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パラメータ制御方式による分子計算

Research Project

Project/Area Number 14085201
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionHokkaido University

Principal Investigator

大内 東  北海道大学, 大学院情報科学研究科, 教授 (50002308)

Co-Investigator(Kenkyū-buntansha) 山本 雅人  北海道大学, 大学院情報科学研究科, 助教授 (40292057)
川村 秀憲  北海道大学, 大学院情報科学研究科, 助教授 (60322830)
Project Period (FY) 2002 – 2006
Project Status Completed (Fiscal Year 2006)
Budget Amount *help
¥45,000,000 (Direct Cost: ¥45,000,000)
Fiscal Year 2006: ¥6,600,000 (Direct Cost: ¥6,600,000)
Fiscal Year 2005: ¥7,500,000 (Direct Cost: ¥7,500,000)
Fiscal Year 2004: ¥9,100,000 (Direct Cost: ¥9,100,000)
Fiscal Year 2003: ¥11,700,000 (Direct Cost: ¥11,700,000)
Fiscal Year 2002: ¥10,100,000 (Direct Cost: ¥10,100,000)
KeywordsDNAコンピューティング / 計算精度 / ハイブリダイゼーション / 塩基配列設計 / 二次構造 / 反応効率 / DNAタイル / アクエアスコンピューティング / 最短経路問題 / PCR
Research Abstract

1.自由エネルギーに基づいたハイブリダイゼーション過程の解析
本研究では,ある一本鎖DNAとその完全相補配列,及び,競合する塩基配列を混合した溶液中で起こるハイブリダイゼーションの特徴を自由エネルギーや融解温度の立場から明らかにした.
ある塩基配列Aと完全相補な塩基配列B,及び,Aと部分的に相補な配列を含む塩基配列Cが競合する反応系において,AとBの結合体の最小自由エネルギー,および,融解温度,また,AとCの結合体の最小自由エネルギー,および,融解温度との関係からAとCが結合してしまうミスハイブリダイゼーションの発生割合の分析を行った.検出にはDNAに修飾した蛍光のクエンチングを利用した.結果的に,最小自由エネルギー,および,融解温度の差がミスハイブリダイゼーションに与える影響について,実験結果からモデル式を導出することに成功した.
2.DNAタイルのための塩基配列設計支援システムの構築
昨年度の研究成果を受けて,DNAタイル設計のための塩基配列設計支援システムの構築を行った.DNAタイルは,ナノ構造の形成やタイル計算に用いることが可能であることから近年注目を浴びている.しかしながら,DNAタイルは何本もの一本鎖DNAの結合体であることからその構造安定性を求めることは困難であり,これまで,ヒューリスティックな方法として,重複する連続した部分塩基配列を避ける方法が使用されてきていた.
本研究では,DNAタイルの構造安定性を見積もる方法として,自由エネルギーを用いることにした.2本の一本鎖DNAからできる主な結合体の自由エネルギーを見積もる方法は,これまでの研究で洗練されたものとなっている.このため,DNAタイルの構造体を2本の一本鎖DNAからなる部分に分けて,DNAタイルが望み通りに生成されたときの結合体の自由エネルギーが最も安定となるような尺度を設計することを目的としている.本研究では,設計支援のためのツールを開発した.DNAタイル設計の際には,各部分配列同士の非特異的結合を避けたり,融解温度やGC含量などを考慮したり必要があり,それらを見積もるツールが必要である.また,作成した配列の解析や,山登り法による最適化手法による配列の自動生成も可能である.

Report

(5 results)
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • 2002 Annual Research Report
  • Research Products

    (45 results)

All 2007 2006 2005 2004 Other

All Journal Article (26 results) Publications (19 results)

  • [Journal Article] Unravel four hairpins!2007

    • Author(s)
      Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Satsuki Yaegashi, Masami Hagiya
    • Journal Title

      Natural Computing (online)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Development of DNA Relational Database and Data Manipulation Experiments2006

    • Author(s)
      Masahito Yamamoto, Yutaka Kita, Satoshi Kashiwamura, Atsushi Kameda, Azuma Ohuchi
    • Journal Title

      DNA Computing (DNA12), Lecture Notes in Computer Science 4287

      Pages: 418-427

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Sequence Design for Stable DNA Tiles2006

    • Author(s)
      Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Atsushi Kameda, Azuma Ohuchi
    • Journal Title

      DNA Computing (DNA12), Lecture Notes in Computer Science 4287

      Pages: 172-181

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Specificity of Hybridization between DNA Sequences Based on Free Energy2006

    • Author(s)
      Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      DNA Computing (DNA11), Lecture Notes in Computer Science 3892

      Pages: 371-379

    • Related Report
      2006 Annual Research Report
  • [Journal Article] DNAタイル構造のための塩基配列設計支援システムの構築2006

