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Design, synthesis and analytical application of peptide-based RNA-binding ligands with high affinity and selectivity

Research Project

Project/Area Number 16H04159
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Analytical chemistry
Research InstitutionTohoku University

Principal Investigator

NISHIZAWA Seiichi  東北大学, 理学研究科, 教授 (40281969)

Co-Investigator(Kenkyū-buntansha) 佐藤 雄介  東北大学, 理学研究科, 助教 (90583039)
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000)
Fiscal Year 2018: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2017: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2016: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000)
KeywordsノンコーディングRNA / siRNA / ペプチド核酸 / 三重鎖核酸 / リガンド / 蛍光プローブ / イメージング / 検出
Outline of Final Research Achievements

We recently proposed a new strategy for analyzing the siRNA delivery process based on affinity labeling with a peptide nucleic acid (PNA)-based fluorescent probe capable of selectively binding to the overhanging structures of siRNAs (Chem. Commun. 2015). Here, we have successfully prepared a new probe with improved binding affinity and imaging ability by conjugation with a cationic oligopeptide (ChemBioChem 2019). In addition, we have developed new fluorogenic sensing probes for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA (J. Am. Chem. Soc. 2016; Chem. Eur. J. 2017; Org . Biomol. Chem. 2017; Org . Biomol. Chem. 2018; RSC Advances 2018). Furthermore, we have developed useful fluorescent indicators for the assessment of the binding capabilities of various test compounds for the internal loop structure of the bacterial ribosomal decoding region of the aminoacyl-tRNA site (A-site) (Chem. Eur. J. 2018; Chem. Commun. 2019).

Academic Significance and Societal Importance of the Research Achievements

本研究は、ポストゲノム時代における生命科学の飛躍的な発展を支える新しい解析技術(RNA結合リガンド)の創製を目指したものである。特に、「二重鎖RNAを塩基配列選択的に検出できる三重鎖形成蛍光プローブ」は、研究代表者らが世界に先駆けて提案したもので、RNAの機能研究(検出・イメージング)における強力な分析ツールになると期待できる。なお、本研究成果の一部は、英国王立化学会速報誌(Chem. Commun.)の表紙および化学学術誌(Wiley-VCH/Chem. Eur. J.)の裏表紙・hot paperとしてハイライトされた。

Report

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

    (58 results)

All 2019 2018 2017 2016 Other

All Journal Article (13 results) (of which Peer Reviewed: 10 results,  Open Access: 7 results,  Acknowledgement Compliant: 3 results) Presentation (43 results) (of which Int'l Joint Research: 7 results,  Invited: 13 results) Remarks (2 results)

  • [Journal Article] Enhanced binding affinity of siRNA overhang-binding fluorescent probes by conjugation with cationic oligopeptides for the improved analysis of siRNA delivery process2019

    • Author(s)
      Y. Sato, M. Kaneko, T. Sato, S. Nakata, Y. Takahashi, and S. Nishizawa
    • Journal Title

      ChemBioChem.

      Volume: 20 Issue: 3 Pages: 408-414

    • DOI

      10.1002/cbic.201800560

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Trimethine cyanine dyes as deep-red fluorescent indicators with high selectivity to the internal loop of the bacterial A-site RNA2019

    • Author(s)
      Y. Sato, S. Yajima, A. Taguchi, K. Baba, M. Nakagomi, Y. Aiba, and S. Nishizawa
    • Journal Title

      Chemical Communications

      Volume: 55 Issue: 22 Pages: 3183-3186

    • DOI

      10.1039/c9cc00414a

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Design and Synthesis of RNA-binding Fluorescent Probes for Analysis of Small RNAs2018

    • Author(s)
      佐藤雄介, 佐藤貴哉, 西澤精一
    • Journal Title

      BUNSEKI KAGAKU

      Volume: 67 Issue: 9 Pages: 531-540

    • DOI

      10.2116/bunsekikagaku.67.531

    • NAID

      130007495780

    • ISSN
      0525-1931
    • Year and Date
      2018-09-05
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Design of a fluorogenic PNA probe capable of simultaneous recognition of 3’-overhang and double-stranded sequences of small interfering RNAs2018

