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Modelling hydration structure of nucleic acid using corresponding gas-phase hydrated clusters: Toward elucidating nucleotide structure

Research Project

Project/Area Number 25410023
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionYokohama City University

Principal Investigator

Saigusa Hiroyuki  横浜市立大学, 生命ナノシステム科学研究科, 教授 (90162180)

Co-Investigator(Kenkyū-buntansha) TSUKAMOTO Masaki  名古屋大学, 情報科学研究科, 助教 (10362295)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2013: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Keywords核酸塩基 / 水和クラスター / 中赤外レーザー / 尿酸 / ローカルモード結合 / 中赤外レーザー分光 / レーザー脱離 / CO伸縮振動 / ペプチド / 水和構造 / 赤外スペクトル / ヌクレオチド / 塩基対生成
Outline of Final Research Achievements

In order to model the hydration structure of nucleic acid systems in relation to their biological functions, we have performed structural characterization of corresponding hydrated clusters isolated in the gas-phase. We have been able to establish an effective strategic method for elucidating hydration structure of nucleotides, in which a sugar-phosphate group is bonded to the base.
With this financial support, we have also developed a novel Mid-IR spectroscopic system and measured CO stretching vibrational spectra of uric acid and its monohydrates.It was found that the two structural isomers of the monohydrated cluster show very different local mode-coupling behavior, depending strongly upon the hydrogen-bonding site. By using this mode coupling scheme, we have been able to identify unambiguously the hydrogen-bonded structure of uric acid-melamine complex.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (27 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (3 results) Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 7 results,  Acknowledgement Compliant: 1 results) Presentation (14 results) (of which Int'l Joint Research: 2 results,  Invited: 6 results) Remarks (2 results) Patent(Industrial Property Rights) (1 results)

  • [Int'l Joint Research] フランス原子エネルギー研究所(CEA)/Dr. Michel Mons(フランス)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] ミュンヘン工科大学化学科/Dr. Deniz Tuna(ドイツ)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] マックス-プランク研究所/Professor Wolfgang Domcke(ドイツ)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Effective strategy for conformer-selective detection of short-lived excited state species: Application to the IR spectroscopy of the N1H keto tautomer of guanine2016

    • Author(s)
      H. Asami, M. Tokugawa, Y. Masaki, S. Ishiuchi, E. Gloaguen, K. Seio, H. Saigusa, M. Fujii, M. Sekine, and M. Mons
    • Journal Title

      Journal of Physical Chemistry A

      Volume: 120 Issue: 14 Pages: 2179-2184

    • DOI

      10.1021/acs.jpca.6b01194

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Hydrogen-bonding interactions of uric acid complexes with water/melamine by mid-infrared spectroscopy2015

    • Author(s)
      H. Saigusa, D. Nakamura, S. Urashima
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 17 Issue: 35 Pages: 23026-23033

    • DOI

      10.1039/c5cp03494a

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Multiple hydrogen-bonding interaction of uric acid/9-methyluric acid with melamine identified by infrared spectroscopy2015

    • Author(s)
      H. Asami, H. Saigusa
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 118 Issue: 18 Pages: 4851-4857

    • DOI

      10.1021/jp502635w

    • Related Report
      2014 Research-status Report 2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Ab Initio Studies on the Photophysics of Uric Acid and Its Monohydrates : Role of the Water Molecule2014

    • Author(s)
      S. Yamazaki, S. Urashima, H. Saigusa, T. Taketsugu
    • Journal Title

      J. Phys. Chem. A

      Volume: 118 Issue: 6 Pages: 1132-1141

    • DOI

      10.1021/jp411880z

    • Related Report
      2014 Research-status Report 2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Synthesis of modified pyrimidine nucleosides via Vorbruuggen-type N-glycosylation catalyzed by 2-methyl-5-phenylbenzoxazolium2014

    • Author(s)
      H. Shirouzu, H. Morita, M. Tsukamoto
    • Journal Title

      Tetrahedron

      Volume: 70 Issue: 22 Pages: 3635-3639

    • DOI

      10.1016/j.tet.2014.03.013

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Stacked base-pair structures of adenine nucleosides stabilized by the formation of hydrogen-bonding network involving sugar groups2013

    • Author(s)
      H. Asami, K. Yagi, M. Ohba, S. Urashima, H. Saigusa
    • Journal Title

      Chemical Physics

      Volume: vol.419 Pages: 84-89

    • DOI

      10.1016/j.chemphys.2013.01.038

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] IR-UV Double Resonance Spectroscopy as Implemented by Polarized Laser Schemes : Probing Orientations of Vibrational Transition Dipole Moments2013

    • Author(s)
      S. Urashima, M. Miyazaki, M. Fujii, H. Saigusa
    • Journal Title

      Chem. Lett.

