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Large Scaled Fast Aqueous Computing with Light Responsive DNA upon Micro Fluidic Devices

Research Project

Project/Area Number 17200022
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionTokyo Institute of Technology

Principal Investigator

YAMAMURA Masayuki  Tokyo Institute of Technology, Interdisciplinary Graduate School of Science and Engineering, Professor, 大学院総合理工学研究科, 教授 (00220442)

Co-Investigator(Kenkyū-buntansha) SEIO Koji  Tokyo Institute of Technology, Frontier Creative Research Center, Associate Professor, フロンティア創造共同研究センター, 助教授 (20313356)
FUJII Teruo  The University of Tokyo, Institute of Industrial Science, Associate Professor, 生産技術研究所, 助教授 (30251474)
FUJIMOTO Kenzo  Japan Advanced Institute of Science and Technology, School of Materials Science, Associate Professor, 材料科学研究科, 助教授 (90293894)
Project Period (FY) 2005 – 2006
Project Status Completed (Fiscal Year 2006)
Budget Amount *help
¥49,530,000 (Direct Cost: ¥38,100,000、Indirect Cost: ¥11,430,000)
Fiscal Year 2006: ¥19,890,000 (Direct Cost: ¥15,300,000、Indirect Cost: ¥4,590,000)
Fiscal Year 2005: ¥29,640,000 (Direct Cost: ¥22,800,000、Indirect Cost: ¥6,840,000)
KeywordsDNA computing / molecular memory / micro fluidic device / light responsive DNA / Aqueous algorithm / NP-complete / massively parallel computing / protecting group / アクエアス・コンピューティング / 分子メモリー / テンプレート法 / 光結合性DNA / ドロップレット
Research Abstract

Early explosion of DNA computing to solve combinatorial problems is now shrinking by three hardness ; (1) code set design, (2) scalability and (3) speed and reliability. This project proposes an implementation of Aqueous memory molecules by using light responsive modification of DNAs and show a series of feasibility experiments. We expect to overcome three difficulties since Aqueous computing is code design free (1), DNA sequence provides arbitrary size of address space (2), and light responsive reaction is fast and reliable (3).
As a result of this project, Yamamura has examined a series of experiments of the write operation with a set of light responsive 11 DNA codes of 20 base pair long and shown a demonstration of Aqueous computing with four bits memory. Fujii has developed a set of necessary techniques to handle droplets on micro fluidic devices so that droplets can be generated and mixed on demand, i.e for arbitrary material, quantity and timing, and also realized continuous DNA-PNA hybridization reaction and gel electrophoresis analysis on a micro fluidic device. Seio has developed a synthesis method of branched DNA with TrS protecting group which can be deprotected by I2-promoted removal of the TrS group, and show high quality branched DNA can be synthesized than conventional method. Fujimoto has developed a method for photo-crosslinking molecules as a write once operation, and also developed a method for photoinduced repair of thymine dimmer as an enzyme free tool for Aqueous computing.

Report

(3 results)
  • 2006 Annual Research Report   Final Research Report Summary
  • 2005 Annual Research Report
  • Research Products

    (38 results)

All 2007 2006 2005

All Journal Article (38 results)

  • [Journal Article] An Implementation of Aqueous Memory Molecules with Light Responsive DNAs2007

    • Author(s)
      M.Yamamura, N.Hirayama, K.Komiya
    • Journal Title

      Proc. CEC2007

      Pages: 6-6

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] A realization of DNA molecular machine that walks autonomously by using a restriction enzyme2007

    • Author(s)
      H.SEKIGUCHI, K.KOMIYA, D.KIGA, M.YAMAMURA
    • Journal Title

      Preliminary Proc. DNA13 1

      Pages: 91-100

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] An Implementation of Aqueous Memory Molecules with Light Responsive DNAs2007

    • Author(s)
      M.Yamamura, N.Hirayama, K.Komiya
    • Journal Title

      Proc.CEC2007 (in press)

      Pages: 6-6

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] A realization of DNA molecular machine that walks autonomously by using a restriction enzyme2007

    • Author(s)
      H.Sekiguchi, K.Komiya, D.Kiga, M.Yamamura
    • Journal Title

      Preliminary Proc.DNA 13

      Pages: 91-100

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] An Implementation of Aqueous Memory Molecules with Light Responsive DNAs2007

    • Author(s)
      Yamamura, M., Hirayama, N.
    • Journal Title

      Proc. CEC 2007

      Pages: 6-6

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A realization of DNA molecular machine that walks autonomously by using a restricion enzyme2007

    • Author(s)
      Hiroyuki SEKIGUCHI, Ken KOMIYA, Daisuke KIGA, Masayuki YAMAMURA
    • Journal Title

      Proc. DNA 13

      Pages: 10-10

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Microfluidic Device for Droplet-based DNA-PNA Hybridization and Separation2006

    • Author(s)
      S.Kaneda, K.Somei, K.Ono, T.Yamamoto, T.Fujii
    • Journal Title

