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2014 Fiscal Year Annual Research Report

遺伝子発現に重要な関与をする核酸の非標準構造のエネルギーデータベース化とその活用

Research Project

Project/Area Number 24245033
Research InstitutionKonan University

Principal Investigator

杉本 直己  甲南大学, 先端生命工学研究所, 教授 (60206430)

Co-Investigator(Kenkyū-buntansha) 建石 寿枝  甲南大学, 先端生命工学研究所, 助教 (20593495)
遠藤 玉樹  甲南大学, 先端生命工学研究所, 講師 (90550236)
Project Period (FY) 2012-04-01 – 2015-03-31
Keywords核酸構造 / 安定化エネルギー / 相互作用エネルギー / 溶液内化学環境 / 分子クラウディング / 四重鎖構造 / 転写反応 / 翻訳反応
Outline of Annual Research Achievements

平成26年度は、『知る』研究、『生む』研究、『活かす』研究を包括的に進め、核酸の非標準構造に関するエネルギーデータベースの活用を行った。『知る』研究では、二重鎖領域末端のダングリングエンドに対する分子クラウディング環境の影響を明らかにした(ChemMedChem, 9, 2150 (2014))。また、計算科学的な手法を用いて微視的観点からDNAと分子イオンとの相互作用をエネルギーレベルで解析し、コリンイオンによる核酸構造の安定性に対する寄与を明らかにした(J. Phys. Chem. B., 118, 9583 (2014)、J. Phys. Chem. B., 118, 379 (2014))。一方で、コリンイオンとグアニン塩基の相互作用により、膜表面上で四重鎖構造が不安定化するという知見を基に、膜の表面上で四重鎖構造を形成するDNAからの転写量を増大させるシステムを『生む』研究へと発展させた(Nucleic Acids Res., 42, 12949 (2014))。また、機能性の人工分子『生む』研究として、アニオン性のフタロシアニンが、二重鎖構造のDNAが多量に存在する条件下でもテロメラーゼの活性を効率的に抑制できることを示した(J. Phys. Chem. B., 118, 2605 (2014))。さらに、人工ペプチド核酸(PNA)を合成し、カルパインでPNAを切断することにより、分子間で形成されていた四重鎖構造を解消させることに成功した(Org. Biomol. Chem., 13, 2022 (2015))。核酸の非標準構造を遺伝子発現制御に『活かす』研究として、これまでの研究から得られている、RNA高次構造の形成におけるステム領域の重要性に着目し、ステム領域を系統的に改変した人工リボスイッチによる遺伝子発現制御システムを構築することに成功した(Angew. Chem. Int. Ed., 54, 905 (2015))。
これらの研究から得られた成果は総説としてまとめ、国際的な学術雑誌に掲載した(Chem. Rev., 114, 2733 (2014)、Nucleic Acids Res., 42, 8831 (2014)など)。

Research Progress Status

26年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

26年度が最終年度であるため、記入しない。

  • Research Products

    (45 results)

All 2015 2014 Other

All Journal Article (13 results) (of which Peer Reviewed: 13 results,  Acknowledgement Compliant: 11 results,  Open Access: 2 results) Presentation (29 results) (of which Invited: 5 results) Book (2 results) Remarks (1 results)

  • [Journal Article] Tuning riboswitch-mediated gene regulation by rational control of aptamer ligand binding properties2015

    • Author(s)
      A. B. Rode, T. Endoh, and N. Sugimoto
    • Journal Title

      Angew. Chem. Int. Ed.

      Volume: 54 Pages: 905-909

    • DOI

      10.1002/anie.201407385

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Effects of molecular crowding on the structures, interactions, and functions of nucleic acids2014

    • Author(s)
      S. Nakano, D. Miyoshi, and N. Sugimoto
    • Journal Title

      Chem. Rev.

      Volume: 114 Pages: 2733-2758

    • DOI

      10.1021/cr400113m

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structure, stability and behavior of nucleic acids in ionic liquids2014

    • Author(s)
      H. Tateishi-Karimata and N. Sugimoto
    • Journal Title

      Nucleic Acids Res.

