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Synthesis and function analysis of mini-chromosome model

Research Project

Project/Area Number 19K22245
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 37:Biomolecular chemistry and related fields
Research InstitutionThe University of Tokyo

Principal Investigator

Okamoto Akimitsu  東京大学, 先端科学技術研究センター, 教授 (60314233)

Project Period (FY) 2019-06-28 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2019: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Keywords化学合成 / クロマチン / DNA / ヒストン / ペプチド / ヌクレオソーム / エピジェネティクス / ライゲーション / 染色体 / 蛍光標識
Outline of Research at the Start

本研究課題では、長鎖DNAの反応解析に存在する構造上の問題点を解消してゲノム機能研究への発展を誘起するために、人工的なミニ染色体モデルの作製とその作製の要素技術を構築する。さらに、獲得したミニ染色体モデルを用いて、構造解析と化学反応解析を進めて、生物機能における染色体構造の役割を明らかにする。

Outline of Final Research Achievements

(1) Chemical synthesis of the mini-chromosome model...We have completed the synthesis of the DNA units to be connected. There are two types of DNA units, each containing the Widom601 DNA sequence, and the units have protruding ends with sequences corresponding to restriction enzymes.
(2) Chemical synthesis of functional histones in mini-chromosome models... We developed a one-pot method for connecting multiple peptides using organoruthenium catalysts that are stable in air. The organoruthenium catalyst was 50 times more active than the conventional palladium complex. Using this organoruthenium catalyst, we synthesized heterochromatin factors with site-specific post-translational modifications such as phosphorylation, ubiquitination, citrullination, and acetylation.

Academic Significance and Societal Importance of the Research Achievements

ミニ染色体モデルを創出する方法を確立することに意義がある。任意の配列を含む染色体構造を人工的に作ることはまだ可能になっていない。この方法が確立できれば、簡便に目的の配列や人工的な機能性修飾を含むミニ染色体モデルを獲得することが可能になり、飛躍的に染色体機能研究が進むと考えられる。また、ミニ染色体モデルを創出することにより、細胞内DNA本来の構造や反応に関わる情報を獲得できるようになる。

Report

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

    (45 results)

All 2021 2020 2019 2018

All Journal Article (20 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 20 results,  Open Access: 7 results) Presentation (25 results) (of which Int'l Joint Research: 4 results,  Invited: 1 results)

  • [Journal Article] Floxuridine Oligomers Activated under Hypoxic Environment2021

    • Author(s)
      Morihiro, K.; Ishinabe, T.; Takatsu, M.; Osumi, H.; Osawa, T.; Okamoto, A.
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 143 Issue: 9 Pages: 3340-3347

    • DOI

      10.1021/jacs.0c10732

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Organoruthenium-Catalyzed Chemical Protein Synthesis to Elucidate the Functions of Epigenetic Modifications on Heterochromatin Factors2021

    • Author(s)
      Kamo, N.; Kujirai, T.; Kurumizaka, H.; Murakami, H.; Hayashi, G.; Okamoto, A.
    • Journal Title

      Chem. Sci.

      Volume: 12 Issue: 16 Pages: 5926-5937

    • DOI

      10.1039/d1sc00731a

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Light-inducible control of cellular proliferation and differentiation by a Hedgehog signaling inhibitor2021

    • Author(s)
      Misawa Ryuji、Minami Tsuyoshi、Okamoto Akimitsu、Ikeuchi Yoshiho
    • Journal Title

      Bioorganic & Medicinal Chemistry

      Volume: 38 Pages: 116144-116144

    • DOI

      10.1016/j.bmc.2021.116144

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Toolbox for chemically synthesized histone proteins2020

    • Author(s)
      Nakatsu, K.; Hayashi, G.; Okamoto, A.
    • Journal Title

      Curr. Opin. Chem. Biol.

      Volume: 58 Pages: 10-19

    • DOI

      10.1016/j.cbpa.2020.04.016

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A light-inducible Hedgehog signaling activator modulates proliferation and differentiation of neural cells.2020

    • Author(s)
      Ryuji Misawa, Tsuyoshi Minami, Akimitsu Okamoto, Yoshiho Ikeuchi.
    • Journal Title

      ACS Chemical Biology

      Volume: - Issue: 6 Pages: 1595-1603

    • DOI

      10.1021/acschembio.0c00195

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fmoc-Compatible and C-terminal-Sequence-Independent Peptide Alkyl Thioester Formation Using Cysteinylprolyl Imide2020

    • Author(s)
      Nakatsu, K.; Yanase, M.; Hayashi, G.; Okamoto, A.
    • Journal Title

      Org. Lett.

