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Novel method for structural analyses of nucleic acids by using orientation dependent FRET system

Research Project

Project/Area Number 16H05925
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Chemical biology
Research InstitutionNagoya University

Principal Investigator

Kashida Hiromu  名古屋大学, 工学研究科, 准教授 (30452189)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥25,350,000 (Direct Cost: ¥19,500,000、Indirect Cost: ¥5,850,000)
Fiscal Year 2019: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2018: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000)
Fiscal Year 2016: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Keywords核酸 / エネルギー移動 / 構造解析 / DNA / RNA
Outline of Final Research Achievements

In this study, we aimed to develop a versatile method to analyze double helical structures of nucleic acids by using orientation dependence of Forster resonance energy transfer (FRET). First, we developed another FRET pair for analyses of larger complexes of nucleic acids. We also found that energy transfer between identical chromophores can also be used for structural analyses. Damaged DNA like gapped DNA, A-tract and RNA structures were successfully analyzed by using the developed method. Furthermore, we succeeded in analyses of the interaction between DNA and small molecules by using orientation dependence of FRET.

Academic Significance and Societal Importance of the Research Achievements

核酸結合タンパク質は核酸構造のわずかな違いを認識して結合することが知られている。従来、核酸構造の解析にはNMRやX線構造解析が利用されてきた。しかしながら、大量のサンプルが必要であり、またサンプル調製や解析が煩雑であるという問題点があった。本研究で開発した核酸構造解析法は少量のサンプルで解析が可能であり、また解析が簡便であるという利点がある。そのため、今後様々な核酸構造を網羅的に解析することによって、生物学や創薬科学に貢献することが期待できる。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (39 results)

All 2020 2019 2018 2017 2016 Other

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 5 results,  Acknowledgement Compliant: 1 results) Presentation (29 results) (of which Int'l Joint Research: 6 results,  Invited: 4 results) Remarks (1 results)

  • [Journal Article] A triplex-forming linear probe for sequence-specific detection of duplex DNA with high sensitivity and affinity2020

    • Author(s)
      Chen Yanglingzhi、Murayama Keiji、Kashida Hiromu、Kamiya Yukiko、Asanuma Hiroyuki
    • Journal Title

      Chemical Communications

      Volume: 印刷中 Issue: 40 Pages: 5358-5361

    • DOI

      10.1039/d0cc01865a

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient Light‐Harvesting Antennae Resulting from the Dense Organization of Dyes into DNA Junctions though d ‐Threoninol2020

    • Author(s)
      Kashida Hiromu、Azuma Hidenori、Maruyama Ryoko、Araki Yasuyuki、Wada Takehiko、Asanuma Hiroyuki
    • Journal Title

      Angewandte Chemie International Edition

      Volume: - Issue: 28 Pages: 11360-11363

    • DOI

      10.1002/anie.202004221

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Selective binding of nucleosides to gapped DNA duplex revealed by orientation and distance dependence of FRET2019

    • Author(s)
      Kashida Hiromu、Kokubo Yuta、Makino Koki、Asanuma Hiroyuki
    • Journal Title

      Organic & Biomolecular Chemistry

      Volume: 17 Issue: 28 Pages: 6786-6789

    • DOI

      10.1039/c9ob00946a

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photo-regulatable DNA isothermal amplification by template-mediated ligation2019

    • Author(s)
      Cheng Bohao、Kashida Hiromu、Shimada Naohiko、Maruyama Atsushi、Asanuma Hiroyuki
    • Journal Title

      Chemical Communications

      Volume: 55 Issue: 8 Pages: 1080-1083

    • DOI

      10.1039/c8cc09218d

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In-stem molecular beacon targeted to a 5′-region of tRNA inclusive of the D arm that detects mature tRNA with high sensitivity2019

    • Author(s)
      Miyoshi Yuichi、Ohtsuki Takashi、Kashida Hiromu、Asanuma Hiroyuki、Watanabe Kazunori
    • Journal Title

      PLOS ONE

      Volume: 14 Issue: 1 Pages: e0211505-e0211505

    • DOI

      10.1371/journal.pone.0211505

    • NAID

      120006767317

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Bifacial Nucleobases for Hexaplex Formation in Aqueous Solution2018

    • Author(s)
      Kashida Hiromu、Hattori Yuhei、Tazoe Kaho、Inoue Tadashi、Nishikawa Keiji、Ishii Kentaro、Uchiyama Susumu、Yamashita Hayato、Abe Masayuki、Kamiya Yukiko、Asanuma Hiroyuki
    • Journal Title

      Journal of the American Chemical Society

      Volume: 140 Issue: 27 Pages: 8456-8462

    • DOI

      10.1021/jacs.8b02807

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantitative evaluation of energy migration between identical chromophores enabled by breaking symmetry2018