      Volume: 42 Pages: 8831-8844

    • DOI

      10.1093/nar/gku499

    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Choline ion interactions with DNA atoms explain unique stabilization of A-T base pairs in DNA duplexes: A microscopic view2014

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

      J. Phys. Chem. B

      Volume: 118 Pages: 379-389

    • DOI

      10.1021/jp406647b

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] In vitro assays predicting of telomerase inhibitory effect of G-quadruplex ligands in cell nuclei2014

    • Author(s)
      H. Yaku, T. Murashima, D. Miyoshi, and N. Sugimoto
    • Journal Title

      J. Phys. Chem. B

      Volume: 118 Pages: 2605-2614

    • DOI

      10.1021/jp410669t

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Reduced graphene oxide upconversion nanoparticle hybrid for electrochemi luminescent sensing of a prognostic indicator in early-stage cancer2014

    • Author(s)
      L. Wu, J. Wang, M. Yin, J. Ren, D. Miyoshi, N. Sugimoto, and X. Qu
    • Journal Title

      Small

      Volume: 10 Pages: 330-336

    • DOI

      10.1002/smll.201301273

    • Peer Reviewed
  • [Journal Article] Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain2014

    • Author(s)
      D. Miyoshi, Y. Ueda, N. Shimada, S. Nakano, N. Sugimoto, A. Maruyama
    • Journal Title

      ChemMedChem

      Volume: 9 Pages: 2156-2163

    • DOI

      10.1002/cmdc.201402157

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Dangling ends perturb the stability of RNA duplex responsive to surrounding condition2014

    • Author(s)
      H. Tateishi-Karimata, S. Pramanik, S. Nakano, D. Miyoshi and N. Sugimoto
    • Journal Title

      ChemMedChem

      Volume: 9 Pages: 2150-2155

    • DOI

      10.1002/cmdc.201402167

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Aptamer-based universal fluorometric sensors based on allosteric modulation of RNA-peptide interactions2014

    • Author(s)
      T. Endoh and N. Sugimoto
    • Journal Title

      ChemMedChem

      Volume: 9 Pages: 2045-2048

    • DOI

      10.1002/cmdc.201402151

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] The affinity of molecular ions for DNA structures is determined by solvent accessible surface area2014

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

      J. Phys. Chem. B

      Volume: 118 Pages: 9583-9594

    • DOI

      10.1021/jp505107g

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription2014

    • Author(s)
      S. Pramanik, H. Tateishi-Karimata, and N. Sugimoto
    • Journal Title

      Nucleic Acids Res.

      Volume: 42 Pages: 12949-12959

    • DOI

      10.1093/nar/gku998

    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Methyl substitution regulates the enantioselectivity of supramolecular complex binding to human telomeric G-Quadruplex DNA2014

    • Author(s)
      B. Xu, C. Zhao, Y. Chen, H. Tateishi-Karimata, J. Ren, N. Sugimoto, and X. Qu
    • Journal Title

      Chem. Eur. J.

      Volume: 20 Pages: 16467-16472

    • DOI

      10.1002/chem.201404854

    • Peer Reviewed
  • [Journal Article] Noncanonical Structures and Their Thermodynamics of DNA and RNA Under Molecular Crowing: Beyond the Watson-Crick Double Helix2014

    • Author(s)
      N. Sugimoto
    • Journal Title

      Int. Rev. of Cell and Mol. Biol.

      Volume: 307 Pages: 205-273

    • DOI

      10.1016/B978-0-12-800046-5.00008-4

    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (1): DNA G-quadruplexes Control RNA-folding and Gene Expression2015

    • Author(s)
      H. Tateishi-Karimata, T. Endoh, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (2): DNA G-triplexes Control Production of RNA Transcript2015

    • Author(s)
      R. Subramaniyam, H. Tateishi-Karimata, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (3): Regulation of Transcription by Cyclic Naphthalene Diimide of G-quadruplex DNA Binding Ligand2015

    • Author(s)
      H. Tateishi-Karimata, Y. Esaki, S. Sato, S. Takeneka, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (4): Interaction of Nucleolin with DNA and RNA G-quadruplexes2015

    • Author(s)
      S. Pramanik, H. Tateishi-Karimata, S. Takahashi, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (6): Binding Mechanism of G-quadruplex and Its Ligands Elucidated by Pressure Effect2015

    • Author(s)
      S. Takahashi, S. Bhowmik, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (7): Molecular Crowding Effect on Ribozyme- or Protein-based Polymerase Reactions2015

    • Author(s)
      H. Okura, S. Takahashi, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (10): Translation Suppression Mediated by Triplex Formed by 2-Aminopyridine-modified PNA and Hairpin RNA2015

    • Author(s)
      T. Endoh, E. Rozners, D. Hnedzko, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (11): Role of Compensatory Base Pair Variation in Stem Regions of FMN Riboswitch Aptamer on Its Gene Regulation2015

