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Elucidating Higher-Order DNA and RNA Structures in Cells via 19F NMR Molecular Technology

Research Project

Project/Area Number 21H02081
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 37030:Chemical biology-related
Research InstitutionUniversity of Miyazaki

Principal Investigator

Xu Yan  宮崎大学, 医学部, 教授 (40506763)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
Fiscal Year 2023: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2022: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2021: ¥7,540,000 (Direct Cost: ¥5,800,000、Indirect Cost: ¥1,740,000)
Keywords19F NMR / 核酸高次構造 / Z-form / G-quadruplex / 四重鎖RNA / 分子プローブ / 19F-NMR / DNA・RNA高次構造
Outline of Research at the Start

ヒト細胞内のDNA及びRNA高次構造は重要な生物学的役割を果たし、いくつかの疾患と重要な関係がある。ヒト細胞内のDNA及びRNA高次構造を調べることは、それら高次構造の生物学的機能の理解と疾患治療薬の開発に役立つ。しかし、現在、最も有力な構造生物学的手法は、生きた細胞に適用できないため、現状では細胞内での高次構造を直接解析する有効な手段は少ない。本研究計画では、フッ素を含む19F-NMRセンサーを創製し、DNA及びRNA配列に導入して、In-Cell 19F-NMRによりヒト細胞中におけるDNA及びRNA高次構造を解析する。またこれらの高次構造とタンパク質の相互作用を解明する。

Outline of Final Research Achievements

Higher-order nucleic acid structures such as Z-form and G-quadruplex play important biological roles. This research aims to elucidate structures like Z-form and G-quadruplex using molecular technologies including 19F NMR, and to establish a foundation for investigating the essential biological functions of these higher-order structures. (1) On the elucidation of Z-form structures and functions: We successfully developed nucleic acid molecules that stabilize the Z-form structure. Collaborative research revealed that severe influenza is associated with left-handed Z-form RNA viruses (Cell 181, 1115, 2020), and that cancer immune checkpoints are linked to left-handed Z-form nucleic acids (Nature 606, 594, 2022). (2) On RNA higher-order structures: We demonstrated that RNA higher-order structures can cause neurological dysfunction via phase transitions into solid-like states (Commun. Biol. 7, 137, 2024).

Academic Significance and Societal Importance of the Research Achievements

本研究のZ型核酸がウイルス感染やがん免疫応答と深く関与することを示した成果は、核酸構造研究に新たな概念をもたらすものであり、核酸の構造と機能を分子レベルで解明する研究基盤を築くものである。またRNAの相転移による神経障害メカニズムの解明は、RNA生物学の新たな展開を示した。Z型RNAがウイルス重症化の要因であること、Z型DNA/RNAががん免疫応答に関与すること、そしてRNA高次構造が神経変性疾患に関与する可能性を示した本研究の成果は、今後の新規治療法の開発に直結する社会的インパクトを待つ。特に、ウイルス感染症やがん、更に神経疾患に対して、構造に基づいた分子標的医療の道を切り開く可能性がある。

Report

(4 results)
  • 2024 Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (28 results)

All 2025 2024 2023 2022 2021 Other

All Int'l Joint Research (4 results) Journal Article (8 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 8 results,  Open Access: 6 results) Presentation (12 results) (of which Int'l Joint Research: 6 results,  Invited: 1 results) Book (2 results) Remarks (2 results)

  • [Int'l Joint Research] Fox Chase Cancer Center(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Liege(ベルギー)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] 貴州医科大学(中国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Fox Chase Cancer Center(米国)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Z-form DNA-RNA hybrid blocks DNA replication2025

    • Author(s)
      Wang Shiyu、Xu Yan
    • Journal Title

      Nucleic Acids Research

      Volume: 53 Issue: 5

    • DOI

      10.1093/nar/gkaf135

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mirror-Image RNA: A Right-Handed Z-Form RNA and Its Ligand Complex2024

