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Molecular recognition and structure formations of nucleic acids under unusual molecular environments

Research Project

Project/Area Number 19760557
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Biofunction/Bioprocess
Research InstitutionKonan University

Principal Investigator

NAKANO Shu-ichi  Konan University, フロンティアサイエンス学部, 准教授 (70340908)

Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥3,720,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥420,000)
Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2008: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2007: ¥1,900,000 (Direct Cost: ¥1,900,000)
Keywords分子クラウディング / ポリエチレングリコール / 金属イオン / DNA構造 / ヘアピン構造 / ハンマーヘッドリボザイム / 結合エネルギー / 核酸 / i-motif構造 / 機能性核酸 / 構造安定性 / 細胞内分子環境 / Z型構造 / リボザイム / PEG / ヘアピンDNA / ポリアミン / 塩基性ペプチド
Research Abstract

DNA is widely used in biotehnology, and the DNA properties under unusual conditions, such as in living cells and on biochips, are the critical issue for the success of biotechnology. Due to the polyelectronic nature of DNA and RNA, significant influences of molecular environment on their functions, including molecular recognitions and structure formations, are expected. Here, we have found facilitations of unusual structure formations of DNA relevant to gene regulations, and enhancements of the catalytic activity of an RNA enzyme. These finding could lead to applications as monitoring molecular environment and design of functional oligonucleotides that efficiently function under unusual conditions applied for biotechnology.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (45 results)

All 2010 2009 2008 2007 Other

All Journal Article (16 results) (of which Peer Reviewed: 13 results) Presentation (19 results) Book (5 results) Remarks (5 results)

  • [Journal Article] Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH.2010

    • Author(s)
      A. Rajendran, S. Nakano, N. Sugimoto
    • Journal Title

      Chem. Commun. 46

      Pages: 1299-1301

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH2010

    • Author(s)
      A.Rajendran, S.Nakano, N.Sugimoto
    • Journal Title

      Chem.Commun. 46

      Pages: 1299-1301

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes.2009

    • Author(s)
      S. Nakano, H.T. Karimata, Y. Kitagawa, N. Sugimoto
    • Journal Title

      J. Am. Chem. Soc. 131

      Pages: 16881-16888

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes2009

    • Author(s)
      S.Nakano, H.T.Karimata, Y.Kitagawa, N.Sugimoto
    • Journal Title

      J.Am.Chem.Soc. 131

      Pages: 16881-16888

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides2009

    • Author(s)
      S.Nakano, H.Oka, Y.Uotani, K.Uenishi, M.Fujii, N.Sugimoto
    • Journal Title

      Biochemistry 48

      Pages: 11304-11311

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence2009

    • Author(s)
      S.Nakano, H.Hirayama, N.Sugimoto
    • Journal Title

      Nucleic Acids Symp.Ser. 53

      Pages: 519-520

    • Related Report
      2009 Annual Research Report
  • [Journal Article] Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media.2008

    • Author(s)
      S. Nakano, L. Wu, H. Oka, H.T. Karimata, T. Kirihata, Y. Sato, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai, N. Sugimoto
    • Journal Title

      Mol. BioSyst. 4

      Pages: 579-588

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Capture of cationic ligands bound diffusely to base pairs during the DNA refolding.2008

    • Author(s)
      S. Nakano, T. Kirihata, N. Sugimoto
    • Journal Title

      Chem. Commun.

      Pages: 700-702

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media2008

    • Author(s)
      S. Nakano, L. Wu, H. Oka, H. T. Karimata, T. Kirihata, Y. Sato, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai. N. Sugimoto
    • Journal Title

      Mol. BioSyst 4

      Pages: 579-588

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Folding and activity of the hammerhead ribozyme facilitated by the molecular crowding by cosolutes2008

    • Author(s)
      S. Nakano, Y. Kitagawa, H. T. Karimata, N. Sugimoto
    • Journal Title

      Nucleic Acids Symp. Ser 52

      Pages: 519-520

    • Related Report
      2008 Annual Research Report
  • [Journal Article] DNAはなぜ二重らせん構造になるのか?-分子間相互作用と分子環境効果を考える-2008

    • Author(s)
      杉本直己・中野修一
    • Journal Title

      現代化学 450

      Pages: 25-30

    • NAID

      40016203606

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Capture of cationic ligands bound diffusely to base pairs during the DNA refolding.2008

    • Author(s)
      S. Nakano, T. Kirihata, and N. Sugimoto
    • Journal Title

      Chem. Commun.

