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Creation of new genome science using chemical tools to precisely detect modification and damage of human genome

Research Project

Project/Area Number 15H02189
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Bio-related chemistry
Research InstitutionNational Institute for Materials Science

Principal Investigator

Komiyama Makoto  国立研究開発法人物質・材料研究機構, 国際ナノアーキテクトニクス研究拠点, NIMS招聘研究員 (50133096)

Co-Investigator(Kenkyū-buntansha) 須磨岡 淳  東京工科大学, 工学部, 教授 (10280934)
徐 岩  宮崎大学, 医学部, 教授 (40506763)
Co-Investigator(Renkei-kenkyūsha) SHIGI Narumi  物質・材料研究機構, 国際ナノアーキテクトニクス研究拠点, NIMS特別研究員 (00396780)
Tanaka Makiko  電気通信大学, 大学院情報理工学研究科, 助教 (90397703)
Rajendran Arivazhagan  京都大学, エネルギー理工学研究所, 講師 (90723122)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥43,290,000 (Direct Cost: ¥33,300,000、Indirect Cost: ¥9,990,000)
Fiscal Year 2017: ¥12,480,000 (Direct Cost: ¥9,600,000、Indirect Cost: ¥2,880,000)
Fiscal Year 2016: ¥12,480,000 (Direct Cost: ¥9,600,000、Indirect Cost: ¥2,880,000)
Fiscal Year 2015: ¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000)
Keywordsゲノム / PNA / インベージョン / ゲノム断片分離 / エピゲノム / DNA結合タンパク質 / DNAメチル化 / テロメア / DNA損傷
Outline of Final Research Achievements

We already developed super artificial restriction enzyme. In this research, we added affinity separating ability to this tool, and constructed the second- generation super artificial restriction enzyme. By modifying biotin to PNA which is a constituent of super restriction enzyme, we successfully extracted desired DNA fragments of several thousand base pairs in high purity and high yield from the human genome with 3 billion base pairs. Furthermore, by combining this biotin-modified PNA with S1 nuclease, we also succeeded in extracting desired DNA fragments from the human genome in one pot.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (19 results)

All 2017 2016 2015

All Journal Article (13 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 13 results,  Open Access: 5 results) Presentation (6 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results)

  • [Journal Article] Inhibition of nonenzymatic depurination of nucleic acids by polycations2017

    • Author(s)
      Ran An, Ping Dong, Makoto Komiyama, Pan, Xiaoming, Xingguo Liang
    • Journal Title

      FEBS OPEN BIO

      Volume: 7 Issue: 11 Pages: 1707-1714

    • DOI

      10.1002/2211-5463.12308

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Applications of PNA-Based Artificial Restriction DNA Cutters2017

    • Author(s)
      Narumi Shigi, Jun Sumaoka, Makoto Komiyama
    • Journal Title

      MOLECULES

      Volume: 22 Issue: 10 Pages: 1586-1586

    • DOI

      10.3390/molecules22101586

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Suppression of Myogenic Differentiation of Mammalian Cells Caused by Fluidity of a Liquid-Liquid Interface2017

    • Author(s)
      Kosuke Minami, Taizo Mori, Waka Nakanishi, Narumi Shigi, Jun Nakanishi, Jonathan P. Hill, Makoto Komiyama, Katsuhiko Ariga
    • Journal Title

      ACS APPLIED MATERIALS & INTERFACES

      Volume: 9 Issue: 36 Pages: 30553-30560

    • DOI

      10.1021/acsami.7b11445

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration2017

    • Author(s)
      Ran An, Qi Li, Yiqiao Fan, Jing Li, Xiaoming Pan, Makoto Komiyama, Xingguo Liang
    • Journal Title

      NUCLEIC ACIDS RESEARCH

      Volume: 45 Issue: 15 Pages: e139-e139

    • DOI

      10.1093/nar/gkx553

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Site-Selective RNA Activation by Acridine-Modified Oligodeoxynucleotides in Metal-Ion Catalyzed Hydrolysis: A Comprehensive Study2017

    • Author(s)
      Akinori Kuzuya, Kenzo Machida, Yun Shi, Keita Tanaka, Makoto Komiyama
    • Journal Title

      ACS OMEGA

      Volume: 2 Issue: 9 Pages: 5370-5377

    • DOI

      10.1021/acsomega.7b00966

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics2017

    • Author(s)
      Makoto Komiyama, Keitaro Yoshimoto, Masahiko Sisido, Katsuhiko Ariga
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 90 Issue: 9 Pages: 967-1004

    • DOI

      10.1246/bcsj.20170156

    • NAID

      130006077919

    • ISSN
      0009-2673, 1348-0634
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Allosteric control of nanomechanical DNA origami pinching devices for enhanced target binding2017