    • Author(s)
      Song Yi、Wang Shiyu、Xu Yan
    • Journal Title

      Molecules

      Volume: 29 Issue: 20 Pages: 4900-4900

    • DOI

      10.3390/molecules29204900

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion2023

    • Author(s)
      Diallo Mamadou Amadou、Pirotte Sebastien、Hu Yunlong、Morvan Lea、Rakus Krzysztof、Suarez Nicolas M、PoTsang Lee、Saneyoshi Hisao、Xu Yan、Davison Andrew J、Tompa Peter、Sussman Joel L、Vanderplasschen Alain
    • Journal Title

      Nucleic Acids Research

      Volume: 51 Issue: 2 Pages: 806-830

    • DOI

      10.1093/nar/gkac761

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An Advanced Detection System for <i>In Situ</i> Hybridization Using a Fluorescence Resonance Energy Transfer-based Molecular Beacon Probe2022

    • Author(s)
      Narantsog Choijookhuu, Yasuaki Shibata, Takumi Ishizuka, Yan Xu, Takehiko Koji, Yoshitaka Hishikawa
    • Journal Title

      ACTA HISTOCHEMICA ET CYTOCHEMICA

      Volume: 55 Issue: 5 Pages: 119-128

    • DOI

      10.1267/ahc.22-00075

    • ISSN
      0044-5991, 1347-5800
    • Year and Date
      2022-10-28
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis2022

    • Author(s)
      Zhang Ting、Yin Chaoran、Fedorov Aleksandr、Qiao Liangjun、Bao Hongliang、Beknazarov Nazar、Wang Shiyu、Gautam Avishekh、Williams Riley M.、Crawford Jeremy Chase、Peri Suraj、Studitsky Vasily、Beg Amer A.、Thomas Paul G.、Walkley Carl、Xu Yan、Poptsova Maria、Herbert Alan、Balachandran Siddharth
    • Journal Title

      Nature

      Volume: 606 Issue: 7914 Pages: 594-602

    • DOI

      10.1038/s41586-022-04753-7

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] ADAR1 masks the cancer immunotherapeutic potential of ZBP1-driven necroptosis2022

    • Author(s)
      Ting Zhang, Chaoran Yin, Aleksandr Fedorov, Liangjun Qiao, Hongliang Bao, Nazar Beknazarov, Shiyu Wang, Avishekh Gautam, Suraj Peri, Vasily Studitsky, Carl Walkley, Yan Xu, Maria Poptsova, Alan Herbert, Riley Williams, Jeremy Crawford, Amer Beg, Paul Thomas, Siddharth Balachandran
    • Journal Title

      Nature

      Volume: -

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Systematic Approach to DNA Aptamer Design Using Amino Acid?Nucleic Acid Hybrids (ANHs) Targeting Thrombin2021

    • Author(s)
      Yum Ji Hye、Ishizuka Takumi、Fukumoto Koyuki、Hori Daisuke、Bao Hong-Liang、Xu Yan、Sugiyama Hiroshi、Park Soyoung
    • Journal Title

      ACS Biomaterials Science & Engineering

      Volume: 7 Issue: 4 Pages: 1338-1343

    • DOI

      10.1021/acsbiomaterials.1c00060

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Small Ligand That Selectively Binds to the G-quadruplex at the Human Vascular Endothelial Growth Factor Internal Ribosomal Entry Site and Represses the Translation2021

    • Author(s)
      Hu Xiao-Xia、Wang Sheng-Quan、Gan Shi-Quan、Liu Lei、Zhong Ming-Qing、Jia Meng-Hao、Jiang Fei、Xu Yan、Xiao Chao-Da、Shen Xiang-Chun
    • Journal Title

      Frontiers in Chemistry

      Volume: 9

    • DOI

      10.3389/fchem.2021.781198

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 5-アミノレブリン酸及びフッ素化官能基を有する4 本鎖(G4)構造RNAを用いた新規光線力学診断技術の探索2024

    • Author(s)
      岩切理絵、岡添隆、太田有羽、徐岩
    • Organizer
      日本核酸医薬学会第9回年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] クリックリリースケージド核酸: 生物機能の制御及び核酸医薬品の応用2024