      Volume: 22 Issue: 12 Pages: 4670-4674

    • DOI

      10.1021/acs.orglett.0c01450

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Single cell array enclosed with a photodegradable hydrogel in microwells for image-based cell classification and selective photorelease of cells2020

    • Author(s)
      Yamaguchi, S.; Takagi, R.; Hosogane, T.; Ohashi, Y.; Sakai, Y.; Sakakihara, S.; Iino, R.; Tabata, K.; Noji, H.; Okamoto, A.
    • Journal Title

      ACS Appl. Bio Mater.

      Volume: 3 Issue: 9 Pages: 5887-5895

    • DOI

      10.1021/acsabm.0c00583

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Monitoring intracellular metal ion complexation with acetylene-tagged ligand by Raman spectroscopy2020

    • Author(s)
      Takemura, S.; Watanabe, H.; Nishihara, T.; Okamoto, A.; Tanabe, K.
    • Journal Title

      RSC Adv.

      Volume: 10 Issue: 59 Pages: 36119-36123

    • DOI

      10.1039/d0ra06329k

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] L-DNA-tagged fluorescence in situ hybridization for highly sensitive imaging of RNAs in single cells2020

    • Author(s)
      Ogata, M.; Hayashi, G.; Ichiu, A.; Okamoto, A.
    • Journal Title

      Org. Biomol. Chem.

      Volume: 18 Issue: 40 Pages: 8084-8088

    • DOI

      10.1039/d0ob01635g

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Acetylation-modulated communication between the H3 N-terminal tail domain and the intrinsically disordered H1 C-terminal domain2020

    • Author(s)
      Hao, F; Murphy, K. J.; Kujirai, T.; Kamo, N.; Kato, J.; Koyama, M.; Okamato, A.; Hayashi, G.; Kurumizaka, H.; Hayes, J. J.
    • Journal Title

      Nucleic Acids Res.

      Volume: 48 Issue: 20 Pages: 11510-11520

    • DOI

      10.1093/nar/gkaa949

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A highly constrained nucleic acid analog based on α-L-threosamine2020

    • Author(s)
      Morihiro, K.; Okamoto, A.
    • Journal Title

      Nucleosides Nucleotides Nucleic Acids

      Volume: 39 Issue: 1-3 Pages: 270-279

    • DOI

      10.1080/15257770.2019.1666278

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Live Cell Sensing of Telomerase Activity Using Hybridization-Sensitive Fluorescent Oligonucleotide Probes2020

    • Author(s)
      Chen, J.; Morihiro, K.; Fukui, D.; Guo, L.; Okamoto, A.
    • Journal Title

      ChemBioChem

      Volume: 21 Issue: 7 Pages: 1022-1027

    • DOI

      10.1002/cbic.201900555

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Efficient Ketose Production by Hydroxyapatite Catalyst in a Continuous Flow Module2019

    • Author(s)
      Usami, K.; Xiao, K.; Okamoto, A.
    • Journal Title

      ACS Sustainable Chem. Eng.

      Volume: 7 Issue: 3 Pages: 3372-3377

    • DOI

      10.1021/acssuschemeng.8b05574

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reversible and Photoresponsive Immobilization of Nonadherent Cells by Spiropyran-Conjugated PEG-Lipids2019

    • Author(s)
      Izuta, S.; Yamaguchi, S.; Kosaka, T.; Okamoto, A.
    • Journal Title

      ACS Appl. Bio Mater.

      Volume: 2 Issue: 1 Pages: 33-38

    • DOI

      10.1021/acsabm.8b00656

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Supramolecular Polymeric Hydrogels for Ultrasound-guided Protein Release2019

    • Author(s)
      Yamaguchi, S; Higashi, K.; Azuma, T.; Okamoto, A.
    • Journal Title

      Biotechnol. J.

