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Quantitative prediction of nucleic acid structures and functions affected by spaciotemporal environmental factors in cells

Research Project

Project/Area Number 22H04975
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Review Section Broad Section E
Research InstitutionKonan University

Principal Investigator

杉本 直己  甲南大学, 学長直属, 特別客員教授 (60206430)

Co-Investigator(Kenkyū-buntansha) 松浦 和則  鳥取大学, 工学研究科, 教授 (60283389)
沼田 圭司  京都大学, 工学研究科, 教授 (40584529)
遠藤 玉樹  甲南大学, フロンティアサイエンス研究科, 准教授 (90550236)
高橋 俊太郎  甲南大学, フロンティアサイエンス研究科, 准教授 (40456257)
建石 寿枝  甲南大学, フロンティアサイエンス研究科, 准教授 (20593495)
Project Period (FY) 2022-04-27 – 2027-03-31
Project Status Granted (Fiscal Year 2024)
Budget Amount *help
¥197,340,000 (Direct Cost: ¥151,800,000、Indirect Cost: ¥45,540,000)
Fiscal Year 2025: ¥29,640,000 (Direct Cost: ¥22,800,000、Indirect Cost: ¥6,840,000)
Fiscal Year 2024: ¥27,690,000 (Direct Cost: ¥21,300,000、Indirect Cost: ¥6,390,000)
Fiscal Year 2023: ¥28,340,000 (Direct Cost: ¥21,800,000、Indirect Cost: ¥6,540,000)
Fiscal Year 2022: ¥83,070,000 (Direct Cost: ¥63,900,000、Indirect Cost: ¥19,170,000)
Keywords核酸構造 / 細胞内環境 / エネルギーデータベース / 熱安定性予測 / 遺伝子発現
Outline of Research at the Start

本研究では、「遺伝情報の保持」と「情報発現の制御」に関与する任意の核酸構造(二重らせん構造および非二重らせん構造)が、細胞内でいつ、どこで、どのように形成し機能するのかを予測する。そのために、細胞内の時空間的な分子環境の変動を考慮して核酸構造の安定性をエネルギーレベルで予測できる、汎用的なパラメータを得る。最終的には生命現象を「可視化」から「数値化」することを念頭に、核酸構造の安定性が生体反応(遺伝子発現など)に与える影響を、その分子機構と共に定量的に解析する。

Outline of Annual Research Achievements

2023年度は、当初の研究計画に従い、細胞内の時空環境による核酸構造への影響を【知る】研究、および任意の時空環境での安定性を予測できるSETUPパラメータを【得る】研究を中心に研究を展開した。
RNA/DNAから形成されるハイブリッド二重らせん構造について、NMRによる二重らせん構造の解析を国際共同研究として行い、配列に依存したエネルギーパラメータの違いを構造学的観点から詳細に解明した。さらに、細胞内でハイブリッド二重らせん構造の形成を直接観測し、予測される安定性と細胞内で形成されるハイブリッド二重らせん構造の割合とが相関する結果を得た(J. Am. Chem. Soc., 145, 23503 (2023))。細胞内の空間的な分子配置を維持したまま核酸構造の物理化学的な解析ができる新たな実験系を構築し、試験管内と細胞内ではカリウムイオンと四重らせん構造の親和性が大きく異なることを示した(J. Am. Chem. Soc., 146, 8005 (2024))。
【知る】研究、【得る】研究で計画以上に研究が進展したため、2023年度はさらに計画を前倒しし、予測した任意の核酸構造の安定性と生体反応への影響との相関を【示す】研究にも着手した。高濃度の分子イオン(コリンイオン)存在下での核酸構造の安定性を解析し、転写反応の活性と相関させて細胞内イオンによる核酸の構造と機能への影響を明らかにした(ACS Omega, 239, 5675 (2024) )。さらに、がん関連遺伝子であるBCL2のプロモーター領域の配列が形成するi-motif構造に低分子化合物であるクリスタルバイオレットが結合し、i-motif構造に依存した転写反応の調節やi-motif構造の細胞内検出に利用できる可能性を示した(Sci. Rep., 13, 14338 (2023))。

Current Status of Research Progress
Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

