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Development of novel platform to rationally design DNA origami

Research Project

Project/Area Number 18K18144
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionTohoku University

Principal Investigator

Kawamata Ibuki  東北大学, 工学研究科, 助教 (30733977)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2020: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
KeywordsDNAオリガミ / DNAナノテクノロジー / DNAコンピュータ / データベース / 設計ソフトウェア / 分子ロボティクス / 分子サイバネティクス / DNA超分子
Outline of Final Research Achievements

In this research about DNA origami nanostructure, (1) a database of design information, (2) a software to design a complex DNA nanostructure, (3) a platform of simulation, were developed. All the tools run on a web browser, which may enable non-experts to benefit from them in a simple manner. Moreover, using the know-how obtained by the research, various DNA origami structures were successfully made and the functionalities of them were experimentally evaluated. The results of them are published in research paper and presented in academic conferences. A book about DNA origami is also planned to be published in May, 2021.

Academic Significance and Societal Importance of the Research Achievements

本研究で開発したDNAオリガミナノ構造体のためのソフトウェアや、本研究期間中に執筆したDNAオリガミに関する書籍は、分野への新規参入者に対する障壁を最小化し、自己組織化を用いた分子ナノテクノロジーの発展に寄与するものと考えている。その例題として申請者は、細胞の膜モデルに穴を開ける筒状のDNAナノ構造や、変形と結合の様式をプログラム可能なのDNAオリガミ分子材料などの開発に成功した。これらの研究は将来的に、スマートな投薬制御や、自己修復材料の創発につながると期待される。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (27 results)

All 2021 2020 2019 2018 Other

All Journal Article (11 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 11 results,  Open Access: 8 results) Presentation (12 results) (of which Int'l Joint Research: 3 results,  Invited: 2 results) Book (3 results) Remarks (1 results)

  • [Journal Article] Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures2021

    • Author(s)
      Yudai Yamashita, Kotaro Watanabe, Satoshi Murata, Ibuki Kawamata
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 21 Issue: 0 Pages: 28-38

    • DOI

      10.1273/cbij.21.28

    • NAID

      130008031759

    • ISSN
      1347-0442, 1347-6297
    • Year and Date
      2021-04-30
    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Large, square-shaped, DNA origami nanopore with sealing function on giant vesicle membrane2021

    • Author(s)
      Shoji Iwabuchi, Ibuki Kawamata, Satoshi Murata, Shin-Ichiro M. Nomura
    • Journal Title

      Chemical Communications

      Volume: 57 Issue: 24 Pages: 2990-2993

    • DOI

      10.1039/d0cc07412h

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Chemo-mechanical Modulation of Cell Motions Using DNA Nanosprings2021

    • Author(s)
      Deepak Karna, Morgan Stilgenbauer, Sagun Jonchhe, Kazuya Ankai, Ibuki Kawamata, Yunxi Cui, Yaorong Zheng, Yuki Suzuki, Hanbin Mao
    • Journal Title

      Bioconjugate Chemistry

      Volume: 32 Issue: 2 Pages: 311-317

    • DOI

      10.1021/acs.bioconjchem.0c00674

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Cascaded pattern formation in hydrogel medium using the polymerisation approach2021

    • Author(s)
      Keita Abe, Satoshi Murata, Ibuki Kawamata
    • Journal Title

      Soft Matter

      Volume: -

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] DNA Ring Motif with Flexible Joints2020

    • Author(s)
      Liu Shiyun、Murata Satoshi、Kawamata Ibuki
    • Journal Title

      Micromachines

      Volume: 11 Issue: 11 Pages: 987-987

    • DOI

      10.3390/mi11110987

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Large deformation of a DNA origami nanoarm through the cumulative actuation of tension-adjustable modules2020

    • Author(s)
      Yuki Suzuki, Ibuki Kawamata, Kohei Mizunom Satoshi Murata
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 59 Issue: 15 Pages: 6230-6234

    • DOI

      10.1002/anie.201916233

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] DNA Origami “Quick” Refolding inside of a Micron-Sized Compartment2020

    • Author(s)
      Taiki Watanabe, Yusuke Sato, Hayato Otaka, Ibuki Kawamata, Satoshi Murata, Shin-Ichiro M. Nomura
    • Journal Title

      Molecules

      Volume: 25 Issue: 1 Pages: 8-8

    • DOI

      10.3390/molecules25010008

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Isothermal amplification of specific DNA molecules inside giant unilamellar vesicles2019

    • Author(s)
      Yusuke Sato, Ken Komiya, Ibuki Kawamata, Satoshi Murata, Shin-ichiro M. Nomura
    • Journal Title

      Chemical Communications

      Volume: 印刷中 Issue: 62 Pages: 9084-9087

    • DOI

      10.1039/c9cc03277k

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Programmable reactions and diffusion using DNA for pattern formation in hydrogel medium2019

    • Author(s)
      Keita Abe, Ibuki Kawamata, Shin-ichiro M. Nomura, Satoshi Murata
    • Journal Title

      Molecular Systems Design & Engineering

      Volume: accepted Issue: 3 Pages: 639-643

    • DOI

      10.1039/c9me00004f

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Pattern Formation on Discrete Gel Matrix based on DNA Computing2019

