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Development of DNA strand displacement reactions using bifacial nucleobases that form both hydrogen-bonded and metal-mediated base pairs

Research Project

Project/Area Number 16K14029
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Bio-related chemistry
Research InstitutionThe University of Tokyo

Principal Investigator

Takezawa Yusuke  東京大学, 大学院理学系研究科(理学部), 助教 (70508598)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
KeywordsDNA / 人工塩基対 / 鎖交換反応 / 金属錯体 / 人工核酸 / 人工DNA / 金属錯体型塩基対 / DNA鎖交換反応 / 核酸化学 / 生体機能関連化学 / 生物無機化学
Outline of Final Research Achievements

We have developed metal-triggered DNA strand displacement reactions by utilizing bifacial unnatural nucleobases that form both hydrogen-bonded base pairs and metal-mediated base pairs. 5-hydroxyuracil (UOH) bases were incorporated into DNA strands and the Gd(III)-triggered strand displacement was demonstrated based on the reversible switching between hydrogen-bonded UOH-A base pairs and metal-mediated UOH-Gd(III)-UOH base pairs. In addition, a 5-carboxyuracil base was found to form both hydrogen-bonded and metal-mediated base pairs in DNA duplexes, and thus would be utilized for metal-triggered strand displacement reactions.

Academic Significance and Societal Importance of the Research Achievements

DNA鎖交換反応は生体内では相同組換えの過程でも見られるが、近年ではDNAナノ構造体の動的変換などDNAナノテクノロジーの分野でも活用されている。本研究で開発した金属錯体形成に基づくDNA鎖交換反応は、金属イオンを外部刺激として駆動するDNA分子マシンの開発や、機能性人工核酸の機能スイッチングなどへの応用が期待される。特に、水素結合型塩基対と金属錯体型塩基対の双方を形成する「ヤヌス型人工核酸塩基」の設計戦略は、外部刺激応答性のDNA材料や機能性核酸の新規なビルディングブロックとして有用であると考えられる。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (53 results)

All 2019 2018 2017 2016 Other

All Journal Article (4 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 4 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (47 results) (of which Int'l Joint Research: 14 results,  Invited: 1 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Synthesis of a Truncated Analog of Amphidinol 3 Corresponding to the C21-C39/C52-C67 Section2017

    • Author(s)
      Makoto Ebine, Yuri Takada, Naoto Yanai, and Tohru Oishi
    • Journal Title

      Chemistry Letters

      Volume: 46 Issue: 5 Pages: 662-664

    • DOI

      10.1246/cl.160985

    • NAID

      130005655669

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Metal-responsive structural transformation between artificial DNA duplexes and three-way junctions2016

    • Author(s)
      Yusuke Takezawa, Shuhei Yoneda, Jean-Louis H. A. Duprey, Takahiro Nakama and Mitsuhiko Shionoya
    • Journal Title

      Chem. Sci.

      Volume: 7 Issue: 5 Pages: 3006-3010

    • DOI

      10.1039/c6sc00383d

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase2016

    • Author(s)
      Yusuke Takezawa, Teruki Kobayashi and Mitsuhiko Shionoya
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 17 Issue: 6 Pages: 906-906

    • DOI

      10.3390/ijms17060906

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] pH-Dependence of the Thermal Stability of Metallo-DNA Duplexes Containing Ligand-Type 5-Hydroxyuracil Nucleobases2016

    • Author(s)
      Kotaro Nishiyama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Journal Title

      Inorg. Chim. Acta

      Volume: 452 Pages: 176-180

    • DOI

      10.1016/j.ica.2016.04.040

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Metal-dependent regulation of DNA duplex stability based on the metal complexation of 5-carboxyuracil nucleobases2019

    • Author(s)
      Yusuke Takezawa, Akira Suzuki, Manabu Nakaya, Mitsuhiko Shionoya
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Metal-dependent orthogonal regulation of DNAzyme activities by the formation of Cu(II)- and Hg(II)-mediated base pairs2019

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 5-ヒドロキシウラシル塩基の金属錯体形成を駆動力とした可逆なDNA鎖交換反応2019

    • Author(s)
      森 圭太・西山 康太郎・竹澤 悠典・塩谷 光彦
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Encapsulation of mononuclear Ni(II) salen-type complexes in an abasic site in DNA duplexes2019