細胞内の時空環境による核酸構造への影響を【知る】研究として、既に、DNA/DNA、RNA/RNA、RNA/DNAという全ての組み合わせの二重らせん構造の安定性を予測できる統合的なエネルギーデータベースを構築し、世界に先駆けてそのデータベースを公開した。本研究課題で構築したデータベースは、核酸の相補性を利用した様々な技術開発を加速的に発展させることができる。本研究課題においても、RNA/RNAの二重らせん構造のエネルギーパラメータを取得した成果(J. Am. Chem. Soc., 145, 23503 (2023))では、共存溶質が存在する環境を想定して予測した二重らせん構造の安定性を基に、細胞内での転写反応やゲノム編集反応の効率、核酸医薬品による遺伝子発現抑制の効率を推察できた。
任意の時空環境での安定性を予測できるSETUPパラメータを【得る】研究においても、当初の研究計画に従い、細胞内の分子配置を維持したまま物理化学的な核酸構造の安定性解析ができる実験系としてSHELLを構築した。この実験系を用いることで、がん疾患の進行に伴う特異的な環境変化が核酸構造の安定性に及ぼす影響を定量的に明らかにした。さらに、このような核酸構造形成とがん疾患の進行度に相関が見出されつつあることから、この成果は非標準核酸構造を標的とした創薬研究を飛躍的に発展させ得る可能性がある(J. Am. Chem. Soc., 146, 8005 (2024))。
以上のように、本研究課題では当初の研究計画に沿って順調に研究成果を発信している。また、ATリッチ配列やGCリッチ配列が形成する二重らせん構造の水和状態が標準的な二重らせん構造とは異なることなど、当初予見し得なかった興味深い成果も得られている。さらに、非二重らせん構造の細胞内での新たな役割なども明らかになりつつあり、本研究課題は期待以上の研究成果を挙げつつある。

Strategy for Future Research Activity

2024年度以降は、これまでに進めてきた、細胞内の時空環境による核酸構造への影響を【知る】研究、任意の時空環境での安定性を予測できるSETUPパラメータを【得る】研究に加え、予測した任意の核酸構造の安定性と生体反応への影響との相関を【示す】研究も同時並行で進める。特に、【示す】研究過程では、これまでに得られたSETUPパラメータを用いて予測した核酸構造の安定性から、それぞれの構造による生体反応への影響まで予測できることを示す。さらに、同じ配列の核酸であっても、時空環境の違いで形成される核酸構造やその安定性が異なり、生体反応への影響も変動することを示す。
研究の一例として、細胞内でpHが異なる核内とミトコンドリア内(ミトコンドリア内は高いpHを示す)において、プラスミドとして導入するレポーター遺伝子の発現を比較する。そして、同じ配列であっても予測されるi-motif構造の安定性の違いで遺伝子発現への影響が異なることを示す。さらに本研究では、SETUPパラメータを活用し、ゲノム上のプロモーター領域で形成され得るグアニン四重らせん構造の安定性をカリウム濃度の影響も踏まえて網羅的に予測する。そして、がんの進行に伴う細胞内カリウム濃度の低下、およびそれに伴う四重らせん構造の安定性の変動により、遺伝子の発現を定量的に予測できることを示す。

Assessment Rating
Interim Assessment Comments (Rating)

A+: In light of the aim of introducing the research area into the research categories, more progress has been made in research than expected.

Report

(5 results)
  • 2024 Interim Assessment (Comments) ( PDF )
  • 2023 Annual Research Report
  • 2022 Abstract ( PDF )   Comments on the Screening Results   Annual Research Report
  • Research Products

    (99 results)

All 2024 2023 2022 Other

All Int'l Joint Research (5 results) Journal Article (17 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 17 results,  Open Access: 10 results) Presentation (72 results) (of which Int'l Joint Research: 32 results,  Invited: 18 results) Book (3 results) Remarks (2 results)

  • [Int'l Joint Research] Slovenian NMR Center(スロベニア)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] MGMARI(インド)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] University of Calcutta(インド)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Nanjing Agricultural University(中国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Reading(英国)

    • Related Report
      2022 Annual Research Report
  • [Journal Article] Development of a Pseudocellular System to Quantify Specific Interactions Determining the G-Quadruplex Function in Cells2024

    • Author(s)
      Tateishi-Karimata Hisae、Kawauchi Keiko、Takahashi Shuntaro、Sugimoto Naoki
    • Journal Title