      Volume: 14 Issue: 5 Pages: 1800530-1800530

    • DOI

      10.1002/biot.201800530

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Cysteinylprolyl imide (CPI) peptide: a highly reactive and easily accessible crypto-thioester for chemical protein synthesis2019

    • Author(s)
      Yanase Masafumi、Nakatsu Koki、Cardos Charlane Joy、Konda Yoshiki、Hayashi Gosuke、Okamoto Akimitsu
    • Journal Title

      Chemical Science

      Volume: 10 Issue: 23 Pages: 5967-5975

    • DOI

      10.1039/c9sc00646j

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Simultaneous and Traceless Ligation of Peptide Fragments on DNA Scaffold.2019

    • Author(s)
      Hayashi G, Yanase M, Nakatsuka Y, Okamoto A.
    • Journal Title

      Biomaclomolecules

      Volume: 20 Issue: 3 Pages: 1246-1253

    • DOI

      10.1021/acs.biomac.8b01655

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Chemical Synthesis of Cys-Containing Protein via Chemoselective Deprotection with Different Palladium Complexes2019

    • Author(s)
      Kamo, N.; Hayashi, G.; Okamoto, A.
    • Journal Title

      Org. Lett.

      Volume: 21 Issue: 20 Pages: 8378-8382

    • DOI

      10.1021/acs.orglett.9b03152

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Photo-responsive materials with strong cell trapping ability for light-guided manipulation of nonadherent cells2019

    • Author(s)
      Jarzebska, N. A.; Yamaguchi, S.; Izuta, S.; Kosaka, T.; Yamahira, S.; Nagamune, T.; Okamoto, A.
    • Journal Title

      Biomater. Sci.

      Volume: 7 Issue: 11 Pages: 4514-4518

    • DOI

      10.1039/c9bm01200a

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study2018

    • Author(s)
      Shiraogawa Takafumi、Candel Gaelle、Fukuda Ryoichi、Ciofini Ilaria、Adamo Carlo、Okamoto Akimitsu、Ehara Masahiro
    • Journal Title

      Journal of Computational Chemistry

      Volume: 40 Issue: 1 Pages: 127-134

    • DOI

      10.1002/jcc.25553

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] ニトロ基およびアゾ基の生体還元を利用したFloxuridineオリゴマーの低酸素活性化2021

    • Author(s)
      森廣 邦彦、石鍋 拓郎、高津 正子、大澤 毅、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 細胞内タンパク質送達を指向した刺激溶解性タンパク質凝集体の開発2021

    • Author(s)
      山本 一穂、山口 哲志、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 光化学インターナリゼーションに有効な近赤外光吸収色素の合成と評価2021

    • Author(s)
      濵邉 美佳子、出羽 和花子、大橋 瑠子、浜窪 隆雄、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 細胞膜透過性を指向する含フッ素オリゴヌクレオチドの合成と評価2021

    • Author(s)
      渡邉 ほの香、相川 光介、森廣 邦彦、岡本 晃充、岡添 隆
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 光誘起型伸長反応を用いたポリユビキチンの鎖長制御手法の確立2021

    • Author(s)
      村山 伊織、古畑 隆史、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 固相合成に適したチオエステル前駆体システイニルプロリルイミドによるタンパク質化学合成2021

    • Author(s)
      中津 幸輝、梁瀬 将史、林 剛介、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 生体分子の選択的可視化を実現する光活性化アルキンタグ2021

    • Author(s)
      中村 聖、山口 哲志、小阪 高広、中村 元直、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 細胞膜裏側の定量的1細胞解析のための細胞膜シートアレイの開発2021

    • Author(s)
      梅田 侑生、山口 哲志、山平 真也、中村 元直、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Ru触媒を用いたリンカーヒストンH1.2とHP1αの化学合成とその翻訳後修飾の機能解析2021

    • Author(s)
      加茂 直己、鯨井 智也、胡桃坂 仁志、村上 裕、林 剛介、岡本 晃充
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] The use of cysteinylprolyl imide peptide as an Fmoc-compatible crypto-thioester2020

    • Author(s)
      Koki Nakatsu、Masafumi Yanase、Gosuke Hayashi、Akimitsu Okamoto
    • Organizer
      第57回ペプチド討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Total chemical synthesis of linker histone H1.2 and heterochromatin protein 1 alpha through one-pot multiple peptide ligation using Ru catalyst2020

    • Author(s)
      Naoki Kamo、Gosuke Hayashi、Tomoya Kujirai、Hitoshi Kurumizaka、Hiroshi Murakami、Akimitsu Okamoto
    • Organizer
      第57回ペプチド討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 低酸素環境下で活性化するFluoxuridineオリゴマーの開発2020