      Proc. μ TAS2006 2

      Pages: 1151-1153

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] マイクロ流体デバイスによるバイオ分析2006

    • Author(s)
      金田祥平, 藤井輝夫
    • Journal Title

      精密工学会誌 72

      Pages: 937-976

    • NAID

      110004799010

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] cis-Tetrahydrofuran-3,4-diol Structure as a Key Skeleton of New Protecting Groups Removable by Self-Cyclization under Oxidative Conditions2006

    • Author(s)
      E.Utagawa, M.Sekine, K.Seio
    • Journal Title

      J. Org. Chem. 71

      Pages: 7668-7677

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Catalytic Repair of a Thymine Dimer in DNA via Carbazole Nucleoside2006

    • Author(s)
      Y.Yoshimura, K.Fujimoto
    • Journal Title

      Chem. Lett. 35・4

      Pages: 386-389

    • NAID

      10018125417

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Photoinduced repair of a thymine dimer in DNA via carbazole nncleoside2006

    • Author(s)
      Y.Yoshimura, K.Fujimoto
    • Journal Title

      Nucleic Acids Symp. Series 50

      Pages: 151-152

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Highly selective and sensitive template-directed photoligation of DNA via 5-carbamoylviny1-2-deoxyuridine2006

    • Author(s)
      Y.Yoshimura, D.Okamura, M.Ogino, K.Fujimoto
    • Journal Title

      Org. Lett. 8・22

      Pages: 5049-5049

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Microfluidic Device for Droplet-based DNA-PNA Hybridization and Separation2006

    • Author(s)
      S.Kaneda, K.Somei, K.Ono, T.Yamamoto, T.Fujii
    • Journal Title

      Proc.μ TAS2006 2

      Pages: 1151-1153

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Microfluidic Devices for Bio Analyses(in Japanese)2006

    • Author(s)
      S.Kaneda, T.Fujii
    • Journal Title

      J.the Japan Society for Precision Engineering 72, 8

      Pages: 937-976

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] cis-Tetrahydrofuran-3,4-diol Structure as a Key Skeleton of New Protecting Groups Removable by Self-Cyclization under Oxidative Conditions2006

    • Author(s)
      E.Utagawa, M.Sekine, K.Seio
    • Journal Title

      J.Org.Chem. 71

      Pages: 7668-7677

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Catalytic Repair of a Thymine Dimer in DNA via Carbazole Nucleoside2006

    • Author(s)
      Y.Yoshimura, K.Fujimoto
    • Journal Title

      Chem.Lett. 35, 4

      Pages: 386-389

    • NAID

      10018125417

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Photoinduced repair of a thymine dimer in DNA via carbazole nucleoside2006

    • Author(s)
      Y.Yoshimura, K.Fujimoto
    • Journal Title

      Nucleic Acids Symp.Series 50

      Pages: 151-152

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Highly selective and sensitive template-directed photoligation of DNA via 5-carbamoylvinyl-2-deoxyuridine2006

    • Author(s)
      Y.Yoshimura, D.Okamura, M.Ogino, K.Fujimoto
    • Journal Title

      Org.Lett. 8, 22

      Pages: 5049-5049

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Microfluidic Device for Droplet-based DNA-PNA Hybridization and Separation2006

    • Author(s)
      S Kaneda, K.Somei, K.Ono, T, Yamamoto, T.Fujii
    • Journal Title

      Proc. μTAS2006 2

      Pages: 1151-1153

    • Related Report
      2006 Annual Research Report
  • [Journal Article] cis-Tetrahydrofuran-3,4-diol Structure as a Key Skeleton of New Protecting Groups Removable by Self-Cyclization under Oxidative Conditions2006

    • Author(s)
      Eri, Utagawa, Mitsuo, Sekine, Kohji, Seio
    • Journal Title

      J. Org. Chem. 71

      Pages: 7668-7677

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Catalytic Repair of a Thymine Dimer in DNA via Carbazole Nucleoside2006

    • Author(s)
      Yoshinaga Yoshimura, Kenzo Fujimoto
    • Journal Title

      Chem. Lett. 35・4

      Pages: 386-389

    • NAID

      10018125417

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Photoindeuce repair of a thymine dimer in DNA via carbazole nucleoside2006

    • Author(s)
      Yoshinaga Yoshimura, Kenzo Fujimoto
    • Journal Title

      Nucleic Acids Symp。Series 50

      Pages: 151-152

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Highly selective and sensitive template-directed photoligation of DNA via 5-carbamoylvinyl-2-deoxyuridine2006

    • Author(s)
      Yoshinaga Yoshimura, Daisuke Okamura, Masayuki Ogino, Kenzo Fujimoto
    • Journal Title

      Org. Lett. 8・22

      Pages: 5049-5049

    • Related Report
      2006 Annual Research Report
  • [Journal Article] 光結合DNAを用いたアクエアスメモリーの作製2006