    • Author(s)
      Takuto Hosoya, Ibuki Kawamata, Shin-ichiro M. Nomura, Satoshi Murata
    • Journal Title

      New Generation Computing

      Volume: 37 Issue: 1 Pages: 97-111

    • DOI

      10.1007/s00354-018-0047-1

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Diffusion modulation of DNA by toehold exchange2018

    • Author(s)
      Thanapop Rodjanapanyakul, Fumi Takabatake, Keita Abe, Ibuki Kawamata, Shin-ichiro M. Nomura, Satoshi Murata
    • Journal Title

      Physical Review E

      Volume: 97 Issue: 5 Pages: 052617-052617

    • DOI

      10.1103/physreve.97.052617

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Presentation] Analysis of wireframe DNA nanostructure based on coarse-grained molecular dynamics simulated on a web server with simple interface2020

    • Author(s)
      Ibuki Kawamata, Yudai Yamashita, Kotaro Watanabe, Sho Aradachi, Satoshi Murata
    • Organizer
      Chem-Bio Informatics Society (CBI) Annual Meeting 2020
    • Related Report
      2020 Annual Research Report
  • [Presentation] 筒状DNAオリガミ構造によるリポソーム内外の分子拡散にむけて2019

    • Author(s)
      川又生吹, 岩渕祥璽, 野村 M. 慎一郎, 村田智
    • Organizer
      SIG-MBI
    • Related Report
      2019 Research-status Report
  • [Presentation] Current and Future Trends of DNA Molecule Computation2019

    • Author(s)
      Ibuki Kawamata
    • Organizer
      SIG-NAC
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] A database to store design information of DNA nanostructure2019

    • Author(s)
      Ibuki Kawamata, Sho Aradachi, Satoshi Murata
    • Organizer
      Molecular Robotics Session, Chem-Bio Informatics Society (CBI) Annual Meeting 2019
    • Related Report
      2019 Research-status Report
  • [Presentation] Toward molecular diffusion through liposome membrane using DNA origami structure2019

    • Author(s)
      Ibuki Kawamata, Shoji Iwabuchi, Shin-ichiro M. Nomura, Satoshi Murata
    • Organizer
      Japanese Society for Cell Synthesis Research 12.0
    • Related Report
      2019 Research-status Report
  • [Presentation] A database of cadnano file to store design information of DNA nanostructure2019

    • Author(s)
      Ibuki Kawamata, Sho Aradachi, Satoshi Murata
    • Organizer
      the 25th International Conference on DNA Computing and Molecular Programming (DNA25)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Toward making a database of design information of DNA nanostructure2019

    • Author(s)
      Ibuki Kawamata, Sho Aradachi, Satoshi Murata
    • Organizer
      Nucleic Acid Nanotechnology: from algorithmic design to biochemical applications (NANTECH2019)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Programming DNA reaction-diffusion system for pattern formation in hydrogel medium2019

    • Author(s)
      Ibuki Kawamata
    • Organizer
      Shaping Self-Assembled Mesoscale (Bio)Materials with Microengineering
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 基礎から学ぶ DNAナノ構造体の設計2018

    • Author(s)
      川又生吹.
    • Organizer
      分子ロボ若手会
    • Related Report
      2018 Research-status Report
  • [Presentation] Modulating diffusion speed of DNA by toehold exchange2018

    • Author(s)
      Ibuki Kawamata, Thanapop Rodjanapanyakul, Fumi Takabatake, Keita Abe, Shin-ichiro M. Nomura, Satoshi Murata
    • Organizer
      The 45th International Symposium on Nucleic Acids Chemistry (ISNAC 2018)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Autonomous and Programmable Strand Generator Implemented as DNA Chemical Reaction Network2018

    • Author(s)
      Ibuki Kawamata, Satoshi Murata
    • Organizer
      The Society of Instrument and Control Engineers Annual Conference (SICE 2018)
    • Related Report
      2018 Research-status Report
  • [Presentation] 基礎から学ぶ DNAナノ構造体の設計2018

    • Author(s)
      川又生吹
    • Organizer
      産総研BMRI若手会・新学術「分子ロボ」若手会ジョイントセミナー
    • Related Report
      2018 Research-status Report
  • [Book] DNA origami入門 基礎から学ぶDNAナノ構造体の設計技法2021

    • Author(s)
      川又生吹, 鈴木勇輝, 村田智
    • Total Pages
      272
    • Publisher
      オーム社
    • ISBN
      9784274227134
    • Related Report
      2020 Annual Research Report
  • [Book] 分子ロボティクス概論 分子のデザインでシステムを創る2019

    • Author(s)
      川又生吹, 他 (分子ロボティクス研究会著), 村田智編
    • Total Pages
      312
    • Publisher
      eBook Series No.3 情報計算化学生物学会 (CBI学会)出版
    • ISBN
      9784990907648
    • Related Report
      2019 Research-status Report
  • [Book] 分子ロボティクス概論2019

    • Author(s)
      分子ロボティクス研究会
    • Total Pages
      302
    • Publisher
      CBI
    • ISBN
      9784990907648
    • Related Report
      2018 Research-status Report
  • [Remarks] Ibuki Kawamata

    • URL

      https://ibuki-kawamata.org/

    • Related Report
      2020 Annual Research Report

URL: 

Published: 2018-04-23   Modified: 2022-01-27  

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