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Creation of functional peptides recognizing a low-molecular compound by evolutionary molecular engineering

Research Project

Project/Area Number 23510253
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Living organism molecular science
Research InstitutionSaitama University

Principal Investigator

NEMOTO Naoto  埼玉大学, 理工学研究科, 准教授 (60509727)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2011: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords進化分子工学 / ペプチド / アプタマー / アミノ基認識 / 分子間相互作用 / 試験管内淘汰 / cDNA display / mRNA display / ペプチドアプタマー / 分子認識 / 架橋構造 / ジスルフィド結合 / 進化工学 / In vitro selection / cDNA display / Peptide aptamer / mRNA/cDNA display / 抗体低分子化 / 低分子認識分子 / 分子間相互作用解析 / 表面プラズモン共鳴法 / プルダウン法
Research Abstract

We have succeeded to improve the preparation of cDNA display molecule easily and efficiently with a one-pot preparational manner. Furthermore, we demonstrated the biotin binding capacity of streptavidin magnetic beads decreased by mRNA-binding ribosomes, resulted in the low yield of cDNA display molecules. Secondly, we developed an easy and rapid molecular-protein interaction analysis using a cell-free translation and a novel puromycin-linker by a pull-down manner. Finally, by using these techniques, in vitro selection using 30 amino acids random library containing cysteine against amino group on the solid-phase was performed. As a result, an amino group-binding peptide aptamer containing two disulfide bonds which have a unique structure has explored. This shows that a peptide has capability to recognize small molecules with a low-molecular weight. In the future, peptides will be more and more applicable for nanotechnology as a recogniton material of nano sturcture.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (49 results)

All 2014 2013 2012 2011 Other

All Journal Article (17 results) (of which Peer Reviewed: 17 results) Presentation (21 results) (of which Invited: 1 results) Book (7 results) Remarks (2 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] Amino group binding peptide aptamers with double disulphide-bridged loops selected by in vitro selection using cDNA display2014

    • Author(s)
      Y. Mochizuki, K. Nishigaki, N. Nemoto
    • Journal Title

      Chem Commun

      Volume: 50 Pages: 5608-5610

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Amino group binding peptide aptamers with double disulphide-bridged loops selected by in vitro selection using cDNA display2014

    • Author(s)
      Yuki Mochizuki, Koichi Nishigaki, and Naoto Nemoto
    • Journal Title

      Chemical Communications

      Volume: 50 Issue: 42 Pages: 5608-5610

    • DOI

      10.1039/c4cc00799a

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] cDNA display による分子デザイン- mRNA display(in vitro virus)からcDNA display へ-2013

    • Author(s)
      根本直人、望月佑樹、上野真吾
    • Journal Title

      生物物理

      Volume: 53 Pages: 250-253

    • NAID

      10031191846

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Increasing the library size in cDNA display by optimizing purification procedures2013

    • Author(s)
      Y. Mochizuki, S. Kumachi, K. Nishigaki, N. Nemoto
    • Journal Title

      Biol Proced Online

      Volume: 15 Pages: 7-7

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A pull-down method with a biotinylated bait protein prepared by cell-free translation using a puromycin-linker2013

    • Author(s)
      Y. Mochizuki, F. Kohno, K. Nishigaki, N. Nemoto
    • Journal Title

      Anal. Biochem

      Volume: 434 Pages: 93-95

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Increasing the library size in cDNA display by optimizing purification procedures2013

    • Author(s)
      Yuki Mochizuki, Shigefumi Kumachi, Koichi Nishigaki and Naoto Nemoto
    • Journal Title

      Biological Procedures Online

      Volume: 15 Issue: 1 Pages: 7-7

    • DOI

      10.1186/1480-9222-15-7

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] cDNA displayによる分子デザイン -mRNA display(in vitro virus)からcDNA displayへ-2013