    • Author(s)
      飯村 直記, 山本 雅人, 田中 文昭, 大内 東
    • Journal Title

      情報処理北海道シンポジウム2006

    • Related Report
      2006 Annual Research Report
  • [Journal Article] DNAを用いたタイル構造における接着結合部の塩基配列設計2006

    • Author(s)
      飯村 直記, 山本 雅人, 田中 文昭, 大内 東
    • Journal Title

      第5回情報科学技術フォーラム(FIT2006)

      Pages: 431-432

    • Related Report
      2006 Annual Research Report
  • [Journal Article] DNA Polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing2006

    • Author(s)
      Ken Komiya, Kensaku Sakamoto, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Dausuke Kiga, Shigeyuki Yokoyama, Masami Hagiya
    • Journal Title

      Biosystems Vol.83, No.1

      Pages: 18-25

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Data Manipulation of DNA Relational Database2006

    • Author(s)
      Yutaka Kita, Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      Proceeding of the 11th International Symposium on Artificial Life and Robotics(AROB 11th '06) Vol.11, No.1

      Pages: 629-632

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Stability evaluation method of DNA tile structure2006

    • Author(s)
      Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Atsushi Kameda, Azuma Ohuchi
    • Journal Title

      Proceeding of the 11th International Symposium on Artificial Life and Robotics(AROB 11th'06) Vol.11, No.1

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNAタイルによる計算論的ナノテクノロジー2006

    • Author(s)
      山本 雅人, 飯村 直記, 田中 文昭, 亀田 充史, 大内 東
    • Journal Title

      第28回日本分子生物学会年会, シンポジウム「ナノバイオテクノロジー・分析からの構築の科学へ」 Vol.28, No1

      Pages: 126-127

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNAタイル構造の安定性評価法2005

    • Author(s)
      飯村 直記, 山本 雅人, 田中 文昭, 亀田 充史, 大内 東
    • Journal Title

      北海道情報処理シンポジウム講演論文集 2005・1

      Pages: 126-127

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNAを記憶素子として用いた分子メモリの開発と大容量化に関する検討2005

    • Author(s)
      柏村 聡, 山本 雅人, 亀田 充史, 大内 東
    • Journal Title

      第4回情報科学技術フォーラム(FIT2005) H-030

      Pages: 357-259

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 自由エネルギーに基づいた塩基配列設計に関する研究2005

    • Author(s)
      田中 文昭, 亀田 充史, 山本 雅人, 大内 東
    • Journal Title

      第4回情報科学技術フォーラム(FIT2005) H-032

      Pages: 375-377

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 自由エネルギーを用いたDNAナノ構造形成のための塩基配列設計2005

    • Author(s)
      飯村 直記, 山本 雅人, 田中 文昭, 亀田 充史, 大内 東
    • Journal Title

      第4回情報科学技術フォーラム(FIT2005) H-031

      Pages: 371-373

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNA分子を利用したリレーショナルデータベースの開発2005

    • Author(s)
      北 豊, 柏村 聡, 亀田 充史, 山本 雅人, 大内 東
    • Journal Title

      第4回情報科学技術フォーラム(FIT2005) A-010

      Pages: 21-23

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNAナノテクノロジー-DNAタイルによる自己組織的ナノ構造制御-2005

    • Author(s)
      山本 雅人
    • Journal Title

      第4回情報科学技術フォーラム(FIT2005)イベント企画チュートリアル「分子計算のしくみ」 Vol.4, No.1

      Pages: 7-11

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Hairpin-based state machine and conformational addressing : Design and experiment2005

    • Author(s)
      Atsushi Kameda, Masahito Yamamoto, Hiroki Uejima, Masami Hagiya, Kensaku Sakamoto, Azuma Ohuchi
    • Journal Title

      Natural Computing Vol.4, No.2

      Pages: 103-126

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Specificity of Hybridization between DNA Sequences Based on Free Energy2005

    • Author(s)
      Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      Proceedings of The 11th International Meeting on DNA Computing Vol.11, No.1

      Pages: 266-375

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Experimental Challenge of Scaled-up Hierarchical DNA Memory Expressing 10,000-Address Space2005

    • Author(s)
      Satoshi Kashiwamura, Masahito Yamamoto, Atsushi Kameda, Azuma Ohuchi
    • Journal Title

      Proceedings of The 11th International Meeting on DNA Computing Vol.11, No.1

      Pages: 396-396

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Potential for Enlarging DNA Memory : Validity of Experimental Operations of Scaled-up Nested Primer Molecular Memory2005

    • Author(s)
      Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      BioSystems : Journal of Biological and Information Processing Science (掲載予定)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Hairpin-based State Machine and Conformational Addressing : Design and Experiment2005

    • Author(s)
      Atsushi Kameda, Masahito Yamamoto, Hiroki Uejima, Masami Hagiya, Kensaku Sakamoto, Azuma Ohuchi
    • Journal Title

