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Study on hairpin DNA molecular device for autonomous molecular computer

Research Project

Project/Area Number 15310084
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Nanomaterials/Nanobioscience
Research InstitutionUniversity of Tokyo

Principal Investigator

SUYAMA Akira  University of Tokyo, Graduate School of Arts and Sciences, Professor, 大学院・総合文化研究科, 教授 (90163063)

Co-Investigator(Kenkyū-buntansha) TAKANO Mitsunori  Waseda University, Science and Engineering, Associate Professor, 理工学部, 助教授 (40313168)
ROSE John  University of Tokyo, Graduate School of Information Science and Technology, Lecturer, 大学院・情報理工学系研究科, 特任講師 (00345125)
HAGIYA Masami  University of Tokyo, Graduate School of Information Science and Technology, Professor, 大学院・情報理工学系研究科, 教授 (30156252)
Project Period (FY) 2003 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥15,700,000 (Direct Cost: ¥15,700,000)
Fiscal Year 2005: ¥1,800,000 (Direct Cost: ¥1,800,000)
Fiscal Year 2004: ¥3,700,000 (Direct Cost: ¥3,700,000)
Fiscal Year 2003: ¥10,200,000 (Direct Cost: ¥10,200,000)
KeywordsDNA computer / molecular computer / nanodevice / nanotechnology / parallel computing / molecular memory
Research Abstract

DNA-based computing is a new computational paradigm that realizes an autonomous and parallel computation by employing DNA molecular reactions. In contrast to a computation on an electronic computer, DNAC can be used to solve biological problems such as gene expression profiling and gene network regulation by using the algorithm of molecular computing because DNAC has a direct interface with biological molecules. A hairpin DNA molecule, which forms a hairpin structure by intra-base pairing, is an effective DNA nano-device for DNAC. For instance, a whiplash PCR system, which is a promising architecture for DNAC, employs recursive and self-catalytic polymerization reactions of hairpin DNA molecules. The rate of hairpin structure formation does not depend on the concentration of hairpin DNA molecules because the hairpin structure formation is an intra-molecular reaction. In massively parallel DNAC, the concentration of DNA molecules that represent individual programs and data is very low. Therefore, the concentration-independent rate of hairpin formation is extremely effective in massively parallel DNAC. In this study the static and kinetic characteristics of structural transition of hairpin DNA molecules were investigated. New hairpin DNA nano devices for DNAC were then developed based on the characteristics of hairpin DNA molecules as well as optimization and extension of the whiplash PCR system. A new architecture for an autonomous DNAC using hairpin DNA molecules as effective computational components was also developed.

Report

(4 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (31 results)

All 2005 2004 2003 Other

All Journal Article (22 results) Book (2 results) Publications (7 results)

  • [Journal Article] Amorphous DNA memory constructed with hairpin DNA immobilized on a soliud surface2005

    • Author(s)
      M.Takinoue, Y.Hatano, Y.Endoh, A.Suyama
    • Journal Title

      Preliminary proceedings of DNA 11

      Pages: 410-410

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Amorphous DNA memory constructed with hairpin DNA immobilized on a soliud surface2005

    • Author(s)
      M.Takinoue, Y.Hatano, Y.Endoh, A.Suyama
    • Journal Title

      Preliminary proceedings of DNA 11 (A.Carbone, M.Daley, L.Kari, I.McQuillan and N.Pierce, Eds.) 410

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Realization of RTRAC : Reverse transcription and Transcription-based Autonomous Computer2005

    • Author(s)
      D.Kiga, T.Mochida, M.Takinoue, A.Suyama
    • Journal Title

      Preliminary proceedings of DNA 11(A.Carbone, M.Daley, L.Kari, I.McQuillan and N.Pierce, Eds)

      Pages: 397-397

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Amorphous DNA memory constructed with hairpin DNA immobilized on a soliud surface2005

    • Author(s)
      M.Takinoue, Y.Hatano, Y.Endoh, A.Suyama
    • Journal Title

      Preliminary proceedings of DNA 11(A.Carbone, M.Daley, L.Kari, I.McQuillan and N.Pierce, Eds.)

      Pages: 410-410

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 細胞の中で働くコンピュータ(前編)2005

    • Author(s)
      陶山 明
    • Journal Title

      BIONICS 7月号 7月号

      Pages: 58-60

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 細胞の中で働くコンピュータ(後編)2005

    • Author(s)
      陶山 明
    • Journal Title

      BIONICS 8月号 8月号

      Pages: 54-56

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Molecular reactions for a molecular memory based on hairpin DNA2004

    • Author(s)
      M.Takinoue, A.Suyama
    • Journal Title

      CBI J. 4・3

      Pages: 93-100

    • NAID

      130004138161

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Autonomous biomolecular computer modeled after retroviral replication2004

    • Author(s)
      N.Nitta, A.Suyama
    • Journal Title

      Lect. Notes Comput. Sc. 2943

      Pages: 203-212

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Physical Modeling of Biomolecular Computers : Models, limitations, and experimental validation2004

