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Development of Photochemical RNA Editing induced by Photothermal Effect

Research Project

Project/Area Number 23350079
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Chemistry related to living body
Research InstitutionJapan Advanced Institute of Science and Technology

Principal Investigator

FUJIMOTO KENZO  北陸先端科学技術大学院大学, マテリアルサイエンス研究科, 教授 (90293894)

Co-Investigator(Kenkyū-buntansha) TSUKAHARA Toshifumi  北陸先端科学技術大学院大学, マテリアルサイエンス研究科, 教授 (60207339)
SAKAMOTO Takashi  北陸先端科学技術大学院大学, マテリアルサイエンス研究科, 助教 (80423078)
Project Period (FY) 2011-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥18,720,000 (Direct Cost: ¥14,400,000、Indirect Cost: ¥4,320,000)
Fiscal Year 2013: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2012: ¥7,540,000 (Direct Cost: ¥5,800,000、Indirect Cost: ¥1,740,000)
Fiscal Year 2011: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Keywords光架橋 / RNA編集 / RNA操作 / 光クロスリンク / 遺伝子変換 / 酵素不要 / RNA / 光編集
Research Abstract

To improve the deamination reaction of cytosine in the photocrosslinked DNA double strand, the effect of additives on the deamination reaction was evaluated. The results indicated that diamine derivatives can accelerate the reaction in a concentration dependent manner. diamine derivatives having more than four carbons distance between two amine groups clearly accelerate the photochemical C-U transition reaction. For spermidine, the acceleration effect was caused by the interaction between spermidine and DNA double strand, although the increase of pH scarcely contributed to the acceleration effect. As the mammalian cells contain millimolars of spermidine and spermine, the acceleration of photochemical C-U transition, that was demonstrated in this study, might occur in mammalian cells. This provides a new design of artificial oligonucleotide having higher photo-editing activity.

Report

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

    (46 results)

All 2013 2012 2011

All Journal Article (13 results) (of which Peer Reviewed: 13 results) Presentation (25 results) (of which Invited: 2 results) Book (1 results) Patent(Industrial Property Rights) (7 results) (of which Overseas: 1 results)

  • [Journal Article] Details of the ultra-fast DNA photocrosslinking reaction of 3-cyanovinylcarbazole nucleoside; Cis-trans isomeric effect and the application for SNP based genotyping2013

    • Author(s)
      Kenzo Fujimoto, Asuka Yamada, Yoshinaga Yoshimura, Tadashi Tsukaguchi and Takashi Sakamoto
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 135 Issue: 43 Pages: 1616-16167

    • DOI

      10.1021/ja406965f

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Geometric Effect on the Photocrosslinking Reaction between 3-Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex2013

    • Author(s)
      Kenzo Fujimoto, Satomi Kishi and Takashi Sakamoto
    • Journal Title

      Photochemistry and Photobiology

      Volume: 89 Issue: 5 Pages: 1095-1099

    • DOI

      10.1111/php.12118

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Quick and Reversible Photocrosslinking Reaction of 3-Cyanovinylcarbazole Nucleoside in DNA Triplex2013

    • Author(s)
      Kenzo Fujimoto, Hiroki Yoshinaga, Yasumasa Yoshio and Takashi Sakamoto
    • Journal Title

      Organic & Biomolecular Chemistry

      Volume: 11 Issue: 31 Pages: 5065-5068

    • DOI

      10.1039/c3ob40915e

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Diamine Derivatives Accelerate Photochemical C→U Transition in DNA Double Strand2013

    • Author(s)
      Kenzo Fujimoto
    • Journal Title

      Chem. Lett.

      Volume: 42 Issue: 3 Pages: 289-291

    • DOI

      10.1246/cl.2013.289

    • NAID

      10031155783

    • Related Report
      2013 Annual Research Report 2013 Final Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand2013

    • Author(s)
      Kenzo Fujimoto
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 14(3) Issue: 3 Pages: 5765-5774

    • DOI

      10.3390/ijms14035765

    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quick Regulation of mRNA Functions by a Few Seconds of Photoirradiation,2012

    • Author(s)
      Atsuo Shigeno
    • Journal Title

      Organic & Biomolecular Chemistry

      Volume: 10(38) Issue: 38 Pages: 7820-7825

    • DOI

      10.1039/c2ob25883h

    • Related Report
      2013 Final Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Specific and reversible photochemical labeling of plasmid DNA using photoresponsive oligonucleotides containing 3-cyanovinylcarbazole2012