    • Author(s)
      Manabu Nakaya, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Construction of DNA three-way junction structures containing thiol ligands at the junction core2019

    • Author(s)
      Nobuyuki Fuse, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 5-カルボキシウラシル塩基のCu(II)錯体形成によるDNA二重鎖安定化:修飾塩基の導入数の効果2018

    • Author(s)
      仲谷 学・鈴木 暁・竹澤 悠典・塩谷 光彦
    • Organizer
      第12回バイオ関連化学シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 5-ヒドロキシウラシル塩基を末端に有するDNA鎖を用いた金属配位駆動型DNA鎖交換反応の開発2018

    • Author(s)
      森 圭太・西山 康太郎・竹澤 悠典・塩谷 光彦
    • Organizer
      第12回バイオ関連化学シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] Development of Metal-responsive DNAzyme through Incorporation of a Cu(II)-mediated Artificial Base Pair2018

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      The 43rd International Conference on Coordination Chemistry (ICCC2018)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Construction of Metallo-DNA Duplexes by Using 5-Substituted Uracil Nucleobases as Metal Ligands2018

    • Author(s)
      Yusuke Takezawa, Kotaro Nishiyama, Akira Suzuki, Mitsuhiko Shionoya
    • Organizer
      The 43rd International Conference on Coordination Chemistry (ICCC2018)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Cu(II)-specific Activation of DNAzyme utilizing Metal-mediated Artificial Base Pairing2018

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      錯体化学会第68回討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Metal-dependent Thermal Stabilization of DNA Duplexes containing 5-Carboxyuracil Nucleobases2018

    • Author(s)
      Yusuke Takezawa, Akira Suzuki, Kotaro Nishiyama, Mitsuhiko Shionoya
    • Organizer
      錯体化学会第68回討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 5-ヒドロキシウラシル塩基の金属錯体形成に基づくDNA 二重鎖の熱的安定化:修飾塩基の導入位置の検討2018

    • Author(s)
      森 圭太・西山 康太郎・竹澤 悠典・塩谷 光彦
    • Organizer
      錯体化学会第68回討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 金属イオン応答性DNAzymeの開発: Cu(II)錯体型人工塩基対を用いた触媒活性の繰返し制御2018

    • Author(s)
      中間 貴寛・竹澤 悠典・塩谷 光彦
    • Organizer
      第16回ホスト_ゲスト・超分子化学シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] Ni(II)-ビピリジン錯体でクロスリンクされた三叉路型DNA超分子の構築:配位子-DNA間のリンカーの構造比較2018

    • Author(s)
      竹澤 悠典・榊原 志織・米田 周平・デュプレー ジャン-ルイ・中間 貴寛・塩谷 光彦
    • Organizer
      第16回ホスト-ゲスト・超分子化学シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] A Synthetic DNAzyme with a Cu(II)-mediated Base Pair for the Metal-dependent Catalytic Activity2018

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      CEMS International Symposium on Supramolecular Chemistry & Functional Materials 2018
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Rational Design of Allosteric DNAzyme utilizing a Cu(II)-mediated Artificial Base Pair2018

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Metal-responsive Structure Conversion of Artificial DNA Three-way Junctions: Development of an Alternative Linker between the Ligand and DNA2018

    • Author(s)
      Shiori Sakakibara, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Metal Assembly inside DNA Duplexes Possessing 5-Carboxyuracil Nucleobases as Ligand Moieties2018

    • Author(s)
      Akira Suzuki, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Enzymatic Synthesis of 5-Hydroxy-2'-deoxyuridine Oligomers toward DNA-templated Metal Assembly2018

    • Author(s)
      Tong Xing, Wenxuan Zhang, Takahiro Nakama, Kotaro Nishiyama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Post-synthetic Modification of Oligonucleotides with Metal Ligands toward Metal-mediated Stabilization of DNA Three-way Junctions2018

    • Author(s)
      Nobuyuki Fuse, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Enzymatic Synthesis of Artificial Metallo-DNA utilizing Two-step Primer Extension2017

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa and Mitsuhiko Shionoya
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶応大学(神奈川県横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] Metal-responsive Triplex-forming Oligonucleotides based on 5-Hydroxyuracil DNA Bases2017