    • Author(s)
      根本直人、望月佑樹、上野真吾
    • Journal Title

      生物物理

      Volume: 53 Pages: 250-253

    • NAID

      10031191846

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A pull-down method with a biotinylated bait protein prepared by cell-free translation using a puromycin-linker2013

    • Author(s)
      Yuki Mochizuki, Fumiaki Kohno, Koichi Nishigaki, Naoto Nemoto
    • Journal Title

      Analytical Biochemistry

      Volume: 434 Issue: 1 Pages: 93-95

    • DOI

      10.1016/j.ab.2012.10.041

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Antagonistic effect of disulfide-rich peptide aptamers selected by cDNA display on interleukin-6-dependent cell proliferation2012

    • Author(s)
      N. Nemoto, C. Tsutsui, J. Yamaguchi, S. Ueno, M. Machida, T. Kobayashi, T. Sakai
    • Journal Title

      Biochem Biophys Res Commun

      Volume: 421 Pages: 129-133

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] In vitro Selection of Peptide Aptamers against Acetylcholine-binding Protein (AChBP) from Disulfide-rich Peptide Library by cDNA Display2012

    • Author(s)
      N. Nemoto, S. Kimura, S. Kumachi, W. Cai, M. Suzuki, K. Nishigaki, and T. Kubo
    • Journal Title

      Peptide Science 2011: K. Sakaguchi (Ed.)

      Pages: 89-90

    • NAID

      10030204056

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Improvement of a puromycin-linker to extend the selection target varieties in cDNA display method.2012

    • Author(s)
      Ueno S, Kimura S, Ichiki T, Nemoto N.
    • Journal Title

      Journal of Biotechnology

      Volume: 162 Issue: 2-3 Pages: 299-302

    • DOI

      10.1016/j.jbiotec.2012.09.003

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] cDNA Display: Rapid Stabilization of mRNA Display2012

    • Author(s)
      Shingo Ueno and Naoto Nemoto
    • Journal Title

      Methods in Molecular Biology

      Volume: 805 Pages: 113-135

    • DOI

      10.1007/978-1-61779-379-0_8

    • ISBN
      9781617793783, 9781617793790
    • Related Report
      2012 Research-status Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Evolution of Disulfide-Rich Peptide Aptamers Using cDNA Display2012

    • Author(s)
      Yuki Mochizuki and Naoto Nemoto
    • Journal Title

      Methods in Molecular Biology

      Volume: 805 Pages: 237-250

    • DOI

      10.1007/978-1-61779-379-0_13

    • ISBN
      9781617793783, 9781617793790
    • Related Report
      2012 Research-status Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] A function of the primitive protein consisting of four kinds of amino acids2012

    • Author(s)
      Shigefumi Kumachi, Miho Suzuki, Koichi Nishigaki, Yuzuru Husimi, Naoto Nemoto
    • Journal Title

      Viva Origino

      Volume: 40 (Supplement) Pages: 47-47

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] An approach towards the origin of primitive translation system from the viewpoint of genotype-phenotype linking strategy2012

    • Author(s)
      Naoto Nemoto, Yuzuru Husimi
    • Journal Title

      Viva Origino

      Volume: 40 (Supplement) Pages: 48-48

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] One-pot preparation of mRNA/cDNA display by a novel and versatile puromycin-linker DNA2011

    • Author(s)
      Y. Mochizuki , M. Biyani , S. T. -Ueno , M. Suzuki , K. Nishigaki , Y. Husimi , and N. Nemoto
    • Journal Title

      ACS Comb. Sci

      Volume: 13 Pages: 478-485

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] One-pot preparation of mRNA/cDNA display by a novel and versatile puromycin-linker DNA2011

    • Author(s)
      Yuki Mochizuki , Manish Biyani , Sachika Tsuji-Ueno , Miho Suzuki , Koichi Nishigaki , Yuzuru Husimi and Naoto Nemoto
    • Journal Title

      ACS Comb. Sci.