    • Author(s)
      T. Tanabe, T. Sato, Y. Sato, and S. Nishizawa
    • Journal Title

      RSC Advances

      Volume: 8 Issue: 73 Pages: 42095-42099

    • DOI

      10.1039/c8ra08759h

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fluorescent trimethylated naphthyridine derivative with an aminoalkyl side chain as the tightest non-aminoglycoside ligand for the bacterial A-site RNA2018

    • Author(s)
      Y. Sato, M. Rokugawa, S. Ito, S. Yajima, H. Sugawara, N. Teramae, and S. Nishizawa
    • Journal Title

      Chem. Eur. J.

      Volume: 24 Issue: 52 Pages: 13862-13870

    • DOI

      10.1002/chem.201802320

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Kinetic and thermodynamic analysis of triplex formation between peptide nucleic acid and double-stranded RNA2018

    • Author(s)
      Sato Takaya、Sakamoto Naonari、Nishizawa Seiichi
    • Journal Title

      Org. Biomol. Chem.

      Volume: 16 Issue: 7 Pages: 1178-1187

    • DOI

      10.1039/c7ob02912h

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Red-emissive triplex-forming PNA probes carrying cyanine base surrogates for fluorescence sensing of double-stranded RNA2017

    • Author(s)
      Chiba Toshiki、Sato Takaya、Sato Yusuke、Nishizawa Seiichi
    • Journal Title

      Org . Biomol. Chem.

      Volume: 15 Issue: 37 Pages: 7765-7769

    • DOI

      10.1039/c7ob02077e

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RNA解析・イメージングのための蛍光性核酸プローブの分子設計2017

    • Author(s)
      佐藤貴哉, 佐藤雄介, 西澤精一
    • Journal Title

      ぶんせき

      Volume: 2017 Pages: 459-463

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-stranded RNA2017

    • Author(s)
      T. Sato, Y. Sato, and S. Nishizawa
    • Journal Title

      Chem. Eur. J.

      Volume: 23 Issue: 17 Pages: 4079-4088

    • DOI

      10.1002/chem.201604676

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] RNA二重鎖を読み解く新技術-三重鎖核酸形成を利用する蛍光プローブ2017

    • Author(s)
      佐藤貴哉, 佐藤雄介, 西澤精一
    • Journal Title

      化学

      Volume: 72(4月号) Pages: 47-52

    • NAID

      40021130141

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Pteridine Derivatives Modified with a Guanidine for Binding and Sensing an Orphan Guanine in RNA duplexes2016

    • Author(s)
      Y. Sato, T. Asami, Y. Toriyabe, T. Sato, N. Teramae, and S. Nishizawa
    • Journal Title

      Chem. Lett.

      Volume: 45 Issue: 8 Pages: 982-984

    • DOI

      10.1246/cl.160425

    • NAID

      130005254494

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Triplex-forming Peptide Nucleic Acid Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA2016

    • Author(s)
      T. Sato, Y. Sato, and S. Nishizawa
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 138 Issue: 30 Pages: 9397-9400

    • DOI

      10.1021/jacs.6b05554

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] siRNA選択性蛍光プローブを用いた細胞内デリバリーイメージング解析2016

    • Author(s)
      佐藤貴哉, 西澤精一
    • Journal Title

      Dojin news

      Volume: 157 Pages: 6-10

    • Related Report
      2016 Annual Research Report
  • [Presentation] RNA高次構造を標的とした蛍光性プローブの開発2019

    • Author(s)
      佐藤 雄介
    • Organizer
      日本化学会 第99春季年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 細胞内RNA解析を指向したRNA選択性赤色蛍光モノメチンシアニン色素の開発2018

    • Author(s)
      芳野幸奈, 佐藤雄介, 西澤精一
    • Organizer
      第78回分析化学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] N末端にpyreneを導入した蛍光性ペプチド核酸プローブによるsiRNA高選択的検出2018

