were carried out. (1) Deuterated Z-DNA d(CGCGCG) could be produced. (2) Large single crystals of Z-DNA d(CGCGCG) were obtained from H2O solution, and TOF neutron experiment was performed using pulsed neutron source. Neutron diffraction spots were detected up to 1.6 -1.8 Angstrom. Protocol for refinements was tested using neutron data sets of protein crystals. X-ray crystallographic analyses were also carried out complementarily, as the result, Z-DNA structures at high and low concentrations of metal salts were determined. Each of these structures had specific features, suggesting that these crystals would be dominant candidates for neutron crystallographic studies.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (23 results)

All 2014 2013 2012 2011

All Journal Article (10 results) (of which Peer Reviewed: 8 results) Presentation (13 results) (of which Invited: 1 results)

  • [Journal Article] Fundamental studies for the proton polarization techniwue in neutron protein crystallography2013

    • Author(s)
      Tanaka I., Kusaka K., Chatake T., Niimura N.
    • Journal Title

      J. Synchrotron Rad

      Volume: 20 Pages: 958-961

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural fluctuation observed in Z-DNA d(CGCGCG)2 in the absence of divalent metal cations and polyamine2013

    • Author(s)
      Chatake T.
    • Journal Title

      J. Synchrotron Rad

      Volume: 20 Pages: 864-868

    • NAID

      120005347088

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] X-ray structure determination and deuteration of nattokinase2013

    • Author(s)
      Yanagisawa, Y. Chatake T.,他9名
    • Journal Title

      J. Synchrotron Rad

      Volume: 20 Pages: 875-879

    • NAID

      120005347089

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] 生体分子の中性子単結晶解析(第一回)蛋白質中性子結晶学の基礎2013

    • Author(s)
      茶竹俊行、森本幸生
    • Journal Title

      日本中性子科学会誌

      Volume: 23 Pages: 81-85

    • Related Report
      2013 Final Research Report
  • [Journal Article] Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl22013

    • Author(s)
      Toshiyuki Chatake, Tomoko Sunami
    • Journal Title

      Journal of Inorganic Biochemistry

      Volume: 123 Pages: 15-25

    • DOI

      10.1016/j.jinorgbio.2013.03.004

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Fundamental studies for the proton polarization technique in neutron protein crystallography2013

    • Author(s)
      Ichiro Tanaka, Katsuhiro Kusaka, Toshiyuki Chatake, Nobuo Niimura
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 20 Issue: 6 Pages: 958-961

    • DOI

      10.1107/s0909049513020815

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural fluctuation observed in Z-DNA d(CGCGCG)2 in the absence of divalent metal cations and polyamines2013

    • Author(s)
      Toshiyuki Chatake
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 20 Issue: 6 Pages: 864-868

    • DOI

      10.1107/s0909049513020773

    • NAID

      120005347088

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] X-ray structure determination and deuteration of nattokinase2013

    • Author(s)
      Yasuhide Yanagisawa, Toshiyuki Chatake, Sawa Naito, Tadanori Ohsugi, Chieko Yatagi, Hiroyuki Sumi, Akio Kawaguchi, Kaori Chiba-Kamosida, Megumi Ogawa, Tatsumi Adachi, Yukio Morimoto
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 20 Issue: 6 Pages: 875-879

    • DOI

      10.1107/s0909049513020700

    • NAID

      120005347089

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 生体分子の中性子単結晶回折(第一回) 蛋白質中性子結晶学の基礎2013

    • Author(s)
      茶竹俊行、森本幸生
    • Journal Title

      日本中性子科学会誌

      Volume: 23 Pages: 81-85

    • NAID

      130007510501

    • Related Report
      2012 Research-status Report
  • [Journal Article] High-resolution X-ray Study of Effects of Deuteration on Crystal Growth and Crystal Structure of Proteinase K2011

    • Author(s)
      T. Chatake, T. Ishikawa, Y. Yanagisawa, T. Yamada, I. Tanaka, S. Fujiwara and Y. Morimoto
    • Journal Title

      Acta Cryst

      Volume: F67 Issue: 11 Pages: 1334-1338

    • DOI

      10.1107/s1744309111031903

    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Presentation] 納豆由来水溶性ビタミンK2の研究2014

    • Author(s)
      茶竹俊行(発表者)、柳澤泰任、松尾龍人、藤原悟、森本幸生
    • Organizer
      京都大学原子炉実験所第48回学術講演会
    • Place of Presentation
      京都大学原子炉実験所(大阪)
    • Related Report
      2013 Final Research Report
  • [Presentation] 納豆由来水溶性ビタミンK2の研究2014