    • Author(s)
      Kotaro Nishiyama, Yusuke Takezawa and Mitsuhiko Shionoya
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶応大学(神奈川県横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] Metal coordination behaviors of 5-carboxyuracil nucleobase inside DNA duplexes2017

    • Author(s)
      Akira Suzuki, Kotaro Nishiyama, Yusuke Takezawa and Mitsuhiko Shionoya
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶応大学(神奈川県横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] Metal-responsive Bifacial Base-pairing Behaviors of 5-Hydroxyuracil DNA Bases2017

    • Author(s)
      Kotaro Nishiyama, Yusuke Takezawa and Mitsuhiko Shionoya
    • Organizer
      NTU-SNU-UTokyo Chemistry Symposium
    • Place of Presentation
      東京大学(東京都文京区)
    • Year and Date
      2017-01-16
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 金属錯体形成に基づく人工DNA 二重鎖・三叉路分岐構造の相互構造変換2017

    • Author(s)
      竹澤 悠典・米田 周平・中間 貴寛・塩谷 光彦
    • Organizer
      第15回ホスト-ゲスト・超分子化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] 鋳型非依存性DNAポリメラーゼを用いた金属錯体型人工DNAオリゴマーの酵素合成2017

    • Author(s)
      竹澤 悠典・小林 輝樹・天野 俊太郎・塩谷 光彦
    • Organizer
      第27回金属の関与する生体関連反応シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] 金属に応答する機能性核酸の開発を目指した金属配位子型人工DNAの酵素合成2017

    • Author(s)
      中間 貴寛・竹澤 悠典・塩谷 光彦
    • Organizer
      第27回金属の関与する生体関連反応シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] Metal-mediated structural conversion between artificial DNA duplexes and three-way junctions2017

    • Author(s)
      Yusuke Takezawa, Shuhei Yoneda, Jean-Louis Duprey, Takahiro Nakama, Mitsuhiko Shionoya
    • Organizer
      The 12th International Symposium on Macrocyclic and Supramolecular Chemistry
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Metal-dependent Thermal Stability of DNA Duplexes containing 5-Hydroxyuracil Nucleobases2017

    • Author(s)
      Yusuke Takezawa, Kotaro Nishiyama, Mitsuhiko Shionoya
    • Organizer
      The 6th Asian Conference on Coordination Chemistry
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 金属錯体形成を駆動力とした人工DNA三叉路分岐モチーフの構造変換2017

    • Author(s)
      竹澤 悠典・米田 周平・榊原 志織・中間 貴寛・Duprey, Jean-Louis・塩谷 光彦
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] 金属錯体型人工DNAの酵素合成および金属イオンに応答するDNA触媒の開発2017

    • Author(s)
      中間 貴寛・竹澤 悠典・塩谷 光彦
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] 5-カルボキシウラシル塩基を導入したDNA二重鎖の金属錯体形成に基づく熱的安定化2017

    • Author(s)
      鈴木 暁・竹澤 悠典・塩谷 光彦
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] 榊原 志織・竹澤 悠典・塩谷 光彦2017

    • Author(s)
      金属錯体形成により安定化される人工DNA三叉路構造:配位子とDNAをつなぐリンカーの設計最適化
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] Enzymatic Synthesis of Ligand-bearing Artificial DNAs toward the Development of Cu(II)-responsive Deoxyribozymes2017

    • Author(s)
      Yusuke Takezawa, Takahiro Nakama, Mitsuhiko Shionoya
    • Organizer
      第67回錯体化学会討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] Construction of Metal-responsive DNAzyme utilizing a Cu(II)-mediated Artificial Base Pair2017

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      3rd International Symposium on Center of Excellence for Innovative Material Sciences Based on Supramolecules
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] DNA-templated Metal Assembly using 5-Modified Uracil Nucleobases2017

    • Author(s)
      Yusuke Takezawa, Kotaro Nishiyama, Akira Suzuki, Mitsuhiko Shionoya
    • Organizer
      3rd International Symposium on Center of Excellence for Innovative Material Sciences Based on Supramolecules
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Polymerase Synthesis of Ligand-bearing Unnatural Oligonucleotides toward Metal-mediated DNA Assembly2017