      Journal of the American Chemical Society

      Volume: 146 Issue: 12 Pages: 8005-8015

    • DOI

      10.1021/jacs.3c11160

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Diholine dihydrogen phosphate destabilizesG-quadruplexes and enhances transcription efficiency invitro and in cells2024

    • Author(s)
      H. Tateishi-Karimata and N. Sugimoto
    • Journal Title

      ACS Omega

      Volume: 9 Issue: 5 Pages: 5675-5682

    • DOI

      10.1021/acsomega.3c08087

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] "In-cell stability prediction of RNA/DNA hybrid duplexes for designing oligonucleotides aimed at therapeutics "2023

    • Author(s)
      D. Banerjee, H. Tateishi-Karimata, M. Toplishek, T. Ohyama,S. Ghosh, S. Takahashi, M. TrajkovskiJ. Plavec, and N. Sugimoto
    • Journal Title

      J. Am. Chem. Soc

      Volume: 145 Issue: 43 Pages: 23503-23518

    • DOI

      10.1021/jacs.3c06706

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet2023

    • Author(s)
      Das Sinjan、Takahashi Shuntaro、Ohyama Tatsuya、Bhowmik Sudipta、Sugimoto Naoki
    • Journal Title

      Scientific Reports

      Volume: 13 Issue: 1 Pages: 14338-14338

    • DOI

      10.1038/s41598-023-39407-9

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Design of an Artificial Peptide Inspired by Transmembrane Mitochondrial Protein for Escorting Exogenous DNA into the Mitochondria to Restore their Functions by Simultaneous Multiple Gene Expression2023

    • Author(s)
      Yoshinaga Naoto、Miyamoto Takaaki、Odahara Masaki、Takeda‐Kamiya Noriko、Toyooka Kiminori、Nara Seia、Nishimura Haruna、Ling Feng、Su'etsugu Masayuki、Yoshida Minoru、Numata Keiji
    • Journal Title

      Advanced Functional Materials

      Volume: 34 Issue: 8 Pages: 2306070-2306070

    • DOI

      10.1002/adfm.202306070

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Advancing Biomolecule Delivery in Plants: Harnessing Synthetic Nanocarriers to Overcome Multiscale Barriers for Cutting-Edge Plant Bioengineering2023

    • Author(s)
      Miyamoto Takaaki、Numata Keiji
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 96 Issue: 9 Pages: 1026-1044

    • DOI

      10.1246/bcsj.20230147

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Simple and fast screening for structure-selective G-quadruplex ligands2023

    • Author(s)
      Y. Hashimoto, Y. Imagawa, K. Nagano, R. Maeda, N. N.agahama, T. Torii, N. Kinoshita, N. Takamiya, K. Kawauchi, H. Tateishi-Karimata, N. Sugimoto and D. Miyoshi
    • Journal Title

      Chem. Commun.

      Volume: 59 Issue: 33 Pages: 4891-4894

    • DOI

      10.1039/d3cc00556a

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase2023

    • Author(s)
      Endoh Tamaki、Takahashi Shuntaro、Sugimoto Naoki
    • Journal Title

      Chemical Communications

      Volume: 59 Issue: 7 Pages: 872-875

    • DOI

      10.1039/d2cc05858h

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Pressure-temperature control of activity of RNA polymerase ribozyme2023

    • Author(s)
      Takahashi Shuntaro、Sugimoto Naoki
    • Journal Title

      Biophysical Chemistry

      Volume: 292 Pages: 106914-106914

    • DOI

      10.1016/j.bpc.2022.106914

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions2022

    • Author(s)
      S. Ghosh, S. Takahashi, D. Banerjee, T. Ohyama, T. Endoh, H. Tateishi-Karimata, and N. Sugimoto
    • Journal Title

      Nucleic Acids Res.,

      Volume: 51 Issue: 9 Pages: 4101-4111

    • DOI

      10.1093/nar/gkad020

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Ruthenium Polypyridyl Complex Bound to a Unimolecular Chair-Form G-Quadruplex2022

    • Author(s)
      K. T. McQuaid, S. Takahashi, L. Baumgaertner, D. J. Cardin, N. G. Paterson, J. P. Hall, N. Sugimoto, and C. J. Cardin
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 144 Issue: 13 Pages: 5956-5964

