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2011 Fiscal Year Final Research Report

Development of novel nucleic acid materials that efficiently work in the intracellular molecular environment

Research Project

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Project/Area Number 21245040
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Chemistry related to living body
Research InstitutionKonan University

Principal Investigator

SUGIMOTO Naoki  甲南大学, フロンティアサイエンス学部, 教授 (60206430)

Co-Investigator(Kenkyū-buntansha) KAWAKAMI Junji  甲南大学, フロンティアサイエンス学部, 教授 (40289012)
NAKANO Shu-ichi  甲南大学, フロンティアサイエンス学部, 准教授 (70340908)
MIYOSHI Daisuke  甲南大学, フロンティアサイエンス学部, 准教授 (50388758)
Project Period (FY) 2009 – 2011
Keywords核酸 / 四重鎖構造 / 相互作用エネルギー / リボザイム / 分子クラウディング / ポリエチレングリコール
Research Abstract

We studied nucleic acid interactions and reactions by using a model experimental system that mimics the intracellular molecular environment. This research provided quantitative insights into influences of the molecular crowding medium on nucleic acid folding, a ribozyme activity, and interactions with proteins and peptides. It is supposed that these data can bridge the gap between the results obtained in vitro and in cells. Based on results regarding the effects of molecular environment, we developed novel nucleic acid materials and sensing methods that efficiently work under unusual conditions such as in living cells.

  • Research Products

    (33 results)

All 2012 2011 2010 2009 Other

All Journal Article (21 results) (of which Peer Reviewed: 21 results) Presentation (8 results) Book (3 results) Remarks (1 results)

  • [Journal Article] Detection of a prognostic indicator in early-stage cancer using functionalized graphene-based peptide sensors.2012

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

      Adv. Mater.

      Volume: 24 Pages: 125-131

    • DOI

      DOI:10.1002/adma.201103205

    • Peer Reviewed
  • [Journal Article] Label-free colorimetric and quantitative detection of cancer marker protein using noncrosslinking aggregation of Au/Ag nanoparticles induced by target-specific peptide probe2011

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

      Biosensors and Bioelectronics

      Volume: 26 Pages: 4804-4809

    • DOI

      DOI:10.1016/j.bios.2011.06.012

    • Peer Reviewed
  • [Journal Article] Measurements of the binding of a large protein using a substrate density-controlled DNA chip.2011

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

      Anal. Chem.

      Volume: 83 Pages: 6368-6372

    • DOI

      DOI:10.1021/bi200477g

    • Peer Reviewed
  • [Journal Article] Effect of locked nucleic acid modification on thermal stability of non-canonical DNA structure2011

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

      Biochemistry

      Volume: 50 Pages: 7414-7425

    • DOI

      DOI:10.1021/bi200477g

    • Peer Reviewed
  • [Journal Article] Rational design of a new IMP aptamer based on a TPP riboswitch and a hypoxanthine aptamer2011

    • Author(s)
      M. Tokui, T. Yamauchi, D. Miyoshi, H. Kamiya, A. Nishimura, and N. Sugimoto
    • Journal Title

      Chem. Lett.

      Volume: 40 Pages: 1313-1314

    • DOI

      DOI:10.1246/cl.2011.1313

    • Peer Reviewed
  • [Journal Article] Effects of protein binding on DNA G-quadruplex structures2011

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

      Int. Rev. Biophys. Chem.

      Volume: 2 Pages: 129-134

    • URL

      http://www.praiseworthyprize.com/IREBIC-latest/IREBIC_vol_2_n_4.html#Effects_of_protein_binding_on_DNA_Gquadruplex_structures

    • Peer Reviewed
  • [Journal Article] Gene regulation system with an artificial RNA switch operating in human cell2011

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

      Chem Bio Chem

      Volume: 12 Pages: 1174-1178

    • DOI

      DOI:10.1002/cbic.201100093

    • Peer Reviewed
  • [Journal Article] Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide2011

    • Author(s)
      S. Pramanik, K. Nakamura, K. Usui, S. Nakano, S. Saxena, J. Matsui, D. Miyoshi, and N. Sugimoto
    • Journal Title

      Chem. Commun.