    • Author(s)
      髙橋勇樹, 田邉貴昭, 佐藤貴哉, 佐藤雄介, 西澤精一
    • Organizer
      第78回分析化学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] RNA選択性を持つlight-up型赤色蛍光プローブの開発2018

    • Author(s)
      芳野幸奈, 佐藤雄介, 西澤精一
    • Organizer
      平成30年度東日本分析化学若手交流会
    • Related Report
      2018 Annual Research Report
  • [Presentation] RNA二重鎖構造を含む高次構造を標的とする蛍光性ペプチド核酸プローブの開発2018

    • Author(s)
      田邉貴昭, 髙橋勇樹, 佐藤貴哉, 佐藤雄介, 西澤精一
    • Organizer
      平成30年度東日本分析化学若手交流会
    • Related Report
      2018 Annual Research Report
  • [Presentation] RNA高次構造を標的とした蛍光性ペプチド核酸プローブの合成と機能評価2018

    • Author(s)
      田邉貴昭, 髙橋勇樹, 佐藤貴哉, 佐藤雄介, 西澤精一
    • Organizer
      日本分析化学会第67年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] RNA選択性を有する赤色蛍光性モノメチンシアニン色素の合成と機能評価2018

    • Author(s)
      芳野幸奈, 佐藤雄介, 西澤精一
    • Organizer
      日本分析化学会第67年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Design and synthesis of fluorescent molecular probes for RNA binding and sensing2018

    • Author(s)
      西澤精一
    • Organizer
      平成30年度化学系学協会東北大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Design of peptid nucleic acid-based fluorescent probes for analysis of siRNA delivery probes2018

    • Author(s)
      Yusuke Sato
    • Organizer
      14th Annual Meeting of the Oligonucletide Therapeutics Society
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] バイオ分析化学~蛍光プローブによる遺伝子検出と細胞内RNAイメージング~2018

    • Author(s)
      西澤精一
    • Organizer
      環境科学コロキウム
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Design and Synthesis of Fluorogenic Molecular Probes for RNA sensing2018

    • Author(s)
      Seiichi Nishizawa
    • Organizer
      Seminar on Analytical Chemistry
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] RNA結合リガンドの設計と合成:塩基欠損部位と三重鎖核酸形成の活用2018

    • Author(s)
      西澤精一
    • Organizer
      シンポジウム「核酸の科学」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Design of Fluorescent Probes Capable of Binding to the Specific Sites in Nucleic Acids and Their Analytical Application2018

    • Author(s)
      Yusuke Sato
    • Organizer
      日本化学会 第98春季年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] RNA選択性を有する赤色蛍光モノメチンシアニン色素の開発2018

    • Author(s)
      芳野幸奈, 佐藤雄介, 西澤精一
    • Organizer
      日本化学会 第98春季年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] RNA二重鎖を標的とする三重鎖形成PNAプローブの開発:シアニン色素擬塩基によるピリミジン含有配列の認識2018

    • Author(s)
      松下史佳, 田邉貴昭, 佐藤貴哉, 佐藤雄介, 西澤精一
    • Organizer
      日本化学会 第98春季年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] N末端にpyreneを導入したsiRNA結合性ペプチド核酸プローブの合成と機能評価2018

    • Author(s)
      高橋勇樹, 田邉貴昭, 佐藤貴哉, 佐藤雄介, 西澤精一
    • Organizer
      日本化学会 第98春季年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 核酸結合プローブの精密設計とRNA検出・細胞内イメージング2017

    • Author(s)
      西澤精一
    • Organizer
      日本化学会 第97春季年会
    • Place of Presentation
      慶應義塾大学 日吉キャンパス
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] RNA構造を識別する蛍光性ペプチド核酸プローブの開発2017

    • Author(s)
      佐藤雄介
    • Organizer
      第77回分析化学討論会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 蛍光性核酸結合リガンドによるRNA検出と細胞内イメージング2017

    • Author(s)
      西澤精一
    • Organizer
      第34回無機・分析化学コロキウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] RNA・エキソソームを認識する分析プローブの開発2017

