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Development of a new method for chemical synthesis of genomic DNAs

Research Project

Project/Area Number 24550184
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Chemistry related to living body
Research InstitutionTokyo Institute of Technology

Principal Investigator

AKIHIRO Ohkubo  東京工業大学, 生命理工学研究科, 准教授 (60376960)

Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2012: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
KeywordsDNA合成 / ホスホロアミダイト / ポーラスガラス / 核酸合成 / DNA / ゲノムDNA / 固相合成
Outline of Final Research Achievements

The final goal of this study is development of a high-throughput method for chemical synthesis of the genomic DNAs of mycoplasma and cyanobacteria. In this research, ‘improvement of chain elongation efficiency’, ‘simplification of purification of oligonucleotides’, and ‘development of a flow-system for synthesis of long oligonucleotides’ was carried out. Specifically, l the 30-mer DNA oligomers was synthesized by using the condensation reaction on the activator-contained solid phase carrier and a capping reaction with diphenylphosphonate. We also prepared a filter-type porous glass carrier for the flow system of DNA synthesis and examined the reactivity on the support in detail.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (20 results)

All 2014 2013 2012 Other

All Journal Article (14 results) (of which Peer Reviewed: 14 results) Presentation (4 results) Remarks (2 results)

  • [Journal Article] Properties of 5- and/or 2-modified 2'-O-cyanoethyl uridine residue: 2'-O-cyanoethyl-5-propynyl-2-thiouridine as an efficient duplex stabilizing component.2014

    • Author(s)
      Masaki Y, Miyasaka R, Hirai K, Kanamori T, Tsunoda H, Ohkubo A, Seio K, Sekine M
    • Journal Title

      Org Biomol Chem.

      Volume: 12 Issue: 7 Pages: 1157-1162

    • DOI

      10.1039/c3ob41983e

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Properties of 5- and/or 2-modified 2'-O-cyanoethyl uridine residue: 2'-O-cyanoethyl-5-propynyl-2-thiouridine as an efficient duplex stabilizing component.2014

    • Author(s)
      Yamada K, Masaki Y, Tsunoda H, Ohkubo A, Seio K, Sekine M.
    • Journal Title

      Org Biomol Chem.

      Volume: 12 Issue: 14 Pages: 1157-62

    • DOI

      10.1039/c3ob42420k

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Synthesis and properties of oligonucleotides modified with 2'-O-(2-carboxyethyl)nucleotides and their carbamoyl derivatives.2014

    • Author(s)
      Yamada T, Masaki Y, Okaniwa N, Kanamori T, Ohkubo A, Tsunoda H, Seio K, Sekine M
    • Journal Title

      Org Biomol Chem.

      Volume: 12 Issue: 33 Pages: 6457-6464

    • DOI

      10.1039/c4ob01260g

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Base recognition of gap sites in DNA-DNA and DNA-RNA duplexes by short oligonucleotides.2013

    • Author(s)
      Yamada K, Ohkubo A, Esaka Y, Kanamori T, Masaki Y, Seio K, Sekine M.
    • Journal Title

      Bioorg Med Chem Lett.

      Volume: 23 Issue: 11 Pages: 3448-51

    • DOI

      10.1016/j.bmcl.2013.03.054

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Fluorescent properties of oligonucleotides doubly modified with an indole-fused cytosine analog and 2-aminopurine2013

    • Author(s)
      Seio, K.; Kanamori, T.; Tokugawa, M.; Ohzeki, H.; Masaki, Y.; Tsunoda, H.; Ohkubo, A.; Sekine, M.
    • Journal Title

      Bioorg. Med. Chem. Lett

      Volume: 23 Issue: 11 Pages: 3197-3201

    • DOI

      10.1016/j.bmc.2013.03.034

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Chemical Synthesis of UlsnRNA Derivatives2013

    • Author(s)
      Ohkubo, A.; Kondo, Y.; Suzuki, M.;Kobayashi, H.;Kanamori, T.; Masaki, Y.; Seio, K.; Nagai, K.; Sekine, M
    • Journal Title

      Org. Lett

      Volume: 15 Issue: 17 Pages: 4386-4389

    • DOI

      10.1021/ol401917r

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Modified oligodeoxynucleotide primers for reversetranscription of target RNAs that can discriminate among length variants at the 3'-terminus2013

    • Author(s)
      Iijima, Y.; Kojima, S.; Kodama, E.; Kurohagi, S.; Kanamori, T.; Masaki, Y.; Ohkubo, A.; Sekine, M.; Seio, K.
    • Journal Title

      Org. Biomol. Chem.

      Volume: 11 Issue: 47 Pages: 8276-8282

    • DOI

      10.1039/c3ob41901k

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Assembly of pyrene-modified DNA/RNA duplexes incorporating a G-rich single strand region. Bioorg2013

    • Author(s)
      Seio, K.; Tokugawa, M.; Tsunoda, H.; Ohkubo, A.; Arisaka, F.; Sekine, M
    • Journal Title

      Med. Chem. Lett

      Volume: 23 Issue: 24 Pages: 6822-6824

    • DOI

      10.1016/j.bmcl.2013.10.012

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Remarkable stabilization of antiparallel DNA triplexes by strong stacking effects of consecutively modified nucleobases containing thiocarbonyl groups.2013

    • Author(s)
      Yamada K, Hattori Y, Inde T, Kanamori T, Ohkubo A, Seio K, Sekine M.
    • Journal Title

      Bioorg Med Chem Lett.