    • Author(s)
      Hiromu Kashida, Hayato Kawai, Ryoko Maruyama, Yuta Kokubo, Yasuyuki Araki, Takehiko Wada, Hiroyuki Asanuma
    • Journal Title

      Communications Chemistry (Nature)

      Volume: 1 Issue: 1 Pages: 91-98

    • DOI

      10.1038/s42004-018-0093-0

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The DNA Duplex as an Aqueous One-Dimensional Soft Crystal Scaffold for Photochemistry2018

    • Author(s)
      Asanuma Hiroyuki、Murayama Keiji、Kamiya Yukiko、Kashida Hiromu
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 91 Issue: 12 Pages: 1739-1748

    • DOI

      10.1246/bcsj.20180278

    • NAID

      130007531017

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes2017

    • Author(s)
      Hiromu Kashida, Ayako Kurihara, Hayato Kawai, Hiroyuki Asanuma
    • Journal Title

      Nucleic Acids Research

      Volume: 印刷中 Issue: 11 Pages: e105-e105

    • DOI

      10.1093/nar/gkx200

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 蛍光色素多数導入多分岐DNAを用いた光捕集アンテナの開発2020

    • Author(s)
      東 秀憲, 樫田 啓, 荒木保幸, 和田健彦, 浅沼浩之
    • Organizer
      日本化学会第100春季年会(開催中止)
    • Related Report
      2019 Annual Research Report
  • [Presentation] 多分岐DNAに多数の蛍光色素を集積した高効率光捕集系の開発2019

    • Author(s)
      東 秀憲, 樫田 啓, 丸山諒子, 浅沼浩之
    • Organizer
      第13回バイオ関連化学シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] DNA junctionに多数の蛍光色素を集積した高効率光捕集系の開発2019

    • Author(s)
      東 秀憲, 樫田 啓, 浅沼浩之
    • Organizer
      第169回東海高分子研究会講演会(夏期合宿)
    • Related Report
      2019 Annual Research Report
  • [Presentation] DNA junctionを利用した高効率光捕集系の開発2019

    • Author(s)
      東 秀憲, 樫田 啓, 浅沼浩之
    • Organizer
      第29回バイオ・高分子シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] 蛍光色素多数導入 DNA を用いた高効率光捕集アンテナの開発2019

    • Author(s)
      東 秀憲, 樫田 啓, 丸山諒子, 浅沼浩之
    • Organizer
      2019年光化学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 単純な構造を持つ核酸の開発及びその応用2019

    • Author(s)
      樫田 啓
    • Organizer
      第5回生体分子科学シンポジウム
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] FRET を用いたギャップ DNA-ヌクレオシド間相互作用の解析2018

    • Author(s)
      小久保祐汰, 樫田 啓, 浅沼浩之
    • Organizer
      第49回 中部化学関係学協会支部連合秋季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] FRET を用いたギャップ DNA-ヌクレオシド挿入反応の解析2018

    • Author(s)
      小久保祐汰, 樫田啓, 浅沼浩之
    • Organizer
      第12回バイオ関連化学シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] FRETを用いたギャップDNA-ヌクレオシド複合体の構造解析2018

    • Author(s)
      小久保祐汰, 樫田啓, 浅沼浩之
    • Organizer
      第165回東海高分子研究会講演会(夏期合宿)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Observation of orientation dependence of FRET by using DNA scaffold2018

    • Author(s)
      Hiromu Kashida
    • Organizer
      International Symposium on Photochemistry (27th PhotoIUPAC)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Orientation Dependent FRET as a Tool to Analyze DNA Structures2018

    • Author(s)
      Hiromu Kashida, Hiroyuki Asanuma
    • Organizer
      INTERNATIONAL CONGRESS ON PURE & APPLIED CHEMISTRY 2018 (ICPAC2018)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] DNAを利用した同種色素間におけるエネルギー移動の検討2017

    • Author(s)
      河合隼人, 丸山諒子, 樫田 啓, 荒木保幸, 和田健彦, 浅沼浩之
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶応義塾大学
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
  • [Presentation] 配向依存型FRETを利用したA-tract含有DNAの構造解析2017

    • Author(s)
      小久保祐汰, 河合隼人, 樫田 啓, 浅沼浩之
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶応義塾大学
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
  • [Presentation] 配向依存FRETを用いた1塩基Gap含有DNA-ヌクレオシド複合体の構造解析2017

    • Author(s)
      小久保祐汰、樫田啓、浅沼浩之
    • Organizer
      第161回東海高分子研究会講演会(夏期合宿)
    • Related Report
      2017 Annual Research Report
  • [Presentation] DNA骨格を利用した同種色素間エネルギー移動の詳細な解析2017