      Volume: 47 Pages: 2790-2792

    • DOI

      DOI:10.1039/C0CC05776B

    • Peer Reviewed
  • [Journal Article] Sole and stable RNA duplexes of G-rich sequences located in the 5'-untranslated region of protooncogenes.2010

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

      Biochemistry

      Volume: 49 Pages: 7190-7201

    • DOI

      DOI:10.1021/bi101093a

    • Peer Reviewed
  • [Journal Article] Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors2010

    • Author(s)
      D. Zhang, T. Fujimoto, S. Saxena, H. Yu, D. Miyoshi, and N. Sugimoto
    • Journal Title

      Biochemistry

      Volume: 49 Pages: 4554-4563

    • DOI

      DOI:10.1021/bi1002822

    • Peer Reviewed
  • [Journal Article] Development of new functional nanostructures consisting of both DNA duplex and quadruplex.2010

    • Author(s)
      K. Dutta, T. Fujimoto, M. Inoue, D. Miyoshi, and N. Sugimoto
    • Journal Title

      Chem. Commun.

      Volume: 46 Pages: 7772-7774

    • DOI

      DOI:10.1039/C0CC00710B

    • Peer Reviewed
  • [Journal Article] Anionic phthalocyanines targeting G-quadruplexes and inhibiting telomerase activity in the presence of excessive DNA duplexes2010

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

      Chem. Commun.

      Volume: 46 Pages: 5740-5742

    • DOI

      DOI:10.1039/C0CC00956C

    • Peer Reviewed
  • [Journal Article] A rapid and sensitive "add-mix-measure" assay for multiple proteinases based on one goldnanoparticle-peptide-fluorophor e conjugate.2010

    • Author(s)
      X. Wang, J. Geng, D. Miyoshi, J. Ren, N. Sugimoto, and X. Qu
    • Journal Title

      Biosensors and Bioelectronics

      Volume: 49 Pages: 743-747

    • DOI

      DOI:10.1016/j.bios.2010.06.046

    • Peer Reviewed
  • [Journal Article] Ultrasensitive and selective detection of a prognostic indicator in early-stage cancer using graphene oxide and carbon nanotubes2010

    • Author(s)
      X. Wang, C. Wang, K. Qu, Y. Song, J. Ren, D. Miyoshi, N. Sugimoto, and X. Qu
    • Journal Title

      Adv. Funct. Mat.

      Volume: 20 Pages: 3967-3971

    • DOI

      DOI:10.1002/adfm.201001118

    • Peer Reviewed
  • [Journal Article] Utilization of salmon milt DNA against UV damage2010

    • Author(s)
      Y. Sasaki, D. Miyoshi, and N. Sugimoto
    • Journal Title

      Applied Biochem. Biotech.

      Volume: 160 Pages: 4554-4563

    • DOI

      DOI:10.1007/s12010-009-8697-6

    • Peer Reviewed
  • [Journal Article] Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides2010

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

      Mol. BioSyst.

      Volume: 6 Pages: 2023-2029

    • DOI

      DOI:10.1039/C0MB00002G

    • 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, and N. Sugimoto
    • Journal Title

      Chem. Commun.

      Volume: 46 Pages: 1299-1301

    • DOI

      DOI:10.1039/B922050J

    • 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, and N. Sugimoto
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 131 Pages: 16881-16888

    • DOI

      DOI:10.1021/ja9066628

    • Peer Reviewed
  • [Journal Article] An approach to peptide-based ATP receptors by a combination of random selection, rational design, and molecular imprinting2009

    • Author(s)
      J. Matsui, J. Nagano, D. Miyoshi, K. Tamaki, and N. Sugimoto
    • Journal Title

      Biosensors and Bioelectronics

      Volume: 25 Pages: 563-567

    • DOI

      DOI:10.1016/j.bios.2009.01.031

    • Peer Reviewed
  • [Journal Article] Stabilization of three-way junctions of DNA under molecular crowding conditions2009

    • Author(s)
      S. Muhuri, K. Mimura, D. Miyoshi, and N. Sugimoto
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 131 Pages: 9268-9280