    • Author(s)
      Akinori Kuzuya, Yusuke Sakai, Takahiro Yamazaki, Yan Xu, Yusei Yamanaka, Yuichi Ohya and Makoto Komiyama
    • Journal Title

      Chemical Communications

      Volume: 53 Issue: 59 Pages: 8276-8279

    • DOI

      10.1039/c7cc03991c

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Design of Highly Active Ce(IV) Catalysts for DNA Hydrolysis and Their Applications2016

    • Author(s)
      Makoto Komiyama
    • Journal Title

      CHEMISTRY LETTERS

      Volume: 45 Issue: 12 Pages: 1347-1355

    • DOI

      10.1246/cl.160786

    • NAID

      130005475734

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ribonuclease A as Effective Promoter for Unimolecular Invasion of Peptide Nucleic Acid to Double-stranded DNA2016

    • Author(s)
      Makiko Tanaka, Narumi Shigi, Makoto Komiyama
    • Journal Title

      CHEMISTRY LETTERS

      Volume: 45 Issue: 7 Pages: 767-769

    • DOI

      10.1246/cl.160340

    • NAID

      130005253013

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Selective Sensing of Tyrosine Phosphorylation in Peptides Using Terbium(III) Complexes2016

    • Author(s)
      Jun Sumaoka, Hiroki Akiba, Makoto Komiyama
    • Journal Title

      INTERNATIONAL JOURNAL OF ANALYTICAL CHEMISTRY

      Volume: 2016 Pages: 1-14

    • DOI

      10.1155/2016/3216523

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fabrication of DNA/RNA hybrids through sequence-specific scission of both strands by pcPNA-SI nuclease combination2016

    • Author(s)
      K. Futai, J. Sumaoka, M. Komiyama
    • Journal Title

      Nucleosides Nucleotides Nucleic Acids

      Volume: 35 Issue: 5 Pages: 233-244

    • DOI

      10.1080/15257770.2015.1131294

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transfection of PNA-NLS Conjugates into Human Cells Using Partially Complementary Oligonucleotides2015

    • Author(s)
      Yuichiro Aiba, Junpei Ohyama, Makoto Komiyama,
    • Journal Title

      CHEMISTRY LETTERS

      Volume: 44 Issue: 11 Pages: 1547-1549

    • DOI

      10.1246/cl.150733

    • NAID

      130005108123

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Affinity-isolation of desired restriction fragment from human genome using double-duplex invasion of biotin-bound pseudo-complementary PNA.2015

    • Author(s)
      N. Shigi, A. Rajendran, X. Wang, H. Kunifuda, J. Sumaoka, M. Komiyama
    • Journal Title

      Chem. Lett.

      Volume: 44 Issue: 11 Pages: 1569-1571

    • DOI

      10.1246/cl.150682

    • NAID

      130005108088

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Presentation] リボヌクレアーゼAによる単一鎖ペプチド核酸の二本鎖DNAへのインベージョン促進2016

    • Author(s)
      田仲真紀子、鴫 成実、小宮山 眞
    • Organizer
      日本化学会 第96春季年会
    • Place of Presentation
      同志社大学 京田辺キャンパス(京都府京田辺市)
    • Year and Date
      2016-03-25
    • Related Report
      2015 Annual Research Report
  • [Presentation] Covalent and Noncovalent Approaches to Promote PNA Invasion for In Vivo Applications2015

    • Author(s)
      Makoto Komiyama
    • Organizer
      The 2015 International Chemical Congress of Pacific Basin Societies
    • Place of Presentation
      Hawaii (USA)
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Chemical Tools to Isolate a Desired Fragment from Human Genome.2015

    • Author(s)
      Makoto Komiyama
    • Organizer
      The 2015 International Chemical Congress of Pacific Basin Societies
    • Place of Presentation
      Hawaii (USA)
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] リボヌクレアーゼAによる単一鎖ペプチド核酸の二本鎖DNAへのインベージョン促進2015

    • Author(s)
      田仲 真紀子、鴫 成実、小宮山 眞
    • Organizer
      第38回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-04
    • Related Report
      2015 Annual Research Report
  • [Presentation] ビオチン化pcPNAプローブによるヒトゲノムの特定領域断片の濃縮法の開発2015

    • Author(s)
      鴫(日野) 成実、アリワラガン ラジェンドラン、王 曉輝、国府田 寛子、須磨岡 淳、小宮山 眞
    • Organizer
      第38回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-03
    • Related Report
      2015 Annual Research Report
  • [Presentation] シクロデキストリン化学の変遷2015

    • Author(s)
      小宮山眞
    • Organizer
      8th Asian Cyclodextrin Conference/第32回シクロデキストリンシンポジウム合同会議
    • Place of Presentation
      くまもと県民交流館パレア(熊本県熊本市)
    • Year and Date
      2015-05-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited

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Published: 2015-04-16   Modified: 2019-03-29  

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