    • Author(s)
      A. B. Rode, T. Endoh, and N. Sugimoto
    • Organizer
      日本化学会第95春季年会
    • Place of Presentation
      日本大学 理工学部船橋キャンパス、千葉
    • Year and Date
      2015-03-26 – 2015-03-29
  • [Presentation] Structures, Interactions, and Functions of Nucleic Acids under Molecular Crowding Conditions2014

    • Author(s)
      N. Sugimoto
    • Organizer
      Asian Chemical Biology Conference (ACBC 2014)
    • Place of Presentation
      Ngee An Kongsi Auditorium, Education resource centre in NUS, Singapore
    • Year and Date
      2014-12-15 – 2014-12-17
    • Invited
  • [Presentation] 核酸の非二重らせん構造に潜む重要な機能2014

    • Author(s)
      杉本直己
    • Organizer
      第14回東北大学多元物質科学研究所 研究発表会
    • Place of Presentation
      東北大学片平さくらホール、宮城
    • Year and Date
      2014-12-05 – 2014-12-05
    • Invited
  • [Presentation] 核酸四重らせん構造を特異的に安定化させる修飾DNAの開発2014

    • Author(s)
      建石寿枝, 村岡貴博, 金原数, 杉本直己
    • Organizer
      第14回東北大学多元物質科学研究所 研究発表会
    • Place of Presentation
      東北大学片平さくらホール、宮城
    • Year and Date
      2014-12-05 – 2014-12-05
  • [Presentation] 核酸の挙動に及ぼす分子クラウディングと圧力の影響2014

    • Author(s)
      杉本直己, 高橋俊太郎
    • Organizer
      第55回高圧討論会
    • Place of Presentation
      徳島大学常三島キャンパス、徳島
    • Year and Date
      2014-11-22 – 2014-11-24
    • Invited
  • [Presentation] テロメアDNA配列のP-T依存的構造変化2014

    • Author(s)
      高橋俊太郎, 杉本直己
    • Organizer
      第55回高圧討論会
    • Place of Presentation
      徳島大学常三島キャンパス、徳島
    • Year and Date
      2014-11-22 – 2014-11-24
  • [Presentation] Effect of Conformational Transition Kinetics of Nascent mRNA on Co-and Post-transcriptional Translation Systems2014

    • Author(s)
      T. Endoh and N. Sugimoto
    • Organizer
      The 41st International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      Kitakyushu International Conference Center, Fukuoka
    • Year and Date
      2014-11-05 – 2014-11-07
  • [Presentation] Large stabilization of G-quadruplexes by tetra-ethylene glycol modified deoxythymines2014

    • Author(s)
      H. Tateishi-Karimata, T. Muraoka, K. Kinbara, P. Podbevsec, J. Plavec, and N. Sugimoto
    • Organizer
      The 41st International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      Kitakyushu International Conference Center, Fukuoka
    • Year and Date
      2014-11-05 – 2014-11-07
  • [Presentation] New insights into the binding nucleolin to nucleic acids from physicochemical analysis2014

    • Author(s)
      S. Pramanik, H. Tateishi-Karimata, S. Takahashi, and N. Sugimoto
    • Organizer
      The 41st International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      Kitakyushu International Conference Center, Fukuoka
    • Year and Date
      2014-11-05 – 2014-11-07
  • [Presentation] Tuning of Riboswitch-mediated Gene Regulation via Rational Control of Aptamer Ligand Binding Properties2014

    • Author(s)
      A. B. Rode, T. Endoh, and N. Sugimoto
    • Organizer
      The 41st International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      Kitakyushu International Conference Center, Fukuoka
    • Year and Date
      2014-11-05 – 2014-11-07
  • [Presentation] Pressure and temperature stability diagram of human telomeric DNA2014

    • Author(s)
      S. Takahashi, S. Bhowmik, and N. Sugimoto
    • Organizer
      The 41st International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      Kitakyushu International Conference Center, Fukuoka
    • Year and Date
      2014-11-05 – 2014-11-07
  • [Presentation] Interesting Behaviors of Nucleic Acids with Unusual Structures2014

    • Author(s)
      T. Endoh, H. Tateishi-Karimata, S. Takahashi, and N. Sugimoto
    • Organizer
      3rd Swiss-Japan Chemical Biology Symposium 2014
    • Place of Presentation
      Bern, Switzerland
    • Year and Date
      2014-10-02 – 2014-10-03
  • [Presentation] 非二重らせん構造に隠された核酸の機能を知る2014