      Pages: 700-702

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of polyethylene glycol on a DNA duplex stability differed by the NaCl concentration.2007

    • Author(s)
      H. Karimata, S. Nakano, N. Sugimoto
    • Journal Title

      Bull. Chem. Soc. Jpn. 80

      Pages: 1987-1994

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides.2007

    • Author(s)
      S. Nakano, T. Kirihata, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai, N. Sugimoto
    • Journal Title

      Nucleic Acids Res. 35

      Pages: 486-494

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Consecutive GC base pairs determine the energy barrier of DNA duplex formation under molecularly crowded conditions.2007

    • Author(s)
      X. Gu, S. Nakano, and N. Sugimoto
    • Journal Title

      Chem. Commun.

      Pages: 2750-2752

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Hydration regulates thermodynamic stability of DNA structures under molecular crowding conditions.2007

    • Author(s)
      H. Karimata, S. Nakano, and N. Sugimoto
    • Journal Title

      Bull. Chem. Soc. Jpn. 80

      Pages: 1987-1994

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] 生命分子の挙動に及ぼす分子環境の効果(3)核酸に対する分子環境効果を調べるためのモデル研究2010

    • Author(s)
      中野修一・平山英伸・北川雄一・杉本直己
    • Organizer
      日本化学会第90春季年会
    • Place of Presentation
      近畿大学
    • Year and Date
      2010-03-27
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] 生命分子の挙動に及ぼす分子環境の効果(1)生体アニオン共存下におけるハンマーヘッドリボザイムの酵素活性2010

    • Author(s)
      北川雄一・中野修一・杉本直己
    • Organizer
      日本化学会第90春季年会
    • Place of Presentation
      近畿大学
    • Year and Date
      2010-03-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] 生命分子の挙動に及ぼす分子環境の効果(2)ポリエチレングリコール存在下におけるRNAとカチオンの結合エネルギーの評価2010

    • Author(s)
      平山英伸・中野修一・杉本直己
    • Organizer
      日本化学会第90春季年会
    • Place of Presentation
      近畿大学
    • Year and Date
      2010-03-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] RNAの機能に及ぼす中性溶質の影響2009

    • Author(s)
      中野修一・北川雄一・平山英伸・杉本直己
    • Organizer
      第32回溶液化学シンポジウム
    • Place of Presentation
      新潟
    • Year and Date
      2009-11-18
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence.2009

    • Author(s)
      S. Nakano, H. Hirayama, N. Sugimoto
    • Organizer
      第6回国際核酸化学シンポジウム(第36回核酸化学シンポジウム)
    • Place of Presentation
      岐阜
    • Year and Date
      2009-09-29
    • Related Report
      2009 Final Research Report
  • [Presentation] Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence2009

    • Author(s)
      中野修一・平山英伸・杉本直己
    • Organizer
      第6回国際核酸化学シンポジウム(第36回核酸化学シンポジウム)
    • Place of Presentation
      岐阜
    • Year and Date
      2009-09-29
    • Related Report
      2009 Annual Research Report
  • [Presentation] NanoBioNow(18) DNAのリン酸負電荷とカチオンのクーロン相互作用に対する定量的アプローチ2009

    • Author(s)
      北川雄一・中野修一・杉本直己
    • Organizer
      日本化学会第89会春季年会
    • Place of Presentation
      日本大学
    • Year and Date
      2009-03-30
    • Related Report
      2008 Annual Research Report
  • [Presentation] Nucleic acid interaction revisited: Cation and water binding to nucleotides.2009

    • Author(s)
      中野修一・杉本直己
    • Organizer
      日本化学会第89会春季年会(アジア国際シンポジウム)
    • Place of Presentation
      日本大学
    • Year and Date
      2009-03-29
    • Related Report
      2009 Final Research Report
  • [Presentation] NanoBioNow(16)ヘアピンRNAの二次構造変化に及ぼすカチオンの静電相互作用の影響2009

    • Author(s)
      平山英伸・中野修一・杉本直己
    • Organizer
      日本化学会第89会春季年会(アジア国際シンポジウム)
    • Place of Presentation
      日本大学
    • Year and Date
      2009-03-29
    • Related Report
      2008 Annual Research Report
  • [Presentation] Nucleic acid interaction revisited : Cation and water binding to nucleotides2009

    • Author(s)
      中野修一・杉本直己
    • Organizer
      日本化学会第89会春季年会(アジア国際シンポジウム)
    • Place of Presentation
      日本大学
    • Year and Date
      2009-03-29
    • Related Report
      2008 Annual Research Report
  • [Presentation] 分子環境がもたらす核酸の機能化2008

    • Author(s)
      中野修一・杉本直己
    • Organizer
      08-01バイオ高分子研究会
    • Place of Presentation
      大阪
    • Year and Date
      2008-09-27
    • Related Report
      2008 Annual Research Report
  • [Presentation] 分子クラウディング環境によってもたらされる核酸とカチオンの結合性の向上とその生物学的意義2008