    • DOI

      10.1021/jacs.2c00178

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs2022

    • Author(s)
      Zhang Yong、Tateishi-Karimata Hisae、Endoh Tamaki、Jin Qiongli、Li Kexin、Fan Xiaoru、Ma Yingjun、Gao Limin、Lu Haiyan、Wang Zhiye、Cho Art E.、Yao Xuefeng、Liu Chunming、Sugimoto Naoki、Guo Shiwei、Fu Xiangdong、Shen Qirong、Xu Guohua、Herrera-Estrella Luis Rafael、Fan Xiaorong
    • Journal Title

      Science Advances

      Volume: 8 Issue: 47

    • DOI

      10.1126/sciadv.adc9785

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Volumetric Strategy for Quantitatively Elucidating a Local Hydration Network around a G-Quadruplex2022

    • Author(s)
      Matsumoto Saki、Takahashi Shuntaro、Bhowmik Sudipta、Ohyama Tatsuya、Sugimoto Naoki
    • Journal Title

      Analytical Chemistry

      Volume: 94 Issue: 20 Pages: 7400-7407

    • DOI

      10.1021/acs.analchem.2c01075

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Controlling liquid-liquid phase separation of G-quadruplex-forming RNAs in a sequence-specific manner2022

    • Author(s)
      Tsuruta Mitsuki、Torii Takeru、Kohata Kazuki、Kawauchi Keiko、Tateishi-Karimata Hisae、Sugimoto Naoki、Miyoshi Daisuke
    • Journal Title

      Chemical Communications

      Volume: 58 Issue: 93 Pages: 12931-12934

    • DOI

      10.1039/d2cc04366a

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] DNA methylation is regulated by both the stability and topology of G-quadruplex2022

    • Author(s)
      Matsumoto Saki、Tateishi-Karimata Hisae、Sugimoto Naoki
    • Journal Title

      Chemical Communications

      Volume: 58 Issue: 89 Pages: 12459-12462

    • DOI

      10.1039/d2cc04383a

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Applicability of Nearest-neighbour Model for Pseudoknot RNAs2022

    • Author(s)
      S. Satpathi, T. Endoh, and N. Sugimoto
    • Journal Title

      Chem. Commun.

      Volume: in press Issue: 40 Pages: 5952-5955

    • DOI

      10.1039/d1cc07094k

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Replication Control of Human Telomere G-Quadruplex DNA by G-Quadruplex Ligands Dependent on Solution Environment2022

    • Author(s)
      S. Takahashi, S. Bhowmik, S. Sato, S. Takenaka, and N. Sugimoto
    • Journal Title

      Life

      Volume: 12 Issue: 4 Pages: 533-533

    • DOI

      10.3390/life12040553

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 細胞内統計熱力学の開拓:核酸機能の理解と制御を夢見て2024

    • Author(s)
      杉本直己
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 核酸化学のNew Data Science (1): 細胞内の核酸構造安定性を予測できる新規の最近接塩基対パラメータの開発2024

    • Author(s)
      杉本直己、S. Ghoshi, 大山達也、遠藤玉樹、高橋俊太郎、建石寿枝
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 核酸化学のNew Data Science (2): 最近接塩基対パラメータとAIを用いたリボザイムの機能予測2024

    • Author(s)
      高橋俊太郎、S. Ghoshi、建石寿枝, 福永津嵩、浜田道昭、杉本直己
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 核酸化学のNew Data Science (3): 最近接塩基対パラメータ、擬似細胞システム、AIを用いたRNAの構造安定性予測2024

    • Author(s)
      D. Banerjee、建石寿枝、高橋俊太郎、福永津嵩、浜田道昭、杉本直己
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 核酸化学のNew Data Science (4): 擬似細胞システムと機械学習を用いたG-四重らせん構造を標的としたハイスループット・スクリーニング法の開発2024

    • Author(s)
      大山達也、建石寿枝、川内敬子、高橋俊太郎、田中成典、杉本直己
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] New Data Science in Nucleic Acids Chemistry (5): Effect of local environments on the stability of nucleic acids in mitochondria2024

    • Author(s)
      S. Ghosh, L. Liu, S. Takahashi, T. Endoh, N. Yoshinaga, K. Numata, N. Sugimoto
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] New Data Science in Nucleic Acids Chemistry (6): Complementary effect of hydrogen bonding and base stacking on the stability of double-stranded nucleic acids2024