    • Author(s)
      杉本直己
    • Organizer
      バイオ・高分子研究会 核酸を科学する
    • Place of Presentation
      にっしょうかん新館・梅松鶴、長崎
    • Year and Date
      2014-09-26 – 2014-09-27
  • [Presentation] Interesting Behaviors of Nucleic Acids under Molecular crowding conditions2014

    • Author(s)
      N. Sugimoto
    • Organizer
      Graduate School of Biostudies & iCeMS Joint Symposium “Hierarchical Dynamics of Nucleic Acids: Synergy between Structure and Function”
    • Place of Presentation
      iCeMS, Kyoto University
    • Year and Date
      2014-09-22 – 2014-09-22
    • Invited
  • [Presentation] 核酸の熱力学的挙動解析と核酸ナノマテリアルの創製2014

    • Author(s)
      杉本直己
    • Organizer
      第64回錯体化学討論会
    • Place of Presentation
      中央大学理工学部 後楽園キャンパス、東京
    • Year and Date
      2014-09-18 – 2014-09-20
    • Invited
  • [Presentation] 高圧力で誘起されるi-motif DNAの構造安定化効果2014

    • Author(s)
      高橋俊太郎, 杉本直己
    • Organizer
      第8回バイオ関連化学シンポジウム
    • Place of Presentation
      岡山大学津島キャンパス、岡山
    • Year and Date
      2014-09-11 – 2014-09-13
  • [Presentation] RNA-ペプチド間のアロステリック相互作用を利用した小分子検出のためのユニバーサルバイオセンサーの構築2014

    • Author(s)
      遠藤玉樹, 杉本直己
    • Organizer
      第8回バイオ関連化学シンポジウム
    • Place of Presentation
      岡山大学津島キャンパス、岡山
    • Year and Date
      2014-09-11 – 2014-09-13
  • [Presentation] DNA四重鎖は転写の二次情報を保持しているか?2014

    • Author(s)
      建石寿枝, 遠藤玉樹, 高橋俊太郎, 杉本直己
    • Organizer
      第8回バイオ関連化学シンポジウム
    • Place of Presentation
      岡山大学津島キャンパス、岡山
    • Year and Date
      2014-09-11 – 2014-09-13
  • [Presentation] Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids: Beyond the Watson-Crick Double Helix2014

    • Author(s)
      S. Nakano, D. Miyoshi, and N. Sugimoto
    • Organizer
      XXI Round Table on Nucleosides, Nucleotides and Nucleic acids (IRT2014)
    • Place of Presentation
      Poznan, Poland
    • Year and Date
      2014-08-24 – 2014-08-28
  • [Presentation] Effect of pressure and molecular crowding on the stability of G-quadruplex DNA2014

    • Author(s)
      S. Takahashi and N. Sugimoto
    • Organizer
      8th International Conference on High Pressure Bioscience and Biotechnology (HPBB)
    • Place of Presentation
      Nantes, France
    • Year and Date
      2014-07-15 – 2014-07-18
  • [Presentation] Thermal Stability and Application of Unusual structures of DNA and RNA, International University2014

    • Author(s)
      N. Sugimoto
    • Organizer
      The 5th International Conference on the Development of Biomedical Engineering
    • Place of Presentation
      Ho Chi Minh, Vietnam
    • Year and Date
      2014-06-16 – 2014-06-18
  • [Presentation] Thermal Stability of Non-cannonical structures in Template DNA and its Effect on Transcription2014

    • Author(s)
      H. Tateishi-Karimata and N. Sugimoto
    • Organizer
      Gordon Research Conference - Biopolymers
    • Place of Presentation
      Salve Regina University, USA
    • Year and Date
      2014-06-01 – 2014-06-06
  • [Book] 高圧力下での核酸の化学的挙動 (CSJカレントレビュー 極限環境の生体分子 過酷な環境下での機能を科学する)2014

    • Author(s)
      高橋俊太郎、杉本直己
    • Total Pages
      9
    • Publisher
      化学同人
  • [Book] Effect of Ionic Liquid and Liposomes on the Structure, Stability, and Function of Nucleic Acids (Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications)2014

    • Author(s)
      N. Sugimoto
    • Total Pages
      18
    • Publisher
      Springer
  • [Remarks] 甲南大学先端生命工学研究所

    • URL

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

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Published: 2016-06-03  

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