      Volume: 42 Issue: 9 Pages: 1070-1072

    • DOI

      10.1246/cl.130425

    • NAID

      10031194345

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] Hydrogen-Bonding Interactions of Uric Acid Complexes with Water/Melamine Identified by Near- and Mid-IR Spectroscopy2015

    • Author(s)
      H. Saigusa
    • Organizer
      The 2015 International Chemical Congress of Pacific Basin Societies (Pacifichem) 2015
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2015-12-15 – 2015-12-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Laser Desorption of Nucleic Acid Components and Their Structural Characterization by IR Spectroscopy2015

    • Author(s)
      H. Saigusa
    • Organizer
      The 2015 International Chemical Congress of Pacific Basin Societies (Pacifichem) 2015
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2015-12-15 – 2015-12-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Structural Investigation of Aspartame, an Artificial Sweetening, and Its Hydrated Clusters in the Gas Phase2015

    • Author(s)
      D. Nakamura, H. Saigusa
    • Organizer
      The 2015 International Chemical Congress of Pacific Basin Societies (Pacifichem) 2015
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2015-12-15 – 2015-12-20
    • Related Report
      2014 Research-status Report
  • [Presentation] Hydrogen-bonding interactions of uric acid complexes with water/melamine identified by near- and mid-IR spectroscopy2015

    • Author(s)
      H. Saigusa
    • Organizer
      Pacifichem 2015
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Laser desorption of nucleic acid components and their structural characterization by IR spectroscopy2015

    • Author(s)
      H. Saigusa
    • Organizer
      Pacifichem 2015
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 中赤外分光による尿酸‐水及びメラミン錯体の水素結合構造解析2015

    • Author(s)
      三枝洋之, 中村大介, 浦島周平
    • Organizer
      第9回分子科学討論会 2015東京
    • Place of Presentation
      東京工業大学 大岡山キャンパス
    • Year and Date
      2015-09-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] 赤外分光法による尿酸-メラミン錯体の多重水素結合構造の決定2014

    • Author(s)
      浅見 祐也, 中村 大介, 三枝 洋之
    • Organizer
      第8回分子科学討論会2014
    • Place of Presentation
      広島大学 東広島キャンパス
    • Year and Date
      2014-09-21 – 2014-09-24
    • Related Report
      2014 Research-status Report
  • [Presentation] 赤外-紫外二重共鳴分光法によるアスパルテーム水和クラスターの気相立体構造解析2014

    • Author(s)
      中村 大介, 三枝 洋之
    • Organizer
      第8回分子科学討論会2014
    • Place of Presentation
      広島大学 東広島キャンパス
    • Year and Date
      2014-09-21 – 2014-09-24
    • Related Report
      2014 Research-status Report
  • [Presentation] Gas-Phase Isolation of Nucleic Acid Components: From Spectroscopy to Biomodelling2014

    • Author(s)
      H. Saigusa
    • Organizer
      Isolated Biomolecules and Biomolecular Clusters (IBBI) 2014
    • Place of Presentation
      Porquerolles Island, France
    • Year and Date
      2014-05-18 – 2014-05-23
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Gas-Phase Isolation of Nucleic Acid Components: From spectroscopy to biomodelling2014

    • Author(s)
      H. Saigusa
    • Organizer
      Isolated Biomolecules and Biomolecular Interactions
    • Place of Presentation
      Porquerolles, France
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] プリン塩基の光物理的挙動に対する一分子水和の影響2014

    • Author(s)
      山崎 祥平,浦島 周平,三枝 洋之,武次 徹也
    • Organizer
      第17回理論化学討論会
    • Place of Presentation
      名古屋大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 赤外-紫外二重共鳴スペクトルの直線偏光二色性測定:遷移双極子モーメントの配向によるグアノシンの局所構造解析

    • Author(s)
      浦島 周平,宮﨑 充彦,藤井 正明,三枝 洋之
    • Organizer
      第7回分子科学討論会2013
    • Place of Presentation
      京都テルサ
    • Related Report
      2013 Research-status Report
  • [Presentation] ナフチル基の光イオン化を利用した核酸塩基のレーザー脱離・超音速ジェット分光―keto体の観測

    • Author(s)
      浅見 祐也,正木 慶昭,石内 俊一,三枝 洋之,関根 光雄,藤井 正明
    • Organizer
      第7回分子科学討論会2013
    • Place of Presentation
      京都テルサ
    • Related Report
      2013 Research-status Report
  • [Presentation] 赤外-紫外二重共鳴分光法による人工甘味料アスパルテームの気相立体構造解析

    • Author(s)
      中村 大介,三枝 洋之
    • Organizer
      第7回分子科学討論会2013
    • Place of Presentation
      京都テルサ
    • Related Report
      2013 Research-status Report
  • [Remarks] 三枝研ホームページ

    • URL

      http://laser.sci.yokohama-cu.ac.jp/

    • Related Report
      2015 Annual Research Report 2014 Research-status Report
  • [Remarks] 三枝研ホームページ

    • URL

      http://laser.sci.yokohama-cu.ac.jp/

    • Related Report
      2013 Research-status Report
  • [Patent(Industrial Property Rights)] ピリミジンヌクレオシド誘導体の新規製造方法2013

    • Inventor(s)
      白水宏、森田裕紀、塚本眞幸
    • Industrial Property Rights Holder
      白水宏、森田裕紀、塚本眞幸
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2013-228375
    • Filing Date
      2013-11-11
    • Related Report
      2013 Research-status Report

URL: 

Published: 2014-07-25   Modified: 2019-07-29  

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