    • Author(s)
      中野修一・桐畑俊正・平山英伸・杉本直己
    • Organizer
      第3回バイオ関連化学合同シンポジウム
    • Place of Presentation
      東京工業大学
    • Year and Date
      2008-09-18
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] ハンマーヘッドリボザイムの切断活性変化を利用したカチオンと共存核酸の結合の評価2008

    • Author(s)
      北川雄一・中野修一・杉本直己
    • Organizer
      第3回バイオ関連化学合同シンポジウム
    • Place of Presentation
      東京工業大学
    • Year and Date
      2008-09-18
    • Related Report
      2008 Annual Research Report
  • [Presentation] Molecular crowding effect on metal ion binding properties of the hammerhead ribozyme2008

    • Author(s)
      S. Nakano, Y. Kitagawa, H. T. Karimata, N. Sugimoto
    • Organizer
      第5回国際核酸化学シンポジウム(第34回核酸化学シンポジウム)
    • Place of Presentation
      東京大学
    • Year and Date
      2008-09-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] Folding and activity of the hammerhead ribozyme facilitated by the molecular crowding by cosolutes2008

    • Author(s)
      S. Nakano, H. T. Karimata, Y. Kitagawa, N. Sugimoto
    • Organizer
      RNA2008
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      2008-07-31
    • Related Report
      2008 Annual Research Report
  • [Presentation] DNA and RNA structures in the presence of a neutral cosolute.2008

    • Author(s)
      中野修一・Lei Wu・岡裕人・狩俣寿枝・桐畑俊正・佐藤雄一・藤井敏司・酒井宏・桑原正靖・澤井宏明・杉本直己
    • Organizer
      Gordon Research Conference on Nucleic Acids
    • Place of Presentation
      Newport, RI, USA
    • Year and Date
      2008-06-05
    • Related Report
      2009 Final Research Report
  • [Presentation] DNA and RNA structures in the presence of a neutral cosolute2008

    • Author(s)
      中野修一・Lei wu・岡裕人・狩俣寿枝・桐畑俊正・佐藤雄一・藤井敏司・酒井宏・桑原正靖・澤井宏明・杉本直己
    • Organizer
      Gordon Research Conference on Nucleic Acids
    • Place of Presentation
      Newport, RI, USA
    • Year and Date
      2008-06-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] NanoBioNow(8)二価金属イオン非存在下で起こるハンマーヘッドリボザイムの切断反応に対するPEGの分子クラウディングの影響2008

    • Author(s)
      北川雄一・狩俣寿枝・中野修一・杉本直己
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Related Report
      2007 Annual Research Report
  • [Presentation] Functional DNA materials controlled by surrounding conditions2007

    • Author(s)
      杉本直己・三好大輔・中野修一・甲元一也・Z.-M. Wang・井上真美子・狩俣寿枝
    • Organizer
      IUPAC 3rd International Symposium on Novel Materials and Synthesis(NMS-III)
    • Place of Presentation
      上海、中国
    • Related Report
      2007 Annual Research Report
  • [Book] 第一節DNAチップの基礎1ハイブリダイゼーション, バイオチップ実用化ハンドブック(金子周一、堀池靖浩監修)2010

    • Author(s)
      杉本直己・中野修一
    • Publisher
      エヌティーエス
    • Related Report
      2009 Final Research Report
  • [Book] シングルセル解析の最前線(神原秀記、松永是、植田充美監修)2010

    • Author(s)
      中野修一・杉本直己
    • Publisher
      シーエムシー出版
    • Related Report
      2009 Final Research Report
  • [Book] シングルセル解析の最前線生体シグナル解析用の機能性核酸センサーの定量的デザイン2010

    • Author(s)
      中野修一・杉本直己
    • Total Pages
      8
    • Publisher
      シーエムシー
    • Related Report
      2009 Annual Research Report
  • [Book] Bottom-up Nanofabrication: Supramolecules, Self-Assemblies, and Organized Films (Eds. By K. Ariga and H.S. Nalwa)2009

    • Author(s)
      S. Nakano, N. Sugimoto
    • Publisher
      American Scientific Publishers
    • Related Report
      2009 Final Research Report
  • [Book] Bottom-up Nanofabrication : Supramolecules, Self-Assemblies, and Organized Films Chapter 8.Energy of Nucleic Acid Self-Assemblies : From Sequence to Function through Structure2009

    • Author(s)
      中野修一・杉本直己
    • Total Pages
      25
    • Publisher
      American Scientific Publishers
    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://www.konan-first.jp/database/search.php

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://www.konan-first.jp/database/search.php

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://www.konan-first.jp/

    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://www.konan-fiber.jp/

    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://fiber.konan-u.ac.jp/

    • Related Report
      2007 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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