    • Author(s)
      佐藤雄介
    • Organizer
      平成29年度日本分析化学会東北支部若手交流会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 三重鎖形成反応とオーバーハング構造認識に基づくsiRNA選択性蛍光プローブの開発2017

    • Author(s)
      田邉貴昭、佐藤貴哉、佐藤雄介、西澤精一
    • Organizer
      平成29年度日本分析化学会東北支部若手交流会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Design of siRNA overhanging structure-selective fluorescent probes2017

    • Author(s)
      Yusuke Sato, Seiichi Nishizawa
    • Organizer
      RSC Tokyo International Conference 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 蛍光性ペプチド核酸プローブによるRNA検出・イメージング2017

    • Author(s)
      西澤精一
    • Organizer
      日本分析化学会第66年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] カチオン性オリゴペプチド導入による蛍光性ペプチド核酸プローブのsiRNA結合能改良2017

    • Author(s)
      中田彩希、金子充雅、佐藤貴哉、佐藤雄介、西澤精一
    • Organizer
      日本分析化学会第66年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 三重鎖形成とオーバーハング構造認識を併用したsiRNA結合性プローブの開発2017

    • Author(s)
      田邉貴昭、佐藤貴哉、佐藤雄介、西澤精一
    • Organizer
      日本分析化学会第66年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] RNA 構造を識別する分子プローブの設計と応用2017

    • Author(s)
      佐藤雄介
    • Organizer
      第21回 次世代医工学研究会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Design and synthesis of fluorescent molecular probes for RNA sensing2017

    • Author(s)
      Seiichi Nishizawa
    • Organizer
      The 17th Beijing Conference and Exhibition on Instrumental Analysis (BCEIA 2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Design of fluorescent peptide nucleic acid probes targeting double stranded-RNAs2017

    • Author(s)
      Yusuke Sato, Takaya Sato, Seiichi Nishizawa
    • Organizer
      ISNAC 2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] Synthetic fluorescent probes capable of selective binding to 3’-overhanging structures in double stranded RNAs for RNA interference study2016

    • Author(s)
      Yusuke Sato
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2016-11-26
    • Related Report
      2016 Annual Research Report
  • [Presentation] DESIGN OF PEPTIDE NUCLEIC ACID-BASED FLUORESCENT PROBES FOR SIRNA DELIVERY ANALYSIS2016

    • Author(s)
      Yusuke Sato, Takaya Sato, Seiichi Nishizawa
    • Organizer
      XVII International Symposium on Luminescence Spectrometry
    • Place of Presentation
      Taipei, Taiwan
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] FLUORESCENCE SENSING OF DOUBLE-STRANDED RNA BY TRIPLEX-FORMING PEPTIDE NUCLEIC ACID PROBES HAVING THIAZOLE ORANGE AS A BASE SURROGATE2016

    • Author(s)
      Seiichi Nishizawa, Takaya Sato, Yusuke Sato
    • Organizer
      XVII International Symposium on Luminescence Spectrometry
    • Place of Presentation
      Taipei, Taiwan
    • Year and Date
      2016-11-23
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RNA二重鎖を解析する蛍光性核酸プローブ2016

    • Author(s)
      佐藤貴哉,佐藤雄介,岩井健太,久下周佐,寺前紀夫,西澤精一
    • Organizer
      みちのく分析化学シンポジウム
    • Place of Presentation
      東北大学理学研究科 青葉サイエンスホール
    • Year and Date
      2016-10-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] γ位修飾ペプチド核酸とRNA二重鎖との三重鎖形成反応の評価2016

    • Author(s)
      清水和也,佐藤貴哉,佐藤雄介,西澤精一
    • Organizer
      みちのく分析化学シンポジウム
    • Place of Presentation
      東北大学理学研究科 青葉サイエンスホール
    • Year and Date
      2016-10-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] 赤色シアニン色素を用いたRNA二重鎖の配列選択的解析2016