    • Author(s)
      山村, 平山, 清尾, 藤本, 藤井
    • Journal Title

      計測自動制御学会 第32回知能システムシンポジウム予稿集

      Pages: 225-228

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Interstrand Photocrosslinking of DNA via p-Carbamoylvinyl Phenol Nucleoside2005

    • Author(s)
      Y.Yoshimura, Y.Ito, K.Fujimoto
    • Journal Title

      Bioorg. Med. Chem. Lett 15・5

      Pages: 1299-1302

    • NAID

      120000861713

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Interstrand Photocrosslinking of DNA via p-Carbamoylvinyl Phenol Nucleoside2005

    • Author(s)
      Y.Yoshimura, Y.Ito, K.Fujimoto
    • Journal Title

      Bioorg.Med.Chem.Lett 15, 5

      Pages: 1299-1302

    • NAID

      120000861713

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Interstrand Photocrosslinking of DNA via p-Carbamoyvinyl Phenol Nucleoside.2005

    • Author(s)
      Yoshimura, Y., Ito, Y., Fujimoto, K.
    • Journal Title

      Bioorganic Medical Chemistry Letters 15(5)

      Pages: 1299-1301

    • Related Report
      2005 Annual Research Report
  • [Journal Article] アクエアス・コンピューティングのスケールアップ2005

    • Author(s)
      山村, 清尾, 藤本
    • Journal Title

      計測自動制御学会 第32回知能システムシンポジウム資料

      Pages: 339-344

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A Novel Method to Synthesize Versatile Multiple-Branched DNA (MB-DNA) by Reversible Photochemical Ligation.2005

    • Author(s)
      Shinzi Ogasawara, Kenzo Fujimoto
    • Journal Title

      ChemBioChem 10(6)

      Pages: 1756-1760

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Solution of a SAT Problem on a Photochemical DNA Computer.2005

    • Author(s)
      Shinzi Ogasawara, Kenzo Fujimoto
    • Journal Title

      Chem.Lett. 34(3)

      Pages: 378-381

    • NAID

      10014464673

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Interstrand Photocrosslinking of DNA via p-Carbamoylvinyl Phenol Nucleoside.2005

    • Author(s)
      Yoshinaga Yoshimura, Yoshiaki Ito, Kenzo Fujimoto
    • Journal Title

      Bioorg.Med.Chem.Lett. 15(5)

      Pages: 1299-1302

    • NAID

      120000861713

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Photoinduced DNA end capping via N3-methyl-5-cyanovinyl-2-deoxyuridine,2005

    • Author(s)
      Kenzo Fujimoto, Yoshinaga Yoshimura, Tadayoshi Ikemoto, Akio Nakazawa, Masayuki Hayashi, Isao Saito
    • Journal Title

      Chemical Communication 24

      Pages: 3177-3179

    • NAID

      120001063261

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Template Directed Photoreversible ligation of DNA via carboxyvinyl-deazaadenosine.2005

    • Author(s)
      Isao Saito, Yohei Miyauchi, Yoshio Saito, Kenzo Fujimoto
    • Journal Title

      Tetrahedron Lett. 46

      Pages: 97-99

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Photochemical ODN Manipulation Based on Reversible DNA Photoligation Mediated by Modified Photoresponsive Base.2005

    • Author(s)
      Masayuki Ogino, Shinzi Ogasawara, Takehiro Ami, Kenzo Fujimoto
    • Journal Title

      Journal of Photopolymer Sciecne and Technology 15(5)

      Pages: 1299-1304

    • NAID

      130004464445

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Template-directed DNA photoligation via a -5-cyanovinyldeoxyuridine.2005

    • Author(s)
      Masayuki Ogino, Yoshinaga Yoshimura, Akio Nakazawa, Isao Saito, Kenzo Fujimoto
    • Journal Title

      Org.Lett. 14

      Pages: 2853-2858

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Photo-triggered ODN manipulation on DNA chip.2005

    • Author(s)
      Shinzi Ogasawara, Kenzo Fujimoto
    • Journal Title

      Nucleic Acid Symp.Series. 49

      Pages: 141-142

    • Related Report
      2005 Annual Research Report
  • [Journal Article] RNA template-directed photoligation via 5-carboxyvinyl-2'-deoxyuridine.2005

    • Author(s)
      Yoshinaga Yoshimura, Yuuki Noguchi, Hideaki Sato, Kenzo Fujimoto
    • Journal Title

      Nucleic Acid Symp.Series. 49

      Pages: 143-144

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A new protecting group for the 5'-hydroxyl group having O-S single bond oxidatively cleavable under mild conditions.2005

    • Author(s)
      E.Utagawa, K.Seio, M.Sekine
    • Journal Title

      Nucleosides Nucleotides Nucleic Acids. 24

      Pages: 927-929

    • Related Report
      2005 Annual Research Report

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Published: 2005-04-01   Modified: 2016-04-21  

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