    • Author(s)
      L. Liu, S. Takahashi, N. Sugimoto
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] New Data Science in Nucleic Acids Chemistry (7): Quantitative study of formation of DNA tetraplexes during cell cycle2024

    • Author(s)
      S. Das, S. Takahashi, N. Sugimoto
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 核酸化学のNew Data Science (8): ハイスピード共焦点イメージングを利用した生細胞内での核酸構造変化の解析2024

    • Author(s)
      遠藤玉樹、建石寿枝、筒井啓太、深谷陽子、築地真也、杉本直己
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] New Data Science in Nucleic Acids Chemistry (9): Conformational transition of nucleic acids with virus genome sequences inside cell-like nanoconfinements2024

    • Author(s)
      S. Sarkar, H. Tateishi-Karimata, K. Maatsuura, T. Endoh, N. Sugimoto
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] New Data Science in Nucleic Acids Chemistry (10): Quantitative analysis for factors affecting i-motif formation in living cells estimated by the pseudo-cellular system2024

    • Author(s)
      K. Chen, H. Tateishi-Karimata, N. Sugimoto
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 核酸化学のNew Data Science (11): G-四重らせんとi-モチーフ構造の形成を介したがん細胞内における転写制御機構の解明2024

    • Author(s)
      建石寿枝、川内敬子、凌一葦、奥田修二郎、杉本直己
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 四重鎖DNAを内包した人工ウイルスキャプシドの創製2024

    • Author(s)
      石井楽乃、稲葉央、遠藤玉樹、建石寿枝、杉本直己、松浦和則
    • Organizer
      日本化学会第104回春季年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Nucleic Acids Chemistry as “Field of Dreams”2024

    • Author(s)
      N. Sugimoto
    • Organizer
      Supra FIBER International Summit for Nucleic Acids (S-FISNA)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] “To B or not to B” in Nucleic Acids Chemistry2023

    • Author(s)
      N. Sugimoto
    • Organizer
      13th International Symposium on Bioorganic Chemistry (ISBOC-13)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] “To B or not to B” of Nucleic Acids Research in Health & Diseases2023

    • Author(s)
      N. Sugimoto
    • Organizer
      International Symposium Current Trends and Future Perspectives of Nucleic Acids Research in Health & Diseases
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Beyond the Watson-Crick Double Helix: Make New History of Nucleic Acids (8)2023

    • Author(s)
      S. Takahashi, N. Sugimoto
    • Organizer
      Asia 3 Roundtable on Nucleic Acids 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] I-motif structure as a binding core for small fluorogens2023

    • Author(s)
      T. Endoh, S. Das, S. Takahashi, N. Sugimoto
    • Organizer
      第50回国際核酸化学シンポジウム (ISNAC2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Twisting of i-motif DNA induced by diverse molecular crowdings2023

    • Author(s)
      S. Takahashi, S. Ghosh, M. Trajkovski, P. Chilka, T. Ohyama, J. Plavec, N. Sugimoto
    • Organizer
      第50回国際核酸化学シンポジウム (ISNAC2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of pseudo-cellular systems to understand G-quadruplex behaviors in cancer progression2023

    • Author(s)
      H. Tateishi-Karimata, K. Kawauchi, S. Takahashi, N. Sugimoto
    • Organizer
      第50回国際核酸化学シンポジウム (ISNAC2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Elucidation of the regulatory mechanism of gene expression for new imperfect G-quadruplexes2023

    • Author(s)
      S. Sarkar, H. Tateishi-Karimata, T. Ohyama, N. Sugimoto
    • Organizer
      第50回国際核酸化学シンポジウム (ISNAC2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effects of intracellular molecular environments during cancer progression on i-motif formations2023

    • Author(s)
      K. Chen, H. Tateishi-Karimata , N. Sugimoto
    • Organizer
      第50回国際核酸化学シンポジウム (ISNAC2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Accumulation behaviors for GGGGCC-repeated RNA with peptide repeats estimated by molecular dynamics simulations2023

    • Author(s)
      T. Ohyama, H. Tateishi-Karimata, S. Tanaka, C. Watanabe, T. Honma, N. Sugimoto
    • Organizer
      第50回国際核酸化学シンポジウム (ISNAC2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chemical targeting of i-motif DNAs for cancer theranostic applications2023