    • Author(s)
      千葉年輝,佐藤貴哉,佐藤雄介,西澤精一
    • Organizer
      みちのく分析化学シンポジウム
    • Place of Presentation
      東北大学理学研究科 青葉サイエンスホール
    • Year and Date
      2016-10-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] チアゾールオレンジを利用するHCV RNA結合リガンドの蛍光スクリーニング2016

    • Author(s)
      山田直樹,伊東良子,佐藤雄介,西澤精一
    • Organizer
      みちのく分析化学シンポジウム
    • Place of Presentation
      東北大学理学研究科 青葉サイエンスホール
    • Year and Date
      2016-10-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] Design and synthesis of RNA-binding fluorescent molecules for analytical applications2016

    • Author(s)
      Seiichi Nishizawa
    • Organizer
      Satellite International Mini Symposium on Middle Molecular Strategy in Sendai
    • Place of Presentation
      IMRAM, Tohoku University
    • Year and Date
      2016-09-20
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 細胞内siRNA解析を目指したペプチド核酸プローブの開発:カチオン性オリゴペプチド導入による機能改良2016

    • Author(s)
      佐藤雄介、佐藤貴哉、金子充雅、西澤精一
    • Organizer
      日本分析化学会第65年会
    • Place of Presentation
      北海道大学工学部
    • Year and Date
      2016-09-16
    • Related Report
      2016 Annual Research Report
  • [Presentation] キラルなペプチド核酸と RNA 二重鎖との三重鎖形成反応の熱力学的解析2016

    • Author(s)
      清水和也、佐藤貴哉、佐藤雄介、西澤精一
    • Organizer
      日本分析化学会第65年会
    • Place of Presentation
      北海道大学工学部
    • Year and Date
      2016-09-15
    • Related Report
      2016 Annual Research Report
  • [Presentation] RNA二重鎖選択性蛍光性プローブの開発と分析化学的応用2016

    • Author(s)
      佐藤貴哉
    • Organizer
      平成28年度東日本分析化学若手交流会
    • Place of Presentation
      日本大学軽井沢研修所
    • Year and Date
      2016-07-02
    • Related Report
      2016 Annual Research Report
  • [Presentation] キラルなペプチド核酸と RNA 二重鎖との三重鎖形成反応の熱力学的解析2016

    • Author(s)
      清水和也、佐藤貴哉、佐藤雄介、西澤精一
    • Organizer
      平成28年度東日本分析化学若手交流会
    • Place of Presentation
      日本大学軽井沢研修所
    • Year and Date
      2016-07-02
    • Related Report
      2016 Annual Research Report
  • [Presentation] RNA構造を識別する蛍光性分子の開発2016

    • Author(s)
      佐藤雄介
    • Organizer
      第33回無機・分析化学コロキウム
    • Place of Presentation
      東北大学川渡共同セミナーセンター
    • Year and Date
      2016-06-04
    • Related Report
      2016 Annual Research Report
  • [Presentation] RNA検出・細胞内イメージングのための蛍光性核酸結合プローブの分子設計2016

    • Author(s)
      西澤精一
    • Organizer
      第76回分析化学討論会
    • Place of Presentation
      岐阜薬科大学・岐阜大学
    • Year and Date
      2016-05-28
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] siRNAデリバリー過程解析を指向した蛍光性プローブの開発2016

    • Author(s)
      佐藤雄介、佐藤貴哉、金子充雅、西澤精一
    • Organizer
      第16回遺伝子デリバリー研究会シンポジウム
    • Place of Presentation
      川崎生命科学・環境研究センター
    • Year and Date
      2016-05-16
    • Related Report
      2016 Annual Research Report
  • [Remarks] 細菌リボソームRNAに対して世界最強の結合力を持つ 非アミノグリコシド系小分子を開発!

    • URL

      http://www.sci.tohoku.ac.jp/news/20180927-9884.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] RNA二重鎖を可視化する新技術を開発!~蛍光性ペプチド核酸プローブ~

    • URL

      http://www.chem.tohoku.ac.jp/research/research_outcome/p001.html

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report

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

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