    • Author(s)
      王詩宇、徐鵬宇、實吉尚郎、徐岩
    • Organizer
      日本核酸医薬学会第9回年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] In Cell 19F NMR for Non-Canonical Structures2024

    • Author(s)
      Yan Xu
    • Organizer
      XXV International Round Table on Nucleosides, Nucleotides and Nucleic Acids
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Liquid to solid phase transition of short RNA promoted by RNA structure in neurodegenerative diseases.2022

    • Author(s)
      Wang, S. Y., Xu, Y.
    • Organizer
      第49回国際核酸化学シンポジウム
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Unusual topological RNA G-quadruplex formed by an RNA duplex: Implications for the dimerization of COVID-19 RNA.2022

    • Author(s)
      Song, Y., Wang, S. Y., Xu, Y.
    • Organizer
      第49回国際核酸化学シンポジウム
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Combination of a near-infrared BODIPY derivative-based turn-on probe and a new norbornene-modified glucosamine derivative for in-cell and in vivo fluorescence imaging.2022

    • Author(s)
      He, Z. Y., Xu, Y.
    • Organizer
      第49回国際核酸化学シンポジウム
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Fluorescence imaging cell using inverse electron demand Diel-Alder reaction2021

    • Author(s)
      Zhiyong He, Yan Xu
    • Organizer
      日本ケミカルバイオロジー学会第15回年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] A novel architecture of RNA G-quadruplex formed by SARS Cov-2 RNA2021

    • Author(s)
      Yi Song, Shi-Yu Wang, Hong-Liang Bao, Yan Xu
    • Organizer
      日本ケミカルバイオロジー学会第15回年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 8-Trifluoromethylated RNA composed of CGG trinucleotide repeats: synthesis, structure and phase transitions2021

    • Author(s)
      Shiyu Wang, Hongliang Bao, Yan Xu
    • Organizer
      日本ケミカルバイオロジー学会第15回年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] RNA二重鎖から形成される新規RNA G-quadruplex:COVID-19 mRNAの二量体化への影響2021

    • Author(s)
      徐岩、宋藝、王詩宇
    • Organizer
      第15回バイオ関連化学シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] Phase Transitions in the Assembly of Trifluoromethylated G-quadruplex RNA by shorter CGG Trinucleotide Repeats2021

    • Author(s)
      Shiyu Wang, Yan Xu
    • Organizer
      第48回国際核酸化学シンポジウム
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dimerization of COVID-19 mRNA formed by an unusual topological RNA G-quadruplex2021

    • Author(s)
      Yi Song, Shiyu Wang, Yan Xu
    • Organizer
      第48回国際核酸化学シンポジウム
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Book] Oligonucleotide Containing 8-Trifluoromethyl-2′-Deoxyguanosine as a Z-DNA Probe. In: Kim, K.K., Subramani, V.K. (eds) Z-DNA.2023

    • Author(s)
      Hong-Liang Bao and Yan Xu
    • Total Pages
      332
    • Publisher
      Humana, New York, NY
    • ISBN
      9781071630839
    • Related Report
      2022 Annual Research Report
  • [Book] In Cell 19F NMR for G-quadruplex. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids.2023

    • Author(s)
      Yan Xu
    • Total Pages
      2650
    • Publisher
      Springer, Singapore
    • ISBN
      9789811613135
    • Related Report
      2022 Annual Research Report
  • [Remarks] 宮崎大学医学部機能制御学講座生命分子科学分野ホームページ

    • URL

      http://www.med.miyazaki-u.ac.jp/MMCCHEM/index.html

    • Related Report
      2023 Annual Research Report
  • [Remarks] 宮崎大学医学部機能制御学講座生命分子科学分野研究室ホームページ

    • URL

      http://www.med.miyazaki-u.ac.jp/MMCCHEM/index.html

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report

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Published: 2021-04-28   Modified: 2026-01-16  

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