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Activities of functional RNA molecules containing unnatural bases in cultured cells

Research Project

Project/Area Number 20710176
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Living organism molecular science
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

KIMOTO Michiko  The Institute of Physical and Chemical Research, 核酸合成生物学研究チーム, 研究員 (20415144)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2009: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2008: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Keywords生体分子 / 核酸 / バイオテクノロジー / 人工塩基対 / 転写 / RNA干渉 / 培養細胞 / 培養
Research Abstract

By using in vitro transcription with our unnatural base pair systems, we prepared shRNA molecules containing a series of unnatural bases at a specific position and evaluated their RNAi activities in cultured cells. We found that the activity was retained by replacement with unnatural bases in some specific positions within the passenger and guide strands of the shRNA molecules, and that the tolerance by unnatural-base replacements depended on the size of the unnatural base.

Report

(3 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • Research Products

    (39 results)

All 2010 2009 2008 Other

All Journal Article (10 results) (of which Peer Reviewed: 4 results) Presentation (15 results) Book (4 results) Remarks (3 results) Patent(Industrial Property Rights) (7 results)

  • [Journal Article] Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis.2010

    • Author(s)
      Y. Hikida, M. Kimoto, S. Yokoyama, I. Hirao
    • Journal Title

      Nature Protocols (in press)

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A unique fluorescent base analogue for the expansion of the genetic alphabet.2010

    • Author(s)
      M. Kimoto, T. Mitsui, S. Yokoyama, I. Hirao
    • Journal Title

      J. Am. Chem. Soc. 132

      Pages: 4988-4989

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules.2009

    • Author(s)
      M. Kimoto, R. Kawai, T. Mitsui, S. Yokoyama, I. Hirao
    • Journal Title

      Nucleic Acids Res. 37

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems.2009

    • Author(s)
      M. Kimoto, A. Sato, R. Kawai, S. Yokoyama, I. Hirao
    • Journal Title

      Nucleic Acids Symp. Ser. 53

      Pages: 73-74

    • Related Report
      2009 Final Research Report
  • [Journal Article] Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems2009

    • Author(s)
      Michiko Kimoto
    • Journal Title

      Nucleic Acids Symp.Ser. 53

      Pages: 73-74

    • Related Report
      2009 Annual Research Report
  • [Journal Article] An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules.2009

    • Author(s)
      木本路子
    • Journal Title

      Nucleic Acids Research 37

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient PCR amplification by an unnatural base pair system.2008

    • Author(s)
      M. Kimoto, R. Kawai, T. Mitsui, S. Yokoyama, I. Hirao
    • Journal Title

      Nucleic Acids Symp. Ser. 52

      Pages: 469-470

    • Related Report
      2009 Final Research Report
  • [Journal Article] Sequences around the unnatural base pair in DNA templates for efficient replication.2008

    • Author(s)
      M. Kimoto, R. Kawai, T. Mitsui, S. Yokoyama, I. Hirao
    • Journal Title

      Nucleic Acids Symp. Ser. 52

      Pages: 457-458

    • Related Report
      2009 Final Research Report
  • [Journal Article] Efficient PCR amplification by an unnatural base pair system.2008

    • Author(s)
      M. Kimoto
    • Journal Title

      Nucleic Acids Symp. Ser. 52

      Pages: 469-470

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Sequences around the unnatural base pair in DNA templates for efficient replication.2008

    • Author(s)
      M. Kimoto
    • Journal Title

      Nucleic Acids Symp. Ser. 52

      Pages: 457-458

    • Related Report
      2008 Annual Research Report
  • [Presentation] PCR amplification and transcription by a hydrophobic unnatural base pair system for site-specific RNA labeling2010

    • Author(s)
      M. Kimoto
    • Organizer
      EVOLVING DNA POLYMERASES: CHEMISTRY MEETS BIOLOGY
    • Place of Presentation
      スイスモンテベリタ
    • Year and Date
      2010-05-10
    • Related Report
      2009 Final Research Report
  • [Presentation] Site-specific fluorescent labling of shRNA by an unnatural base pair system2009

    • Author(s)
      S. Liu
    • Organizer
      第19回アンチセンス-第5回OTS(Oligonucleotide Therapeutics Society)年会合同国際学会
    • Place of Presentation
      福岡
    • Year and Date
      2009-11-04
    • Related Report
      2009 Final Research Report
  • [Presentation] Site-specific fluorescent labeling of shRNA by an unnatural base pair system2009