      Volume: 13 Issue: 5 Pages: 478-485

    • DOI

      10.1021/co2000295

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] ペプチドで広がる医療・診断技術 - ペプチドアプタマーを中心にして -2013

    • Author(s)
      根本直人
    • Organizer
      第4回 「医工連携によるイノベーション創出研究会」
    • Place of Presentation
      さいたま市
    • Year and Date
      2013-12-11
    • Related Report
      2013 Final Research Report
  • [Presentation] cDNA display 法を用いた TNFα に対するシステインリッチペプチドライブラリの試験管内淘汰実験2013

    • Author(s)
      澤田 貴宏,望月 佑樹、鈴木 美穂,西垣功一、根本 直人
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸
    • Year and Date
      2013-12-05
    • Related Report
      2013 Final Research Report
  • [Presentation] 標的分子の多様性を拡張するペプチドアプタマー取得ための cDNA display 法2013

    • Author(s)
      根本直人
    • Organizer
      Biotech 2013
    • Place of Presentation
      東京(東京ビックサイト)
    • Year and Date
      2013-05-09
    • Related Report
      2013 Final Research Report
  • [Presentation] Easy-to-use and Rapid Molecular Interaction Analysis by Combination of Pull-down method with mRNA Display2012

    • Author(s)
      F. Kono, Y. Mochizuki, M. Suzuki, K. Nishigaki, N. Nemoto
    • Organizer
      The 35th Annual Meeting of the Molecular Biology Society of Japan
    • Place of Presentation
      Fukuoka
    • Year and Date
      2012-12-12
    • Related Report
      2013 Final Research Report
  • [Presentation] Optimization of In Vitro Protein Selection using mRNA/cDNA Display Method to Search Functional Peptides and Proteins Rapidly2012

    • Author(s)
      Y. Mochizuki, N. Nemoto
    • Organizer
      Protein & Peptide Conference 2012
    • Place of Presentation
      Beijing, China
    • Year and Date
      2012-03-25
    • Related Report
      2013 Final Research Report
  • [Presentation] Molecular Interactions Analysis by Fluorescence Correlation Spectroscopy(FCS) Method and Rapid Fluorescence Labeling of Proteins with a cell-free Translation System2012

    • Author(s)
      Shigefumi Kumachi, Miho Suzuki, Koichi Nishigaki, Naoto Nemoto
    • Organizer
      The 35th Annual Meeting of the Molecular Biology Society of Japan, (Fukuoka, 2012)
    • Place of Presentation
      福岡 (福岡国際会議場)
    • Related Report
      2012 Research-status Report
  • [Presentation] Optimization of In Vitro Protein Selection using mRNA/cDNA Display Method to Search Functional Peptides and Proteins Rapidly2012

    • Author(s)
      Yuki Mochizuki & Naoto Nemoto
    • Organizer
      Protein & Peptide Conference2012(招待講演)
    • Place of Presentation
      Beijing International Convention Center, Beijing, China
    • Related Report
      2011 Research-status Report
  • [Presentation] 4種類のアミノ酸(GADV)からなる原始タンパク質の機能2012

    • Author(s)
      熊地 重文 、鈴木 美穂 、西垣 功一 、伏見 譲 、根本 直人
    • Organizer
      生命の起源および進化学会第37回学術講演会
    • Place of Presentation
      大阪薬科大学 (高槻)
    • Related Report
      2011 Research-status Report
  • [Presentation] In vitro evolution of peptide aptamers against survivin from a novel three-finger scaffold library by cDNA display2011

    • Author(s)
      Y. Yotsumoto,Y. Mochizuki,M. Suzuki,K. Nishigaki,N. Nemoto
    • Organizer
      第34回日本分子生物学会年会(MBSJ2011)
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-13
    • Related Report
      2013 Final Research Report
  • [Presentation] cDNA display 法によるジスルフィド結合を複数含むペプチドライブラリからのアセチルコリン結合タンパク質結合ペプチドアプタマーの試験管内淘汰2011