    • Author(s)
      Kenzo Fujimoto
    • Journal Title

      Molecular BioSystems

      Volume: 8 (2) Issue: 2 Pages: 491-494

    • DOI

      10.1039/c2mb05422a

    • Related Report
      2013 Final Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 5-Methylcytosine Selective Photoligation Using Photoresponsive, Oligonucleotides Containing Various 5-Vinyl-2’-deoxyuridines Having an Aromatic Group2012

    • Author(s)
      Takashi Sakamoto
    • Journal Title

      Chem. Lett

      Volume: 41(1) Issue: 1 Pages: 47-49

    • DOI

      10.1246/cl.2012.47

    • NAID

      130004426322

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Template Directed Reversible Photochemical Ligation of Oligodeoxynucleotides2012

    • Author(s)
      Shigetaka Nakamura
    • Journal Title

      Molecules

      Volume: 17 Issue: 1 Pages: 163-178

    • DOI

      10.3390/molecules17010163

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Signal turn-on probe for nucleic acid detection based on 19F nuclear magnetic resonance2011

    • Author(s)
      Takashi Sakamoto, Yu-ki Shimizu, Jun Sasaki, Hikaru Hayakawa, Kenzo Fujimoto
    • Journal Title

      Bioorg.Med.Chem.Lett

      Volume: 21 Issue: 1 Pages: 303-206

    • DOI

      10.1016/j.bmcl.2010.11.013

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Possibility of genetic restoration for a disease treatment2011

    • Author(s)
      Toshifumi Tsukahara, Yu Ooka, Shafiul Alam, Hitoshi Suzuki, Kenzo Fujimoto
    • Journal Title

      IEEE ICMSAO

      Volume: 4 Pages: 1-4

    • DOI

      10.1109/icmsao.2011.5775517

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Construction of branched DNA for SNP determination on glass-chip using photochemical ligation2011

    • Author(s)
      Minhaz Uddin Ahmed, Yoshinaga Yoshimura, M.Mosharraf Hossain, Eiichi Tamiya, Kenzo Fujimoto
    • Journal Title

      BioChip J.

      Volume: 5 Issue: 3 Pages: 206-221

    • DOI

      10.1007/s13206-011-5303-0

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Stabilization of DNA nanostructures by photo-cross-linking2011

    • Author(s)
      Miho Tagawa, Koh-ichiroh Shohda, Kenzo Fujimotoc, Akira Suyama
    • Journal Title

      Soft Matter

      Volume: 7 Issue: 22 Pages: 10931-10934

    • DOI

      10.1039/c1sm06303k

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] Details of the ultra-fast DNA photocrosslinking reaction of 3-cyanovinylcarbazole nucleoside2013

    • Author(s)
      Takashi Sakamoto, Asuka Yamada, Yoshinaga Yoshimura, Kenzo Fujimoto
    • Organizer
      Internal Symposium of Nucleic Acids Chemistry 2013
    • Place of Presentation
      Kanagawa Univ. (神奈川県)
    • Related Report
      2013 Final Research Report
  • [Presentation] Possibility of Genetic Code Restoration by Chemical RNA Editing2013

    • Author(s)
      Toshifumi Tsukahara, Vu Thi Luyen, Hitoshi Suzuki, and Kenzo Fujimoto
    • Organizer
      BIT' s Biopharmaceutical Summit 2013
    • Place of Presentation
      Boston, USA
    • Related Report
      2013 Final Research Report
  • [Presentation] Development of cyanovinylcarbazole mediated photocrosslinking reaction toward for regulation of RNA2013

    • Author(s)
      Atsuo Shigeno , Takashi Sakamoto, Kenzo Fujimoto
    • Organizer
      40th Annual Meeting & Exposition of the Controlled Release Society
    • Place of Presentation
      Hawaii, USA
    • Related Report
      2013 Annual Research Report 2013 Final Research Report
  • [Presentation] 超高速光DNA・RNA操作法の開発2013

    • Author(s)
      藤本健造
    • Organizer
      バイオアカデミックフォーラム2013
    • Place of Presentation
      東京ビッグサイト(東京)
    • Related Report
      2013 Final Research Report
  • [Presentation] Details of the ultra-fast DNA photocrosslinking reaction of 3-cyanovinylcarbazole nucleoside2013

    • Author(s)
      Takashi Sakamoto, Asuka Yamada, Yoshinaga Yoshimura, Kenzo Fujimoto
    • Organizer
      Internal Symposium of Nucleic Acids Chemistry 2013
    • Place of Presentation
      Kanagawa Univ.
    • Related Report
      2013 Annual Research Report
  • [Presentation] Possibility of Genetic Code Restoration by Chemical RNA Editing2013