    • Author(s)
      樫田啓、河合隼人、荒木保幸、和田健彦、浅沼浩之
    • Organizer
      2017年光化学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 配向依存型FRETを利用したDNA-ヌクレオシド間の相互作用解析2017

    • Author(s)
      小久保祐汰、樫田啓、浅沼浩之
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] DNAを光反応場として利用した同種色素間エネ ルギー移動の解析2017

    • Author(s)
      樫田啓、河合隼人、荒木保幸、和田健彦、浅沼浩之
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] Analysis of energy transfer between dyes by using DNA scaffold2017

    • Author(s)
      Hiromu Kashida
    • Organizer
      第53回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Molecular design of pseudo base pairs for functionalization of DNA2017

    • Author(s)
      Hiromu Kashida
    • Organizer
      Annual Spring Meeting of Polymer Society of Korea
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Accumulation of dyes into DNA for efficient light-harvesting2016

    • Author(s)
      Hiromu Kashida, Ryoko Maruyama, Hayato Kawai, Yasuyuki Araki, Takehiko Wada and Hiroyuki Asanuma
    • Organizer
      The 11th SPSJ International Polymer Conference (IPC 2016)
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2016-12-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structural analysis of modified DNA by using FRET system2016

    • Author(s)
      Hayato Kawai, Tetsuya Doi, Hiromu Kashida and Hiroyuki Asanuma
    • Organizer
      The 11th SPSJ International Polymer Conference (IPC 2016)
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2016-12-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structural analyses of nicked and gapped DNA duplexes by using orientation dependence of FRET2016

    • Author(s)
      Hiromu Kashida, Ayako Kurihara, Hiroyuki Asanuma
    • Organizer
      The 43rd International Symposium on Nucleic Acid Chemistry (ISNAC2016)
    • Place of Presentation
      熊本大学
    • Year and Date
      2016-09-27
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 配向依存型FRETを用いたスチルベン導入型DNAの構造解析2016

    • Author(s)
      河合隼人、土居哲也、樫田 啓、浅沼浩之
    • Organizer
      第65回高分子討論会
    • Place of Presentation
      神奈川大学
    • Year and Date
      2016-09-14
    • Related Report
      2016 Annual Research Report
  • [Presentation] DNA骨格を利用したエネルギーマイグレーションの検討2016

    • Author(s)
      樫田 啓、丸山諒子、河合隼人、荒木保幸、和田健彦、浅沼浩之
    • Organizer
      2016年光化学討論会
    • Place of Presentation
      東京大学
    • Year and Date
      2016-09-06
    • Related Report
      2016 Annual Research Report
  • [Presentation] 配向異存型FRETを利用したDNA二重鎖中におけるスチルベン会合体の構造解析2016

    • Author(s)
      河合隼人、土居哲也、樫田 啓、浅沼浩之
    • Organizer
      2016年光化学討論会
    • Place of Presentation
      東京大学
    • Year and Date
      2016-09-06
    • Related Report
      2016 Annual Research Report
  • [Presentation] FRETを利用したDNA二重鎖中における色素会合体の構造解析2016

    • Author(s)
      河合隼人、土居哲也、樫田 啓、浅沼浩之
    • Organizer
      第157回東海高分子研究会講演会(夏期合宿)
    • Place of Presentation
      長良川観光ホテル石金
    • Year and Date
      2016-09-02
    • Related Report
      2016 Annual Research Report
  • [Presentation] FRETの距離・配向依存性を利用した核酸構造解析法の開発2016

    • Author(s)
      樫田 啓、栗原綾子、浅沼浩之
    • Organizer
      第26回バイオ・高分子シンポジウム
    • Place of Presentation
      東京工業大学
    • Year and Date
      2016-07-28
    • Related Report
      2016 Annual Research Report
  • [Presentation] FRETの配向依存性を利用したスチルベン導入型DNAの構造解析2016

    • Author(s)
      河合隼人、土居哲也、樫田 啓、浅沼浩之
    • Organizer
      第26回バイオ・高分子シンポジウム
    • Place of Presentation
      東京工業大学
    • Year and Date
      2016-07-28
    • Related Report
      2016 Annual Research Report
  • [Presentation] 高効率光捕集系の構築に向けた蛍光色素集積化DNAの調製2016

    • Author(s)
      樫田 啓, 丸山 諒子, 栗原 綾子, 浅沼 浩之
    • Organizer
      第65回高分子学会年次大会
    • Place of Presentation
      神戸国際会議場
    • Year and Date
      2016-05-25
    • Related Report
      2016 Annual Research Report
  • [Remarks]

    • URL

      http://www.nubio.nagoya-u.ac.jp/seigyo1/index.html

    • Related Report
      2017 Annual Research Report

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Published: 2016-04-21   Modified: 2021-02-19  

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