    • Author(s)
      根本直人、木村真之介、熊地重文、Cai Weiyan、鈴木美穂、西垣功一、久保 泰
    • Organizer
      第48回ペプチド討論会
    • Place of Presentation
      札幌
    • Year and Date
      2011-09-29
    • Related Report
      2013 Final Research Report
  • [Presentation] タンパク/ペプチドの簡易で迅速な精製・ビオチン化法2011

    • Author(s)
      根本直人
    • Organizer
      イノベーション・ジャパン2011「新技術説明会」
    • Place of Presentation
      東京
    • Year and Date
      2011-09-21
    • Related Report
      2013 Final Research Report
  • [Presentation]2011

    • Author(s)
      T. Fukushima, W. Cai, M. Suzuki, K. Nishigaki, T. Kubo, N. Nemoto
    • Organizer
      第49回日本物理学会年会
    • Place of Presentation
      姫路
    • Year and Date
      2011-09-17
    • Related Report
      2013 Final Research Report
  • [Presentation] cDNA display 法による新機能分子の創出2011

    • Author(s)
      根本直人
    • Organizer
      理研シンポジウム 第6回「バイオものづくり」シンポジウム
    • Place of Presentation
      和光
    • Year and Date
      2011-05-10
    • Related Report
      2013 Final Research Report
  • [Presentation] cDNA display法による新機能分子の創出2011

    • Author(s)
      根本直人
    • Organizer
      理研シンポジウム 第6回 「バイオものづくり」シンポジウム」(招待講演)
    • Place of Presentation
      理化学研究所 (埼玉県・和光)
    • Related Report
      2011 Research-status Report
  • [Presentation] 抗体に代るペプチドを用いた分子認識材料(ペプチドアプタマー)の迅速な創製2011

    • Author(s)
      根本直人
    • Organizer
      H23年度首都圏北部4大学新技術説明会(招待講演)
    • Place of Presentation
      JST/サイエンスプラザ (東京)
    • Related Report
      2011 Research-status Report
  • [Presentation] 抗体に代るペプチドを用いた分子認識材料(ペプチドアプタマー)の迅速な創製2011

    • Author(s)
      根本直人
    • Organizer
      埼玉大学地域オープンイノベーションセンター産学官協議会第12回定期総会(招待講演)
    • Place of Presentation
      大宮ソニックシティ (大宮)
    • Related Report
      2011 Research-status Report
  • [Presentation] タンパク/ペプチドの簡易で迅速な精製・ビオチン化法2011

    • Author(s)
      根本直人
    • Organizer
      イノベーション・ジャパン2011「新技術説明会」(招待講演)
    • Place of Presentation
      東京国際フォーラム (東京)
    • Related Report
      2011 Research-status Report
  • [Presentation] cDNA display法によるジスルフィド結合を複数含むペプチドライブラリからのアセチルコリン結合タンパク質結合ペプチドアプタマーの試験管内淘汰2011

    • Author(s)
      根本直人、木村真之介、熊地重文、Cai Wei yan、鈴木美穂、西垣功一、久保 泰
    • Organizer
      第48回ペプチド討論会
    • Place of Presentation
      札幌コンベンションセンター (札幌)
    • Related Report
      2011 Research-status Report
  • [Presentation] In vitro evolution of peptide aptamers against survivin from a novel three-finger scaffold library by cDNA display2011

    • Author(s)
      Yuya Yotsumoto,Yuki Mochizuki,Miho Suzuki,Koichi Nishigaki,Naoto Nemoto
    • Organizer
      第34回日本分子生物学会年会(MBSJ2011)
    • Place of Presentation
      パシフィコ横浜 (横浜)
    • Related Report
      2011 Research-status Report
  • [Presentation] Generation of functional peptides consisting of four kinds of amino acids by in vitro selection-An approach to the origin of translation2011