    • Author(s)
      Toshifumi Tsukahara, Vu Thi Luyen, Hitoshi Suzuki, and Kenzo Fujimoto
    • Organizer
      BIT's Biopharmaceutical Summit 2013
    • Place of Presentation
      Boston, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] 超高速光DNA・RNA操作法の開発2013

    • Author(s)
      藤本健造
    • Organizer
      バイオアカデミックフォーラム2013
    • Place of Presentation
      東京ビッグサイト
    • Related Report
      2013 Annual Research Report
  • [Presentation] Ultrafast reversible DNA photocrosslinking in triplex DNA2012

    • Author(s)
      Hiroki Yoshinaga, Yasumasa Yoshio, Takashi Sakamoto, Kenzo Fujimoto
    • Organizer
      Internal Symposium of Nucleic Acids Chemistry 2012
    • Place of Presentation
      Nagoya Univ. (愛知県)
    • Related Report
      2013 Final Research Report
  • [Presentation] Development of Photochemical DNA and RNA Manipulation2012

    • Author(s)
      Kenzo Fujimoto
    • Organizer
      International Symposium on SYNTHESIZING LIFE AND BIOLOGICAL SYSTEMS
    • Place of Presentation
      SENRI LifeScieence Center(大阪)
    • Related Report
      2013 Final Research Report
  • [Presentation] Development about Photochemical RNA Manipulation2012

    • Author(s)
      Kenzo Fujimoto
    • Organizer
      14th RNA Meeting
    • Place of Presentation
      Tohoku Univ. (宮城県)
    • Related Report
      2013 Final Research Report
  • [Presentation] Template directed DNA photochemical ligation toward for construction of DNA architecure2012

    • Author(s)
      Shigetaka Nakamura, Kenzo Fujimoto
    • Organizer
      13th Tetrahedron Symposium
    • Place of Presentation
      Amsterdam, Nederland
    • Related Report
      2013 Final Research Report
  • [Presentation] Development about Photochemical RNA Manipulation2012

    • Author(s)
      Kenzo Fujimoto
    • Organizer
      14th RNA Meeting
    • Place of Presentation
      Tohoku Univ.
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 光化学的なDNA及びRNA操作法の開発2012

    • Author(s)
      藤本 健造
    • Organizer
      関西大学 研究部門発表会
    • Place of Presentation
      関西大学
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 高速光架橋能をもつアンチセンス核酸による細胞内遺伝子発現制御2012

    • Author(s)
      藤本 健造
    • Organizer
      アンチセンス・遺伝子・デリバリーシンポジウム2012
    • Place of Presentation
      仙台市民会館
    • Related Report
      2012 Annual Research Report
  • [Presentation] Development of Photochemical DNA and RNA Manipulation2011

    • Author(s)
      Kenzo Fujimoto
    • Organizer
      34th Annual Meeting of the Molecular Biology Society of Japan
    • Place of Presentation
      Pacifico YOKOHAMA(神奈川県)(Invited)
    • Year and Date
      2011-12-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] Regulation of gene expression by photocrosslinking antisense oligonucleotide containing of carbazole derivative2011

    • Author(s)
      Atsuo Shigeno, Takashi Sakamoto, Kenzo Fujimoto
    • Organizer
      34th Annual Meeting of the Molecular Biology Society of Japan
    • Place of Presentation
      Pacifico YOKOHAMA(神奈川県)
    • Year and Date
      2011-12-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] 酵素を使わずに化学の力でDNAを操る2011

    • Author(s)
      藤本健造
    • Organizer
      日本化学会東北支部主催会員増強のための講演会
    • Place of Presentation
      東北大学(宮城県)(招待講演)
    • Year and Date
      2011-11-25
    • Related Report
      2011 Annual Research Report
  • [Presentation] Rice genome screening by photo-reactive DNA probes2011

    • Author(s)
      Takematsu Yuuki, Yoshinaga Yoshimura, Sakamoto Takashi, Fujimoto Kenzo
    • Organizer
      The 38th International Symposium on Nucleic Acid Chemistry
    • Place of Presentation
      Hokkaido Univ.(北海道)
    • Year and Date
      2011-11-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] Site-specific transition of cytosine to uracil by reversible DNA and RNA photo-crosslinking2011

    • Author(s)
      Futamura Daiki, Yoshinaga Yoshimura, Sakamoto Takashi, Fujimoto Kenzo
    • Organizer
      The 38th International Symposium on Nucleic Acid Chemistry
    • Place of Presentation
      Hokkaido Univ.(北海道)
    • Year and Date
      2011-11-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] Photochemical DNA manipulation toward for DNA computing2011