    • Author(s)
      Shuang Liu
    • Organizer
      第19回アンチセンス-第5回OTS(Oligonucleotide Therapeutics Society)年会合同国際学会
    • Place of Presentation
      福岡
    • Year and Date
      2009-11-04
    • Related Report
      2009 Annual Research Report
  • [Presentation] Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems2009

    • Author(s)
      M. Kimoto
    • Place of Presentation
      岐阜県高山市
    • Year and Date
      2009-10-01
    • Related Report
      2009 Final Research Report
  • [Presentation] Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems2009

    • Author(s)
      木本路子
    • Organizer
      第6回国際核酸化学シンポジウム
    • Place of Presentation
      岐阜県高山市
    • Year and Date
      2009-10-01
    • Related Report
      2009 Annual Research Report
  • [Presentation] PCRと転写で機能する人工塩基対による機能性コンポーネントのRNA中への位置選択的取り込み2009

    • Author(s)
      木本路子
    • Organizer
      第11回rnaミーティング
    • Place of Presentation
      新潟
    • Year and Date
      2009-07-29
    • Related Report
      2009 Final Research Report
  • [Presentation] PCRと転写で機能する人工塩基対による機能性コンポーネントのRNA中への位置選択的取り込み2009

    • Author(s)
      木本路子
    • Organizer
      第11回RNAミーティング
    • Place of Presentation
      新潟
    • Year and Date
      2009-07-29
    • Related Report
      2009 Annual Research Report
  • [Presentation] Efficient PCR amplification functionalization by an unnatural base pair system2009

    • Author(s)
      M. Kimoto
    • Organizer
      ACS 237th National Meeting
    • Place of Presentation
      米国ユタ
    • Year and Date
      2009-03-23
    • Related Report
      2009 Final Research Report
  • [Presentation] 高効率でPCR増幅可能な人工塩基対システムの構築2008

    • Author(s)
      木本路子
    • Organizer
      分子生物学会
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-10
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] Efficient PCR amplification by an unnatural base pair system2008

    • Author(s)
      I. Hirao
    • Organizer
      Joint Symposium of 18th International Roundtable on Nucleosides, Nucleotides and Nucleic Acids (IRTXVIII) and 35th International Symposium on Nucleic Acids Chemistry (SNAC)
    • Place of Presentation
      京都
    • Year and Date
      2008-09-09
    • Related Report
      2009 Final Research Report
  • [Presentation] Sequences around the unnatural base pair in DNA templates for efficient replication2008

    • Author(s)
      M. Kimoto
    • Organizer
      Joint Symposium of 18th International Roundtable on Nucleosides, Nucleotides and Nucleic Acids (IRTXVIII) and 35th International Symposium on Nucleic Acids Chemistry (SNAC)
    • Place of Presentation
      京都
    • Year and Date
      2008-09-09
    • Related Report
      2009 Final Research Report
  • [Presentation] Site-specific fluorescent labeling of RNA fragments by transcription using an unnatural base pair system2008

    • Author(s)
      M. Kimoto
    • Organizer
      ACS 236th National Meeting
    • Place of Presentation
      米国フィラデルフィア
    • Year and Date
      2008-08-20
    • Related Report
      2009 Final Research Report
  • [Presentation] Site-specific fluorescent labeling of RNA fragments by transcription using an unnatural base pair system2008

    • Author(s)
      M. Kimoto
    • Organizer
      ACS 236th National Meeting
    • Place of Presentation
      Philadelphia
    • Year and Date
      2008-08-20
    • Related Report
      2008 Annual Research Report
  • [Presentation] Site-specific incorporation of fluorescent 2-amino-6-(2-thienyl)purine into RNA by transcription using an unnatural base pair system2008

    • Author(s)
      M. Kimoto
    • Organizer
      XIVth symposium on chemistry of nucleic acid components
    • Place of Presentation
      チェコチェスキークルムロフ
    • Year and Date
      2008-06-10
    • Related Report
      2009 Final Research Report
  • [Presentation] Site-specific incorporation of fluorescent 2-amino-6-(2-thienyl)purine in to RNA by transcription using an unnatural base pair2008

    • Author(s)
      M. Kimoto
    • Organizer
      XIVth symposium on chemistry of nucleic acid components
    • Place of Presentation
      Czech Republic
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report
  • [Book] Methods in Molecular Biology(Site-Specific Incorporation of Extra Components into RNA by Transcription Using Unnatural Base Pair Systems.)2010