      Natural Computing (掲載予定)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Design of nucleic acid sequences for DNA computing based on a thermodynamic approach2005

    • Author(s)
      Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      Nucleic Acids Research 33・3

      Pages: 903-911

    • NAID

      120005955486

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Development, Evaluation and Benchmarking of Simulation Software for Biomolecule-based Computing2004

    • Author(s)
      Derrel Blain, Max Garzon, Soo-Yong Shin, Byoung-Tak Zhang, Satoshi Kashiwamura, Masahito Yamamoto, Atsuhi Kameda, Azuma Ohuchi
    • Journal Title

      Natural Computing 3・4

      Pages: 427-422

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Aqueous Computing with DNA Hairpin-based RAM2004

    • Author(s)
      Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      Preliminary Proceedings of the Tenth International Meeting on DNA Based Computers (DNA10)

      Pages: 50-59

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Thermodynamic Parameters Based on a Nearest-Neighbor Model for DNA Sequences with a Single-Bulge Loop2004

    • Author(s)
      Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      Biochemistry 43・22

      Pages: 7143-7150

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Two-Step Search for DNA Sequence Design2004

    • Author(s)
      Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
    • Journal Title

      IEICE E87-A

      Pages: 1446-1553

    • NAID

      110003213054

    • Related Report
      2004 Annual Research Report
  • [Publications] 山本雅人, 大内 東: "DNAコンピューティングと最適化"平成16年電気学会全国大会講演論文集. 4-S19. 13-16 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi: "General Protocol for Evaluating the Degree of Occurrence of Mis-Hybridization"Proceedings of the Ninth International Symposium on Artificial Life and Robotics (AROB 9th '04). 303-308 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi: "Construction and Verification of DNA Hairpin-based RAM"Proceedings of the Ninth International Symposium on Artificial Life and Robotics (AROB 9th '04). 388-391 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Masashi Nakatsugawa, Masahito Yamamoto, Azuma Ohuchi: "Study of the Efficient Parameter Setting based on Mahalanobis-Taguchi Strategy"Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03). 640-643 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi: "Two Step Search for DNA Sequence Design"Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03). 1815-1818 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Keisuke Hashimoto, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi: "State Transition Model Based on DNA Polymerization"Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03). 1889-1892 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, Azuma, Ohuchi: "Construction of DNA Hairpin based RAM"Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03). 1897-1900 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi: "The Effect on a Bonding Strength by the Freedom of Movement of a DNA strand on a Solid Support in DNA Computing"Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03). 1901-1904 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi: "Nearest-Neighbor Thermodynamics of DNA Sequences with Single Bulge Loop"Proceedings of 9th International Meetings on DNA Based Computers (DNA9). 180-159 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] A.Kameda, M.Yamamoto, H.Uejima, M.Hagiya, K.Sakamoto, A.Ohuchi: "Conformational Addressing using the Hairpin Structure of Single-strand DNA"Proceedings of 9th International Meetings on DNA Based Computers (DNA9). 197-201 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 大内 東, 山本雅人, 川村秀憲, 柴肇一, 高柳俊明, 當間愛晃, 遠藤聡志: "相互作用科学シリーズ生命複雑系からの計算パラダイム"森北出版株式会社. 201 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Masahito Yamamoto: "A Separation Method for DNA Computing Based on Concentration Control"New Generation Computing. 20. 251-261 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Toshikazu Shiba: "Constructions of Security System for Information Encoded by DNA"Preliminary Proceedings of Eighth International Meeting on DNA Based Computers (DNA8). 337-337 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Masashi Nakatsugawa: "Improvement of the Reliability of Experiments in DNA Computing"Preliminary Proceedings of Eighth International Meeting on DNA Based Computers (DNA8). 333-333 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Satoshi Kashiwamura: "Hierarchical DNA Memory based on Nested PCR"Preliminary Proceedings of Eighth International Meeting on DNA Based Computers (DNA8). 231-240 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Atsushi Kameda: "An Analysis of Computational Efficiency on DNA Computing"Proceedings of 3rd International Conference on Unconventional Models of Computation (UMC'02). 191-198 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Yumi Kawazoe: "A Security System for Personal Genome Information at DNA level"Proceedings of IEEE Computer Society Bioinformatics Conference. 314-320 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Masashi Nakatsugawa: "Towards a High Reliability of the PCR Amplification Process in DNA Computing"The International Journal of Computational Intelligence and Applications (IJCIA). 2(4). 423-432 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Masahito Yamamoto: "Local Search by Concentration Controlled DNA Computing"The International Journal of Computational Intelligence and Applications (IJCIA). 2(4). 447-456 (2002)

    • Related Report
      2002 Annual Research Report

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Published: 2002-04-01   Modified: 2018-03-28  

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