    • Author(s)
      S. Das, S. Takahashi, T. Ohyama, S. Bhowmik, N. Sugimoto
    • Organizer
      第50回国際核酸化学シンポジウム (ISNAC2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RNAの複製エラーに対する高圧力の効果2023

    • Author(s)
      高橋俊太郎、杉本直己
    • Organizer
      第64回高圧討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Physical Chemistry of Nucleic Acids: “To B or not to B”2023

    • Author(s)
      S. Takahashi, S. Ghosh, H. Tateishi-Karimata, D. Banerjee, T. Endoh, T. Ohyama, N. Sugimoto
    • Organizer
      Advances in Noncanonical Nucleic Acids “ANNA2023”
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Versatile binding core for small fluorogens consisting of noncanonical base pairs2023

    • Author(s)
      T. Endoh, J.-H. Tan, S.-B. Chen, S. Das, S. Takahashi, N. Sugimoto
    • Organizer
      Advances in Noncanonical Nucleic Acids “ANNA2023”
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Development of pseudo-cellular systems to understand effects of molecular environments on G-quadruplex behaviors depending on the type of cells2023

    • Author(s)
      H. Tateishi-Karimata, K. Kawauchi, S. Takahashi, N. Sugimoto
    • Organizer
      Advances in Noncanonical Nucleic Acids “ANNA2023”
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Prediction of Duplex Stability of Nucleic Acids in Diverse in vitro and Cellular-like Crowding Conditions2023

    • Author(s)
      S. Ghosh, D. Banerjee, S. Takahashi, H. Tateishi-Karimata, T. Endoh, T. Ohyama, N. Sugimoto
    • Organizer
      第72回高分子討論会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 高圧力を用いたグアニン四重鎖DNAへのリガンド結合解析2023

    • Author(s)
      高橋俊太郎、松本咲、大山達也、S. Bhowmik、杉本直己
    • Organizer
      第72回高分子討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Nucleic Acids Research in the post-COVID-19 Era2023

    • Author(s)
      N. Sugimoto
    • Organizer
      日本分析化学会第72年会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 新型コロナウィルスのRNA合成反応を阻害する細胞内在性の四重らせんRNA2023

    • Author(s)
      遠藤玉樹、高橋俊太郎、杉本直己
    • Organizer
      第17回バイオ関連化学シンポジウム
    • Related Report
      2023 Annual Research Report
  • [Presentation] RNA複製におけるRNA二重鎖の最近接塩基対の効果2023

    • Author(s)
      高橋俊太郎、建石寿枝、杉本直己
    • Organizer
      第17回バイオ関連化学シンポジウム
    • Related Report
      2023 Annual Research Report
  • [Presentation] リピートRNAの細胞毒性凝集体の形成を抑制するリガンドの深索2023

    • Author(s)
      松本咲、建石寿枝、大山達也、杉本直己
    • Organizer
      第17回バイオ関連化学シンポジウム
    • Related Report
      2023 Annual Research Report
  • [Presentation] “To B or not to B” in Nucleic Acids Chemistry2023

    • Author(s)
      N. Sugimoto
    • Organizer
      Asian Chemical Biology Conference 2023 (ACBC)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 新型コロナウイルスのRNA依存性RNAポリメラーゼ活性を抑制できるヒト内在性RNAの取得2023

    • Author(s)
      遠藤玉樹、高橋俊太郎、杉本直己
    • Organizer
      日本核酸医薬学会第8回年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] シトシン四重らせん構造によるがん遺伝子発現の制御2023

    • Author(s)
      建石寿枝、川内敬子、杉本直己
    • Organizer
      日本核酸医薬学会第8回年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] “To B or not to B” in Nucleic Acids Research2023

    • Author(s)
      N. Sugimoto
    • Organizer
      Nucleic Acids; Prospect and Therapeutic Applications
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions2023

    • Author(s)
      N. Sugimoto
    • Organizer
      Gordon Research Conference (Nucleosides, Nucleotides and Oligonucleotides)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] “To B or not to B” in Nucleic Acid Therapeutics. Sungkyunkwan University2023

    • Author(s)
      N. Sugimoto
    • Organizer
      Sungkyunkwan University Nucleic Acid Forum (SKKU NAF 2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] “To B or not to B” in Nucleic Acids Research2023

    • Author(s)
      N. Sugimoto
    • Organizer
      The 6th Conference on Frontiers in Water Biophysics (FWB)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] バイオ・高分子材料のビッグデータ構築と材料開発への利用 / Digital transformation in biological and polymeric materials2023