    • Author(s)
      Shigefumi Kumachi, Miho Suzuki, Koich Nishigaki, Yuzuru Husimi, Naoto Nemoto
    • Organizer
      第49回日本物理学会年会
    • Place of Presentation
      兵庫県立大学 (姫路)
    • Related Report
      2011 Research-status Report
  • [Presentation] ペプチドで広がる医療・診断技術 ー ペプチドアプタマーを中心にして -

    • Author(s)
      根本直人
    • Organizer
      第4回 「医工連携によるイノベーション創出研究会」
    • Place of Presentation
      大宮ビジネスセンター
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] 遺伝子型-表現型対応付け技術,『進化分子工学-高速分子進化によるタンパク質・核酸の開発-』 第2編 第3章2013

    • Author(s)
      根本直人
    • Publisher
      (株)エヌ・ティー・エス
    • Related Report
      2013 Final Research Report
  • [Book] 『進化分子工学-高速分子進化によるタンパク質・核酸の開発-』2013

    • Author(s)
      根本直人
    • Total Pages
      20
    • Publisher
      (株)エヌ・ティー・エス
    • Related Report
      2013 Annual Research Report
  • [Book] Evolutionary Molecular Engineering to Efficiently Direct in vitro Protein Synthesis, CELL-FREE PROTEIN SYNTHESIS (Edited by Manish Biyani)2012

    • Author(s)
      M. Biyani, M. Biyani, N. Nemoto, Y. Husimi
    • Publisher
      InTech
    • Related Report
      2013 Final Research Report
  • [Book] Evolution of Disulfide-Rich Peptide Aptamers Using cDNA Display, Methods in Mol. Biol2012

    • Author(s)
      Y. Mochizuki, N. Nemoto
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] cDNA Display : Rapid Stabilization of mRNA Display, Methods in Mol. Biol2012

    • Author(s)
      S. Ueno, N. Nemoto
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] CELL-FREE PROTEIN SYNTHESIS (Edited by Manish Biyani)2012

    • Author(s)
      Manish Biyani, Madhu Biyani, Naoto Nemoto and Yuzuru Husimi
    • Total Pages
      135
    • Publisher
      InTech
    • Related Report
      2012 Research-status Report
  • [Book] Peptide Science 2011: K. Sakaguchi (Ed.)2012

    • Author(s)
      Naoto Nemoto, Shinnosuke Kimura, Shigefumi Kumachi, Weiyan Cai, Miho Suzuki, Koichi Nishigaki, and Tai Kubo
    • Total Pages
      431
    • Publisher
      In vitro Selection of Peptide Aptamers against Acetylcholine-binding Protein (AChBP) from Disulfide-rich Peptide Library by cDNA Display
    • Related Report
      2011 Research-status Report
  • [Remarks] ホームページ等

    • URL

      http://park.saitama-u.ac.jp/~nemoto/

    • Related Report
      2013 Final Research Report
  • [Remarks] 埼玉大学工学部機能材料工学科 根本研究室

    • URL

      http://park.saitama-u.ac.jp/~nemoto/

    • Related Report
      2012 Research-status Report
  • [Patent(Industrial Property Rights)] 特許2012

    • Inventor(s)
      根本直人、熊地重文、塩野博文
    • Industrial Property Rights Holder
      埼玉大学、(株)ニコン
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2012-255737
    • Filing Date
      2012-11-21
    • Related Report
      2012 Research-status Report
  • [Patent(Industrial Property Rights)] スリーフィンガー構造を有するリガンド、及びそれを用いた分子の検出2011

    • Inventor(s)
      根本直人、四本勇也
    • Industrial Property Rights Holder
      根本直人、四本勇也
    • Industrial Property Number
      2011-253311
    • Filing Date
      2011
    • Related Report
      2011 Research-status Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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