    • Author(s)
      Nakamura Shigetaka, Ogasakawa Shinzi, Fujimoto Kenzo
    • Organizer
      17th International Conference on. DNA Computing and Molecular Programming
    • Place of Presentation
      LA, USA
    • Year and Date
      2011-09-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] 光化学的な新規遺伝子操作法の開発とその応用2011

    • Author(s)
      藤本健造
    • Organizer
      日本化学会中国四国支部愛媛地区化学講演会
    • Place of Presentation
      愛媛大学(愛媛県)(招待講演)
    • Year and Date
      2011-09-14
    • Related Report
      2011 Annual Research Report
  • [Presentation] 光応答性人工核酸分子の合成と応用2011

    • Author(s)
      藤本健造
    • Organizer
      第28回有機合成化学セミナー
    • Place of Presentation
      天童(山形県)(招待)
    • Year and Date
      2011-08-31
    • Related Report
      2011 Annual Research Report
  • [Presentation] Catalytic Repair of a Thymine Dimer in DNA via Carbazole Nucleoside : Its Application for DNA nanotechnology2011

    • Author(s)
      Nakamura Shigetaka, Ogasakawa Shinzi, Fujimoto Kenzo
    • Organizer
      International Conference of Photochemistry 2011
    • Place of Presentation
      Beijing, China
    • Year and Date
      2011-08-06
    • Related Report
      2011 Annual Research Report
  • [Presentation] Photochemical site specific DNA and RNA transition2011

    • Author(s)
      Fujimoto Kezno, Hiratsuka Kaoru, Shigeno Atsuo
    • Organizer
      12th Tetrahedron Symposium
    • Place of Presentation
      Sgiches, Spain
    • Year and Date
      2011-06-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] Development of Phototriggered DNA and RNA Manipulation2011

    • Author(s)
      Kenzo Fujimoto
    • Organizer
      5th Pacific Symposium on Radical Chemistry
    • Place of Presentation
      Shirahama, WAKAYAMA(Invited)
    • Related Report
      2011 Annual Research Report
  • [Book] 光で操るDNA, パリティ特集「DNAの物理」2011

    • Author(s)
      藤本健造
    • Publisher
      丸善出版株式会社
    • Related Report
      2013 Final Research Report
  • [Patent(Industrial Property Rights)] 光架橋形成抑制方法, 及び自己架橋体形成抑制型光応答性核酸2013

    • Inventor(s)
      藤本健造, 中村重孝
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013-10-30
    • Related Report
      2013 Final Research Report
  • [Patent(Industrial Property Rights)] 鎖交換された二重鎖オリゴヌクレオチドの製造方法2013

    • Inventor(s)
      藤本健造, 中村重孝, 橋本浩寿, 小林聡
    • Industrial Property Rights Holder
      陸先端科学技術大学院大学, 電気通信大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013-06-25
    • Related Report
      2013 Final Research Report
  • [Patent(Industrial Property Rights)] 光クロスリンク能を有する光応答性ヌクレオチドアナログ2013

    • Inventor(s)
      藤本健造, 坂本隆, 田中佑弥
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013-03-28
    • Related Report
      2013 Final Research Report
  • [Patent(Industrial Property Rights)] 光クロスリンク能を有する光応答性人工ヌクレオチド2013

    • Inventor(s)
      藤本健造, 吉村嘉永
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013-05-09
    • Related Report
      2013 Final Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] 光架橋形成抑制方法、及び自己架橋体形成抑制型光応答性核酸2013

    • Inventor(s)
      藤本健造、中村重孝
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2013-225799
    • Filing Date
      2013-10-30
    • Related Report
      2013 Annual Research Report
  • [Patent(Industrial Property Rights)] 鎖交換された二重鎖オリゴヌクレオチドの製造方法2013

    • Inventor(s)
      藤本健造、中村重孝、橋本浩寿、小林聡
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学、電気通信大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2013-133163
    • Filing Date
      2013-06-25
    • Related Report
      2013 Annual Research Report
  • [Patent(Industrial Property Rights)] 光クロスリンク能を有する光応答性ヌクレオチドアナログ2013

    • Inventor(s)
      藤本健造、坂本隆、 田中佑弥
    • Industrial Property Rights Holder
      国立大学法人 北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2013-070381
    • Filing Date
      2013-03-28
    • Related Report
      2012 Annual Research Report

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Published: 2011-04-06   Modified: 2019-07-29  

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