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Synthetic study of functional mismatch binding molecules for selective hydrolysis of expanded repeat RNAs

Research Project

Project/Area Number 17K14516
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Bio-related chemistry
Research InstitutionOsaka University

Principal Investigator

YAMADA Takeshi  大阪大学, 産業科学研究所, 助教 (80633263)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2018: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2017: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
KeywordsDNA / トリヌクレオチドリピート / 低分子 / ミスマッチ塩基対 / RNA / ミスマッチ / チオール / イミダゾール / 生体関連化学 / 核酸 / 有機合成化学 / ケミカルバイオロジー / トリプレットリピート / 有機合成
Outline of Final Research Achievements

To develop small molecules that selectively hydrolyze repeat RNAs that cause neurodegenerative diseases, various NCD derivatives, comprised from NCD moiety and various nucleophilic functional groups, were synthesized. Then the effects of these derivatives on the hydrolysis of mismatch RNAs were analyzed by RP-HPLC and MALDI-TOF-MASS. Although those results confirmed that the C-C mismatch site in the RNA duplex was prone to be hydrolyzed in the presence of compounds, selective hydrolysis of the CGG repeat RNA were not observed. However, it was clarified NCD-SH and NCD-CC modified with thiol groups rapidly dimerize on CGG repeats and bind tightly to their targets, and NCD-IMI, a derivative of NCD modified with imidazole groups, can efficiently place metal complexes on DNA. Those derivatives were published in three different theses in peer-reviewed journal.

Academic Significance and Societal Importance of the Research Achievements

遺伝子中のトリヌクレオチドリピートの異常伸長は脆弱X症候群・ハンチントン病など、多くの神経変成疾患の原因となるが、発症・重症化のメカニズムは不明な部分が多い。本研究の成果であるNCD-SHやNCD-CCは、脆弱X症候群の原因であるCGGリピートDNAと強固に結合するため、脆弱X症候群を解明するための分子プローブとしての利用が期待できる。また、DNA中のCGG/CGG特異的に結合して二重鎖DNA上に金属錯体を配置することができるNCD-IMIは、DNAオリガミなどのDNAナノテクノロジーへの応用が期待できる。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (20 results)

All 2020 2019 2018 2017

All Journal Article (3 results) (of which Peer Reviewed: 3 results) Presentation (17 results) (of which Int'l Joint Research: 6 results,  Invited: 1 results)

  • [Journal Article] Assembly of ruthenium complexes on double stranded DNA using mismatch binding ligands2020

    • Author(s)
      Ni Lu、Yamada Takeshi、Nakatani Kazuhiko
    • Journal Title

      Chemical Communications

      Volume: 56 Issue: 39 Pages: 5227-5230

    • DOI

      10.1039/d0cc01863e

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CGG repeat DNA assisted dimerization of CGG/CGG binding molecule through intermolecular disulfide formation2018

    • Author(s)
      Yamada Takeshi、Miki Shouta、Ni Lu、Nakatani Kazuhiko
    • Journal Title

      Chemical Communications

      Volume: 54 Issue: 93 Pages: 13072-13075

    • DOI

      10.1039/c8cc06757k

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Synthesis of Naphthyridine Carbamate Dimer (NCD) Derivatives Modified with Alkanethiol and Binding Properties of G?G Mismatch DNA2017

    • Author(s)
      Yamada Takeshi、Miki Shouta、Ul’Husna Anisa、Michikawa Akiko、Nakatani Kazuhiko
    • Journal Title

      Organic Letters

      Volume: 19 Issue: 16 Pages: 4163-4166

    • DOI

      10.1021/acs.orglett.7b01632

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] Structural analysis and functionalization of naphthyridine dimer derivatives bound to CGG repeats2020

    • Author(s)
      ○Takeshi Yamada, Shuhei Sakurabayashi, Kyoko Huruitab, Chojiro Kojima, Kazuhiko Nakatani
    • Organizer
      The 23rd SANKEN INTERNATIONAL SYMPOSIUM
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] NMR structural analysis of naphthyridine dimer derivatives binding to CGG/CGG triplets in DNAs2020