    • Author(s)
      M. Kimoto, I. Hirao
    • Publisher
      The Humana Press Inc.(in press)
    • Related Report
      2009 Final Research Report
  • [Book] The Chemical Biology of Nucleic Acids(Expansion of the Genetic Alphabet in Nucleic Acids by Creating New Base Pairs.)2010

    • Author(s)
      I. Hirao, M. Kimoto
    • Publisher
      John Wiley & Sons(in press)
    • Related Report
      2009 Final Research Report
  • [Book] The Chemical Biology of Nucleic Acids, Expansion of the Genetic Alphabet in Nucleic Acids by Creating New Base Pairs2010

    • Author(s)
      Ichiro Hirao
    • Publisher
      John Wiley & Sons(in press)
    • Related Report
      2009 Annual Research Report
  • [Book] Methods in Molecular Biology, Site-Specific Incorporation of Extra Components into RNA by Transcription Using Unnatural Base Pair Systems2010

    • Author(s)
      Ichiro Hirao
    • Publisher
      The Humana Press Inc., NJ, USA(in press)
    • Related Report
      2009 Annual Research Report
  • [Remarks] 研究室ホームページURL

    • URL

      http://protein.gsc.riken.jp/hirao/index.html

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://protein.gsc.riken.jp/hirao/index.html

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://protein.gsc.riken.go.jp/hirao/index.html

    • Related Report
      2008 Annual Research Report
  • [Patent(Industrial Property Rights)] 消光性ならびに蛍光性の核酸塩基類似体とその応用2010

    • Inventor(s)
      尾一郎、平尾路子、横山茂之、三井雅雄、山重りえ
    • Industrial Property Rights Holder
      理化学研究所、タグシクス・バイオ株式会社
    • Industrial Property Number
      2010-098319
    • Filing Date
      2010-04-21
    • Related Report
      2009 Final Research Report
  • [Patent(Industrial Property Rights)] 機能性核酸分子の安定化法2010

    • Inventor(s)
      平尾一郎、平尾路子、劉爽、野澤巌
    • Industrial Property Rights Holder
      理化学研究所、タグシクス・バイオ株式会社
    • Industrial Property Number
      2010-965201
    • Filing Date
      2010-04-19
    • Related Report
      2009 Final Research Report
  • [Patent(Industrial Property Rights)] 新規蛍光人工塩基対2009

    • Inventor(s)
      平尾一郎, 平尾路子, 横山茂之, 三井雅雄
    • Industrial Property Rights Holder
      理化学研究所、タグシクス・バイオ株式会社
    • Industrial Property Number
      2009-232776
    • Filing Date
      2009-10-06
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Patent(Industrial Property Rights)] 特異な塩基対を形成する人工塩基対2009

    • Inventor(s)
      :平尾一郎,平尾路子,横山茂之
    • Industrial Property Rights Holder
      :理化学研究所、タグシクス・バイオ株式
    • Industrial Property Number
      2009-232851
    • Filing Date
      2009-10-06
    • Related Report
      2009 Final Research Report
  • [Patent(Industrial Property Rights)] 特異な塩基対を形成する人工塩基対2009

    • Inventor(s)
      平尾一郎, 平尾路子, 横山茂之
    • Industrial Property Rights Holder
      理化学研究所、タグシクス・バイオ株式会社
    • Industrial Property Number
      2009-232851
    • Filing Date
      2009-10-06
    • Related Report
      2009 Annual Research Report
  • [Patent(Industrial Property Rights)] 高選択性・高効率でPCR増幅が可能なDNA2008

    • Inventor(s)
      平尾一郎, 平尾路子, 横山茂之
    • Industrial Property Rights Holder
      理化学研究所、タグシクス・バイオ株式会社
    • Industrial Property Number
      2008-094255
    • Filing Date
      2008-03-27
    • Related Report
      2009 Final Research Report
  • [Patent(Industrial Property Rights)] 高選択性・高効率でPCR増幅が可能なDNA2008

    • Inventor(s)
      平尾一郎, 木本路子, 横山茂之
    • Industrial Property Rights Holder
      理化学研究所、タグシクスバイオ株式会社
    • Industrial Property Number
      2008-094255
    • Filing Date
      2008-03-27
    • Related Report
      2008 Annual Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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