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Efficient functional design of artificial DNA using order-N elongation method

Research Project

Project/Area Number 25810103
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Bio-related chemistry
Research InstitutionKyushu University

Principal Investigator

ORIMOTO YUUICHI  九州大学, グリーンアジア国際リーダー教育センター, 助教 (00398108)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2013: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywords機能性人工核酸 / DNA / 電子状態計算 / O(N) Elongation法 / スルースペース/ボンド相互作用解析法 / 導電性・半導体性 / 強磁性 / 非線形光学(NLO)特性 / 導電性
Outline of Final Research Achievements

We aim to develop a new theoretical method to design functions of artificial DNA (ADNA) using our developed linear-scaling elongation (ELG) method. In the ELG method, the electronic structure of a large system can be elongated sequentially with keeping high computational accuracy. For the purpose, a “property optimization ELG method” was developed and applied to the optimization of non-linear optical properties in DNA. It was found that the method can automatically choose appropriate base pair unit for each ELG step according to an optimization condition defined in advance. Then, its effectiveness was confirmed by test optimizations. Furthermore, we obtained useful knowledge for the functional design by investigating the change in frontier orbitals of various chemically-modified ADNAs, pitch angle dependence of magnetic property in metal-mediated ADNAs, and so on.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (9 results)

All 2015 2014 2013

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Acknowledgement Compliant: 1 results) Presentation (7 results) (of which Int'l Joint Research: 2 results)

  • [Journal Article] Elongation method for electronic structure calculations of random DNA sequences2015

    • Author(s)
      Yuuichi Orimoto, Kai Liu, and Yuriko Aoki
    • Journal Title

      J. Comput. Chem.

      Volume: 36 Issue: 28 Pages: 2103-2113

    • DOI

      10.1002/jcc.24047

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems2015

    • Author(s)
      Yuuichi Orimoto, Ryohei Yamamoto, Peng Xie, Kai Liu, Akira Imamura, and Yuriko Aoki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 142 Issue: 10 Pages: 104111-104111

    • DOI

      10.1063/1.4913931

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Computational functional design of artificial DNAs: application of elongation method and through-space /bond interaction analysis2015

    • Author(s)
      Yuuichi Orimoto and Yuriko Aoki
    • Organizer
      The 42th International Symposium on Nucleic Acids Chemistry (ISNAC2015)
    • Place of Presentation
      Himeji(JAPAN): I-messae hall
    • Year and Date
      2015-09-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 機能性人工核酸の理論的分子設計~導電性・強磁性・非線形光学特性~2015

    • Author(s)
      折本 裕一、青木 百合子
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京(東京工業大学 大岡山キャンパス)
    • Year and Date
      2015-09-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] Highly efficient electronic structure calculations of biomaterials for their functional design2015

    • Author(s)
      Yuuichi Orimoto and Yuriko Aoki
    • Organizer
      2015 International Symposium for Advanced Materials Research (ISAMR 2015)
    • Place of Presentation
      Sun Moon Lake (Taiwan): Sun Moon Lake Teachers' Hostel
    • Year and Date
      2015-08-19
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] π電子集積体としての天然・人工DNAの超効率的O(N)電子状態計算とその特性解析2014

    • Author(s)
      折本 裕一、河村 祐希、Kai Liu、青木 百合子
    • Organizer
      第63回高分子討論会
    • Place of Presentation
      長崎大学 文教キャンパス
    • Year and Date
      2014-09-25
    • Related Report
      2014 Research-status Report
  • [Presentation] 超効率的電子状態計算と軌道間相互作用解析による人工DNAの理論的機能設計2014

    • Author(s)
      折本 裕一、河村 祐希、Liu Kai、青木 百合子
    • Organizer
      第8回分子科学討論会
    • Place of Presentation
      広島大学 東広島キャンパス
    • Year and Date
      2014-09-22
    • Related Report
      2014 Research-status Report
  • [Presentation] Functional design of natural and artificial nucleic acids via ab initio order-N elongation method: computational approaches2013

    • Author(s)
      Yuuichi Orimoto, Liu Kai, and Yuriko Aoki
    • Organizer
      The 40th International Symposium on Nucleic Acids Chemistry (ISNAC2013)
    • Place of Presentation
      Kanagawa University
    • Related Report
      2013 Research-status Report
  • [Presentation] Highly effcient O(N) calculations of natural and artificial DNAs by elongation method2013

    • Author(s)
      Y. Orimoto, L. Kai, and Y. Aoki
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都テルサ(京都府民総合交流プラザ)
    • Related Report
      2013 Research-status Report

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Published: 2014-07-25   Modified: 2019-07-29  

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