      Volume: 23 Issue: 3 Pages: 776-8

    • DOI

      10.1016/j.bmcl.2012.11.079

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Prediction of the stability of modified RNA duplexes based on deformability analysis: 0ligoribonucleotide derivatives modified with 2'O-cyanoethyl- 5-propynyl-2-thiouridine as a promising component2012

    • Author(s)
      Masaki, Y.; Miyasaka, R.;Hirai, K.;Tsunoda, H.; Ohkubo, A.;Seio, K.;Sekine, M
    • Journal Title

      Chem. Commun

      Volume: 48 Issue: 58 Pages: 7313-7315

    • DOI

      10.1039/c2cc33409g

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Synthesis and properties of cationic 2' -O-[N-(4-aminobutyl)carbamoyl]modified oligonucleotides2012

    • Author(s)
      Seio, K.; Tokugawa, M.; Kanamori, T.; Tsunoda, H.; Ohkubo, A.; Sekine, M.
    • Journal Title

      Bioorg. Med. Chem. Lett

      Volume: 22 Issue: 7 Pages: 2470-2473

    • DOI

      10.1016/j.bmcl.2012.02.012

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Formation of New Base Pairs between Inosine and 5-Methyl-2-thiocytidine Derivatives2012

    • Author(s)
      Ohkubo, A.; Nishino, Y.; Ito, Y.; Tsunoda, H.; Seio, K.; Sekine
    • Journal Title

      Org.Biomol.Chem.

      Volume: 10 Issue: 10 Pages: 2008-2010

    • DOI

      10.1039/c2ob06641f

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Development of an efficient method for phosphorodiamidate bond formation by using inorganic salts.2012

    • Author(s)
      T. Harakawa, H. Tsunoda, A. Ohkubo, K. Seio, and M. Sekine,
    • Journal Title

      Bioorg. Med. Chem. Lett.

      Volume: 22 Issue: 3 Pages: 1445-1447

    • DOI

      10.1016/j.bmcl.2011.12.021

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Synthesis of 5'-Terminal Capped Oligonucleotides Using O-N Phosphoryl Migration of Phosphoramidite Derivatives2012

    • Author(s)
      Ohkubo, A.;Tago, N.;Nishino, Y.;Yamada, K.; Tsunoda, H.:Seio, K.:Sekine, M
    • Journal Title

      Org. Lett

      Volume: 14 Issue: 1 Pages: 10-13

    • DOI

      10.1021/ol2026075

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] Synthesis of oligodeoxynucleotides incorporating conformational restriction at the 5’-terminus and their application to discrimination of RNA length variants2013

    • Author(s)
      Yoshihiro Iijima, Sayako Kurohagi, Erika Kodama, Shun Kojima, Takashi Kanamori, Yoshiaki Masaki, Akihiro Ohkubo, Mitsuo Sekine, Kohji Seio
    • Organizer
      The 40th international symposium on nucleic acids chemistry
    • Place of Presentation
      Kanagawa University (Yokohama)
    • Related Report
      2013 Research-status Report
  • [Presentation] Chemical synthesis of U1 snRNA derivatives2013

    • Author(s)
      Haruki Kobayashi, Akihiro Ohkubo, Makoto Suzuki, Takashi Kanamori, Yoshiaki Masaki, Kohji Seio, Mitsuo Sekine, Hideya Yuasa
    • Organizer
      The 40th international symposium on nucleic acids chemistry
    • Place of Presentation
      Kanagawa University (Yokohama)
    • Related Report
      2013 Research-status Report
  • [Presentation] Development of fluorescent turn-on sensor for triplex formation and its application to nucleosides and oligonucleotides sensing2012

    • Author(s)
      Takashi Kanamori, Hiroki Ohzeki, Yuki Oda, Akihiro Ohkubo, Mitsuo Sekine, Kohji Seio
    • Organizer
      The 39th International Symposium onNucleic Acids Chemistry
    • Place of Presentation
      Nagoya, Japan
    • Related Report
      2012 Research-status Report
  • [Presentation] Synthesis and properties of new triplex forming oligonucleotides capable of recognizing TA and CG base pairs in parallel orientation2012

    • Author(s)
      Kenji Yamada, Yu Ito, Kiichi Yoshimura, Takashi Kanamori, Akihiro Ohkubo, Kohji Seio, Mitsuo Sekine
    • Organizer
      The 39th International Symposium onNucleic Acids Chemistry
    • Place of Presentation
      Nagoya, Japan
    • Related Report
      2012 Research-status Report
  • [Remarks] 湯浅・大窪研究室

    • URL

      http://www.yuasa-lab.bio.titech.ac.jp/

    • Related Report
      2013 Research-status Report
  • [Remarks] 湯浅・大窪研究室

    • URL

      http://www.yuasa-lab.bio.titech.ac.jp/

    • Related Report
      2012 Research-status Report

URL: 

Published: 2013-05-31   Modified: 2019-07-29  

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