    • Author(s)
      茶竹俊行、柳澤泰任、松尾龍人、藤原悟、森本幸生
    • Organizer
      第48回京都大学原子炉実験所学術講演会
    • Place of Presentation
      京都大学原子炉実験所
    • Related Report
      2013 Annual Research Report
  • [Presentation] 生体高分子の昨日発現に重要な役割を持つ水分子およびプロトン化状態の直接観察2013

    • Author(s)
      樋口芳樹(発表者)、茶竹俊行、横山武司、山田太郎
    • Organizer
      2012年度第2回水和ナノ構造研究会
    • Place of Presentation
      新世代研究所(東京)
    • Year and Date
      2013-02-23
    • Related Report
      2013 Final Research Report
  • [Presentation] 核酸科学を中心とした中性子結晶構造解析2013

    • Author(s)
      茶竹俊行
    • Organizer
      第一回Neutron in Biology研究会
    • Place of Presentation
      京都大学東京オフィス(東京)
    • Related Report
      2013 Final Research Report
  • [Presentation] 核酸科学を中心とした中性子結晶構造解析2013

    • Author(s)
      茶竹俊行
    • Organizer
      第1回Neutron in Biology研究会
    • Place of Presentation
      京都大学東京オフィス (東京都)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 生体高分子の機能発現に重要な役割をもつ水分子およびプロトン化状態の直接観測2013

    • Author(s)
      樋口芳樹、 茶竹俊行、 横山武司、 山田太郎 (代表発表者: 樋口芳樹)
    • Organizer
      2012年第2回水和ナノ構造研究会
    • Place of Presentation
      新世代研究所 (東京都)
    • Related Report
      2012 Research-status Report
  • [Presentation] 高塩状態で誘導されるDNA会合の研究2012

    • Author(s)
      茶竹俊行
    • Organizer
      蛋白質の異常凝集とその防御修復機構に関する研究会
    • Place of Presentation
      京都大学原子炉実験所(大阪)
    • Year and Date
      2012-11-02
    • Related Report
      2013 Final Research Report
  • [Presentation] 生体試料解析のための重水素化手法の確立2012

    • Author(s)
      森本幸生(発表者)、杉山正明、茶竹俊行、藤井紀子、齊藤毅、藤原悟、日高雄二
    • Organizer
      京都大学原子炉実験所第46回学術講演会
    • Place of Presentation
      京都大学原子炉実験所(大阪)
    • Year and Date
      2012-02-02
    • Related Report
      2013 Final Research Report 2011 Research-status Report
  • [Presentation] 高塩状態で誘導されるDNA会合の研究2012

    • Author(s)
      茶竹俊行
    • Organizer
      タンパク質の異常凝集とその防御修復機構に関する研究会
    • Place of Presentation
      京都大学原子炉実験所 (大阪府)
    • Related Report
      2012 Research-status Report
  • [Presentation] Time of Flight Neutron Crystallographic analysis of Human Carbomonoxyhemoglobin2011

    • Author(s)
      T. Chatake(発表者)、N. Shibayama、S.Y. Park、K. Tomoyori、H. Hosoya、T. Ohara、K. Kusaka、I. Tanaka、N. Niimura, Y. Morimoto
    • Organizer
      1st Asia- Oceania Conference on Neutron Scattering
    • Place of Presentation
      エポカル筑波(茨城)
    • Year and Date
      2011-11-23
    • Related Report
      2013 Final Research Report
  • [Presentation] DNAの水和構造における水分子と金属イオン2011

    • Author(s)
      茶竹俊行
    • Organizer
      2011年第1回バイオ単分子・水罠の構造合同研究会
    • Place of Presentation
      パウエル箱根(神奈川)
    • Year and Date
      2011-09-22
    • Related Report
      2013 Final Research Report
  • [Presentation] Time of Flight Neutron Crystallographic analysis of Human Carbonmonoxyhemoglobin2011

    • Author(s)
      T. Chatake, N. Shibayama, S.Y. Park, K. Tomoyori, T. Hosoya, T. Ohara, K. Kusaka, K. Kurihara, I. Tanaka, N. Niimura, Y. Morimoto
    • Organizer
      1st Asia-Oceania Conference on Neutron Scattering
    • Place of Presentation
      エポカル筑波(茨城)
    • Related Report
      2011 Research-status Report
  • [Presentation] DNAの水和構造における水分子と金属イオン2011

    • Author(s)
      茶竹俊行
    • Organizer
      2011年第1回バイオ単分子・水和ナノ構造合同研究会
    • Place of Presentation
      パウエル箱根(神奈川)
    • Related Report
      2011 Research-status Report

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

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