    • DOI

      DOI:10.1021/ja900744e

    • Peer Reviewed
  • [Journal Article] Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions2009

    • Author(s)
      D. Miyoshi, K. Nakamura, H. T. Karimata, T. Ohmichi, and N. Sugimoto
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 131 Pages: 3522-3531

    • DOI

      DOI:10.1021/ja805972a

    • Peer Reviewed
  • [Presentation] Quantitative analysis of adsorption and desorption of DNA secondary structures on graphene oxide2011

    • Author(s)
      T. Fujimoto, S. Nakano, N. Sugimoto, and D. Miyoshi
    • Organizer
      The 38th International Symposium on Nucleic Acid Chemistry
    • Place of Presentation
      北海道大学(北海道)
    • Year and Date
      2011-11-10
  • [Presentation] Control of gene expression through an allosteric interaction of transactivator protein and its target RNA2010

    • Author(s)
      T. Endoh, and N. Sugimoto
    • Organizer
      The 37th International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      はまぎんホール・ヴィアマーレ(横浜)
    • Year and Date
      2010-11-11
  • [Presentation] Evaluation of the cation binding for the RNA dimerization under molecular crowding condition2010

    • Author(s)
      H. Hirayama, S. Nakano, D. Miyoshi, and N. Sugimoto
    • Organizer
      The 37th International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      はまぎんホール・ヴィアマーレ(横浜)
    • Year and Date
      2010-11-11
  • [Presentation] Molecular crowding effect on functional nucleic acids2010

    • Author(s)
      N. Sugimoto
    • Organizer
      The 1st Asian Chemical Biology Conference(ACBC2010)
    • Place of Presentation
      ソウル大学(韓国)
    • Year and Date
      2010-06-26
  • [Presentation] Stabilization and function of nucleic acids under molecular crowding conditions2010

    • Author(s)
      N. Sugimoto
    • Organizer
      Symposium on Nucleic Acid Chemistry(Structure and Interactions)
    • Place of Presentation
      Gorica(スロベニア)
    • Year and Date
      2010-05-30
  • [Presentation] Thermodynamic parameters for reliable prediction of RNA structures2009

    • Author(s)
      Y. Tanaka, K. Kishimoto, N. Sugimoto, and J. Kawakami
    • Organizer
      Joint Symposium of the 5th Annual Meeting of the Oligonucleotide Therapeutics Society and the 19th Antisense Symposium
    • Place of Presentation
      九州大学(福岡)
    • Year and Date
      2009-11-05
  • [Presentation] Formation of three-way junctions of DNA under molecular crowding conditions2009

    • Author(s)
      S. Muhuri, D. Miyoshi, and N. Sugimoto
    • Organizer
      Gordon Research Conference(Nucleosides, Nucleotides & Oligonucleoties)
    • Place of Presentation
      Newport(アメリカ)
    • Year and Date
      2009-07-07
  • [Presentation] 共存溶質によるテロメラーゼ活性の制御2009

    • Author(s)
      三好大輔, Hai-Quing Yu, 杉本直己
    • Organizer
      日本ケミカルバイオロジー学会第4回年会
    • Place of Presentation
      神戸市産業振興センター(神戸)
    • Year and Date
      2009-05-18
  • [Book] G-quartet, G-quadruplex, and G-wire regulated by chemical stimuli DNA2011

    • Author(s)
      D. Miyoshi and N. Sugimoto
    • Total Pages
      93-104
  • [Book] 機能性核酸のテーラーメード設計超分子サイエンス & テクノロジー2009

    • Author(s)
      杉本直己, 三好大輔
    • Total Pages
      921-929
    • Publisher
      エヌ・ティー・エス
  • [Book] Chapter 8.Energy of Nucleic Acid Self-Assemblies : From Sequence to Function through Structure. Bottom-up Nanofabrication : Supramolecules, Self-Assemblies, and Organized Films2009

    • Author(s)
      S. Nakano and N. Sugimoto
    • Total Pages
      191-215
    • Publisher
      American Scientific Publishers
  • [Remarks]

    • URL

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

URL: 

Published: 2013-07-31  

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