    • Author(s)
      J.A.Rose, A.Suyama
    • Journal Title

      Natural Computing 3

      Pages: 411-426

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Statistical thermodynamic analysis and design of DNA-based Computers2004

    • Author(s)
      J.A.Rose, R.J.Deaton, A.Suyama
    • Journal Title

      Natural Computing 3

      Pages: 443-459

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Molecular reactions for a molecular memory based on hairpin DNA2004

    • Author(s)
      M.Takinoue, A.Suyama
    • Journal Title

      CBI J. 4(3)

      Pages: 93-100

    • NAID

      130004138161

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Satistical thermodynamic analysis and design of DNA-based Computers2004

    • Author(s)
      J.A.Rose, R.J.Deaton, A.Suyama
    • Journal Title

      Natural Computing 3

      Pages: 443-459

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Stability of double-stranded DNA : Its theory and application2004

    • Author(s)
      J.A.Rose, A.Suyama
    • Journal Title

      YODOSHA. (書名)

      Pages: 140-140

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Autonomous biomolecular computer modeled after retroviral replication2004

    • Author(s)
      N.Nitta, A.Suyama
    • Journal Title

      Lect.Notes Comput.Sc. 2943

      Pages: 203-212

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Parallel translation of DNA clusters by VCSEL array trapping and temperature control with laser illumination2004

    • Author(s)
      Y.Ogura, T.Kawakami, F.Sumiyama, A.Suyama, J.Tanida
    • Journal Title

      Lect.Notes Comput.Sc. 2943

      Pages: 10-18

    • Related Report
      2004 Annual Research Report
  • [Journal Article] DNAコンピュータとナノテクノロジー2004

    • Author(s)
      陶山 明
    • Journal Title

      細胞工学 23(2)

      Pages: 241-246

    • Related Report
      2004 Annual Research Report
  • [Journal Article] DNAコンピュータの現状と将来2004

    • Author(s)
      陶山 明
    • Journal Title

      臨時別冊・数理科学 SGCライブラリ31

      Pages: 129-135

    • Related Report
      2004 Annual Research Report
  • [Journal Article] バイオコンピュータ・DNAデバイス2004

    • Author(s)
      陶山 明
    • Journal Title

      新訂版・表面科学の基礎と応用 (日本表面科学学会編)

      Pages: 1365-1367

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Statistical thermodynamic analysis and design of DNA-based computers2004

    • Author(s)
      J.A.Rose, R.J.Deeaton, A.Suyama
    • Journal Title

      International Journal of Natural Computing 3

      Pages: 443-459

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Physical modeling of biomolecular computers : Models, limitations and experimental validation2004

    • Author(s)
      J.A.Rose, A.Suyama
    • Journal Title

      International Journal of Natural Computing 3

      Pages: 411-426

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Molecular reactions for a molecular memory based on hairpin DNA2004

    • Author(s)
      M.Takinoue, A.Suyama
    • Journal Title

      CBI J. 4

      Pages: 112-120

    • NAID

      130004138161

    • Related Report
      2004 Annual Research Report
  • [Journal Article] A DNA-computing-based genetic program for in vitro protein evolution via constrained pseudomodule shuffling2003

    • Author(s)
      J.A.Rose, M.Takano, M.Hagiya, A.Suyama
    • Journal Title

      Genetic Programming and Evolvable Machines 4

      Pages: 139-152

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] DNA二重らせんの安定性を解く-その理論と応用2004

    • Author(s)
      J.A.Rose, 陶山明
    • Total Pages
      140
    • Publisher
      羊土社
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] 東京大学バイオインフォマティクス集中講義 DNA二重らせんの安定性を解く-その理論と応用2004

    • Author(s)
      J.A.Rose, 陶山 明
    • Total Pages
      140
    • Publisher
      羊土社
    • Related Report
      2004 Annual Research Report
  • [Publications] N.Nitta その他: "Autonomous biomolecular computer modeled after retroviral reprication"Lect.Notes Comput.Sc.. (In press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] J.A.Rose その他: "A DNA-computing-based genetic program for in vitro protein evolution via constrained pseudomodule shuffling"Genetic Programming and Evolvable Machines. 4. 139-152 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] J.A.Rose 他: "A PNA-mediated whiplash PCR-based program for in vitro protein evolution"Lect.Notes Comput.Sc.. 2568. 47-60 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 陶山 明: "自律的に動作するin vivo DNAコンピュータ"細胞工学. 22(11). 1244-1249 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 陶山 明: "DNAコンピュータとナノテクノロジー"細胞工学. 23(2). 241-246 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] 陶山 明: "DNAコンピュータ"応用物理学会薄膜・表面物理セミナー「有機分子ナノテクノロジー」. AP032326. 53-58 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] John Rose その他: "DNA解析科学入門 バイオインフォマティクス概論 (高木利久編)"羊土社(In press). (2004)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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