    • Author(s)
      ○YAMADA Takeshi
    • Organizer
      2nd Indo-Japan (NCBS/inStem-ISIR, Osaka University) Meeting: Interfacing Chemistry and Biology
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Assembly of ruthenium complexes on dsDNA using mismatch binding ligand2020

    • Author(s)
      ○Lu Ni, Takeshi Yamada, Kazuhiko Nakatani,
    • Organizer
      日本化学会第100春季年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Synthesis and the properties of NA Dimer2020

    • Author(s)
      ◯Chen Qingwen, Yamada Takeshi, Murata Asako, Nakatani Kazuhiko
    • Organizer
      日本化学会第100春季年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Synthesis and properties of 13C-labeled naphthyridine derivative2020

    • Author(s)
      ○Shuhei Sakurabayashi, Takeshi Yamada, Gota Kawai, Kazuhiko Nakatani
    • Organizer
      日本化学会第100春季年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] XGGリピートDNA中のピリミジン塩基を選択的に酸化するリガンドの開発2020

    • Author(s)
      ◯八木 勇樹、山田 剛史、中谷 和彦
    • Organizer
      日本ケミカルバイオロジー学会 第14回年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] The methylation effect for binding of dimeric 2-amino-1,8-naphthyridine derivatives to CGG/CGG triad in DNA2020

    • Author(s)
      ○Takeshi Yamada, Shuhei Sakurabayashi, Kazuhiko Nakatani
    • Organizer
      The Commemorative International Symposium of the Japan Society of Nucleic Acids Chemistry (CISNAC 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Research on NCD (Naphthyridine Carbamate Dimer) Linked Arene-Ruthenium(II) Half-Sandwich Complexes2019

    • Author(s)
      Ni Lu, Takeshi Yamada
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 配列選択的ピリミジン塩基の酸化を指向した、ナフチリジンカルバメートダイマー誘導体の合成とその評価2019

    • Author(s)
      ○八木勇樹、山田剛史、中谷和彦
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 7位修飾ナフチリジンカルバメートダイマーの合成と結合特性2019

    • Author(s)
      櫻林 修平、山田 剛史、中谷 和彦
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 金属に配位可能な側鎖をもつアミノ酸で修飾したミスマッチDNA結合性小分子の合成と性質2018

    • Author(s)
      三木 翔太・山田 剛史・中谷 和彦
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2018 Research-status Report 2017 Research-status Report
  • [Presentation] Repeat-Assisted Dimerization of Thiol Modified Mismatch Binding Ligand2018

    • Author(s)
      YAMADA Takeshi, NAKATANI Kazuhiko
    • Organizer
      International Roundtable of Nucleosides, Nucleotides, and Nucleic Acids (IRT)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Functional Regulation of Epigenetic DNA Modifications using Photoreactive Oligonucleotides2018

    • Author(s)
      Asako Yamayoshi, Takayuki Shibata, Yui Sakai, Takeshi Yamada, Tsuyoshi Yamamoto, Takehiko Wada, Kazuhiko Nakatani
    • Organizer
      International Symposium on Nucleic Acids Chemistry (ISNAC) 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Repeat DNA assisted dimerization of mismatch binding molecules through intermolecular disul de formation2018

    • Author(s)
      Takeshi Yamada, Kazuhiko Nakatani
    • Organizer
      International Symposium on Nucleic Acids Chemistry (ISNAC) 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Toward site selective modification of pyrimidine bases flipped out by naphthyridine cabamate dimer binding.2018

    • Author(s)
      ○Yuki Yagi, Takeshi Yamada, Kazuhiko Nakatani
    • Organizer
      JSPS日中韓フォーサイト事業 アジア化学プローブ研究拠点 第3回A3若手研究者ミーティング
    • Related Report
      2018 Research-status Report
  • [Presentation] Thiol Modified Naphthyridine Carbamate Dimer Accumulated on CGG Repeat DNA2017

    • Author(s)
      ○Takeshi Yamada, Shouta Miki, Kazuhiko Nakatani
    • Organizer
      ISNAC2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] RNA切断活性をもつミスマッチ結合性リガンドの開発2017

    • Author(s)
      三木 翔太・山田 剛史・中谷 和彦
    • Organizer
      日本化学会第97春季年会
    • Related Report
      2017 Research-status Report

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Published: 2017-04-28   Modified: 2021-02-19  

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