    • Author(s)
      森廣 邦彦、石鍋 拓郎、高津 正子、岡本 晃充
    • Organizer
      第14回バイオ関連化学シンポジウム
    • Related Report
      2020 Annual Research Report
  • [Presentation] 金属イオン曝露によるDNAメチル化レベル変化の蛍光解析2020

    • Author(s)
      森廣 邦彦、劉 杉、竹内 芙美香、岡本 晃充
    • Organizer
      第42回日本光医学・光生物学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 感光性クリック試薬を用いた異種細胞位置制御技術の開発2019

    • Author(s)
      小阪 高広、山口 哲志、泉田 森、岡本 晃充
    • Organizer
      生体機能関連化学部会若手の会 第31回サマースクール
    • Related Report
      2019 Research-status Report
  • [Presentation] タンパク質化学合成を指向したチオエステル前駆体CPI(Cysteinylprolyl imide) の設計と機能評価2019

    • Author(s)
      中津 幸輝、梁瀬 将史、林 剛介、岡本 晃充
    • Organizer
      生体機能関連化学部会若手の会 第31回サマースクール
    • Related Report
      2019 Research-status Report
  • [Presentation] 細胞内分子動態解析のための光活性化アルキンタグ2019

    • Author(s)
      中村 聖、山口 哲志、小阪 高広、岡本 晃充
    • Organizer
      2019年度生物工学若手研究者の集い(若手会)夏のセミナー
    • Related Report
      2019 Research-status Report
  • [Presentation] ターンオン型蛍光プローブを用いたテロメラーゼ活性の生細胞内センシング2019

    • Author(s)
      森廣 邦彦、Jiazhuo Chen, 福井 大介、Guo Lihao、岡本 晃充
    • Organizer
      第41回日本光医学・光生物学会
    • Related Report
      2019 Research-status Report
  • [Presentation] Inorganic reactions for analysis of epigenetically modified DNA2019

    • Author(s)
      Akimitsu Okamoto
    • Organizer
      19th International Conference on Biological Inorganic Chemistry (ICBIC-19)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 細胞運理を志向した光溶解性ゲル充填マイクロウェルアレイ2019

    • Author(s)
      山口 哲志、細金 剛、大橋 友紀、榊原 昇一、田端 和仁、野地 博行、岡本 晃充
    • Organizer
      第13回バイオ関連化学シンポジウム
    • Related Report
      2019 Research-status Report
  • [Presentation] ターンオン型蛍光オリゴヌクレオチドプローブを用いたテロメラーゼ活性の生細胞内センシング2019

    • Author(s)
      森廣 邦彦、Chen Jiazhuo、福井 大介、Guo Lihao、岡本 晃充
    • Organizer
      第13回バイオ関連化学シンポジウム
    • Related Report
      2019 Research-status Report
  • [Presentation] 1細胞間相互作用解析のための光誘導型クリック反応表面2019

    • Author(s)
      小阪 高広、山口 哲志、泉田 森、岡本 晃充
    • Organizer
      第13回バイオ関連化学シンポジウム
    • Related Report
      2019 Research-status Report
  • [Presentation] Chemical Reactions for Analysis of Epigenetically Modified DNA2019

    • Author(s)
      Akimitsu Okamoto
    • Organizer
      Epigenetics & Bioengineering Coference (EpiBio 2019)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 光反応性クリック試薬を用いた細胞間相互作用解析手法の開発2019

    • Author(s)
      小阪 高広、山口 哲志、泉田 森、岡本 晃充
    • Organizer
      第68回高分子討論会
    • Related Report
      2019 Research-status Report
  • [Presentation] Photo-responsive cell immobilization reagents for cell manipulation on solid phase2019

    • Author(s)
      Satoshi Yamaguchi, Shin Izuta, Shinya Yamahara, Teruyuki Nagamune, Akimitsu Okamoto
    • Organizer
      The 18th Asian Pacific Confederation of Chemical Engineering Congress (APCChE2019)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Live-Cell Sensing of Telomerase Activity2019

    • Author(s)
      Akimitsu Okamoto, Kunihiko Morihiro, Jiazhuo Chen, Daisuke Fukui and Lihao Guo
    • Organizer
      Asia 3 Roundtable of Nucleic Acid 2019 (A3RONA)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited

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Published: 2019-07-04   Modified: 2022-01-27  

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