    • Author(s)
      Yusuke Takezawa, Teruki Kobayashi, Mitsuhiko Shionoya
    • Organizer
      The 44th International Symposium on Nucleic Acids Chemistry
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Metal-dependent regulation of structures and functions of DNA supramolecules2017

    • Author(s)
      Yusuke Takezawa
    • Organizer
      Symposium on Frontier of Biofunctional Chemistry (ISBC 2017 Pre-Symposium Meeting)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Metal-mediated Stabilization and Structural Induction of Bipyridine-modified DNA Three-way Junction Structures2017

    • Author(s)
      Yusuke Takezawa, Shuhei Yoneda, Shiori Sakakibara, Takahiro Nakama, Jean-Louis Duprey, Mitsuhiko Shionoya
    • Organizer
      The 2nd International Symposium on Biofunctional Chemistry (ISBC2017)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Allosteric Regulation of DNAzyme Activity by the Formation of a Cu(II)-mediated Artificial Base Pair2017

    • Author(s)
      Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    • Organizer
      The 2nd International Symposium on Biofunctional Chemistry (ISBC2017)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Metal-triggered Structural Rearrangement between Artificial DNA Duplexes and Three-way Junctions2016

    • Author(s)
      Yusuke Takezawa, Shuhei Yoneda, Jean-Louis H. A. Duprey, Takahiro Nakama and Mitsuhiko Shionoya
    • Organizer
      2nd International Symposium on Center of Excellence for Innovative Material Science Based on Supramolecules 2016
    • Place of Presentation
      石川県文教会館(石川県金沢市)
    • Year and Date
      2016-10-26
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Metal-responsive Bifacial Nucleobase Pairing of 5-Hydroxyuracils inside DNA Duplexes2016

    • Author(s)
      Kotaro Nishiyama, Yusuke Takezawa and Mitsuhiko Shionoya
    • Organizer
      The 43rd International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      熊本大学(熊本県熊本市)
    • Year and Date
      2016-09-27
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Enzymatic synthesis of ligand-bearing artificial DNAs toward metal-mediated DNA assembly2016

    • Author(s)
      Yusuke Takezawa, Teruki Kobayashi and Mitsuhiko Shionoya
    • Organizer
      第66回錯体化学会討論会
    • Place of Presentation
      福岡大学(福岡県福岡市)
    • Year and Date
      2016-09-10
    • Related Report
      2016 Research-status Report
  • [Presentation] 5-ヒドロキシウラシル塩基のpH依存的金属錯体形成を利用したDNA二重鎖の安定性制御2016

    • Author(s)
      西山 康太郎・竹澤 悠典・塩谷 光彦
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県立音楽堂(石川県金沢市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] 鋳型非依存DNA ポリメラーゼによる金属配位子型人工DNA の合成:マグネシウムイオンの影響2016

    • Author(s)
      小林 輝樹・竹澤 悠典・塩谷 光彦
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県立音楽堂(石川県金沢市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] 天然鎖を鋳型としたプライマー伸長による金属配位子型人工DNAの酵素合成2016

    • Author(s)
      中間 貴寛・竹澤 悠典・塩谷 光彦
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県立音楽堂(石川県金沢市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] Enzymatic Synthesis of Artificial Metallo-DNAs Using a Template-independent DNA Polymerase2016

    • Author(s)
      竹澤 悠典・小林 輝樹・坂本 晶・塩谷 光彦
    • Organizer
      第16回 東京大学 生命科学シンポジウム
    • Place of Presentation
      東京大学(東京都目黒区)
    • Year and Date
      2016-04-23
    • Related Report
      2016 Research-status Report
  • [Book] Comprehensive Supramolecular Chemistry II2017

    • Author(s)
      Yusuke Takezawa, Jens Mueller and Mitsuhiko Shionoya
    • Publisher
      Elsevier
    • Related Report
      2016 Research-status Report
  • [Remarks] 東京大学大学院理学系研究科化学専攻 生物無機化学研究室ウェブサイト

    • URL

      http://www.chem.s.u-tokyo.ac.jp/~bioinorg/

    • Related Report
      2016 Research-status Report

URL: 

Published: 2016-04-21   Modified: 2020-03-30  

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