    • Author(s)
      沼田圭司
    • Organizer
      JapanNano第21回マテリアル戦略総合シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] Fluorescence light-up through binding of dye molecules to specific loop sequences of i-motif DNA2023

    • Author(s)
      Sinjan Das, Shuntaro Takahashi, Naoki Sugimoto
    • Organizer
      日本化学会第103回春季年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Applications of nearest-neighbor parameters for RNA/DNA hybrid duplexes in the advancement of therapeutics2023

    • Author(s)
      Dipanwita Banerjee, Hisae Tateishi-Karimata, Saptarshi Ghosh, Shuntaro Takahashi, Tatsuya Ohyama, Tamaki Endoh, Maria Toplishek, Marko Trajkovski , Janez Plavec, Naoki Sugimoto
    • Organizer
      日本化学会第103回春季年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Stability prediction of RNA duplexes under various molecular crowding in vitro and in cell2023

    • Author(s)
      Saptarshi Ghosh, Shuntaro Takahashi, Dipanwita Banerjee, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi-Karimata, Naoki Sugimoto1
    • Organizer
      日本化学会第103回春季年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 高圧力を用いたグアニン四重鎖の水和解析によるリガンド結合予測2023

    • Author(s)
      高橋 俊太郎、松本 咲、大山 達也、Sudipta Bhowmik、杉本 直己
    • Organizer
      日本化学会第103回春季年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] がん細胞内環境変化に応答したC四重らせん構造の形成機構の解明2023

    • Author(s)
      建石 寿枝、川内 敬子、杉本 直己
    • Organizer
      日本化学会第103回春季年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] G4C2 繰り返し配列をもつ RNA 四重鎖とジペプチドの集積メカニズムの解析2023

    • Author(s)
      大山 達也、建石 寿枝、田中 成典、杉本 直己
    • Organizer
      日本化学会第103回春季年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Adventures of Non-Double Helical Nucleic Acids in Molecular Crowding World, Marienbad2022

    • Author(s)
      N. Sugimoto
    • Organizer
      8th International Meeting on Quadruplex Nucleic Acids
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 核酸構造の定量的解析を基にしたC9orf72由来のリピートRNAとペプチドの相互作用制御法の開発2022

    • Author(s)
      建石寿枝, 松本咲, 大山達也, Ye Teng, 田中成典, 杉本直己
    • Organizer
      日本核酸医薬学会第7回年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Nucleotides and Nucleic Acids: Prediction of structure and stability of nucleic acids under molecular crowding: To B or not to B2022

    • Author(s)
      N. Sugimoto
    • Organizer
      XXIV International Round Table on Nucleosisdes
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Role of macromolecular crowding in the cells on the structures and functions of nucleic acids2022

    • Author(s)
      N. Sugimoto
    • Organizer
      India|EMBO Lecture Course: Functional nucleic acids: Recent landscapes and therapeutic applications
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 自己複製人工ウイルスキャプシドの創製に向けた mRNA 内包人工ウイルスキャプシドの設計と構築2022

    • Author(s)
      坂本健太郎,稲葉央,岩崎崇,松浦和則
    • Organizer
      第32回バイオ・高分子シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] i-motif 型 DNA 構造に対する分子クラウディング効果の定量的解析2022

    • Author(s)
      高橋俊太郎, S. Ghosh, P. Chilka, 大山達也, 杉本直己
    • Organizer
      第71回高分子討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] シグナルペプチドを利用した遺伝子送達の現状2022

    • Author(s)
      沼田圭司
    • Organizer
      遺伝子デリバリー研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 神経変性疾患に関わるリピートRNAとペプチドの相互作用解析2022

    • Author(s)
      建石 寿枝, 大山達也, 田中成典, 杉本 直己
    • Organizer
      第16回バイオ関連化学シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] グアニン四重らせん構造の安定性とトポロジーによるDNAメチル化制御2022

    • Author(s)
      松本咲, 建石寿枝, 杉本直己
    • Organizer
      第16回バイオ関連化学シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] SARS-CoV-2由来RNA依存性RNAポリメラーゼの複製反応におけるグアニン四重鎖の効果とその制御2022

    • Author(s)
      高橋俊太郎, 松本咲, 建石寿枝, Byeang Hyean Kim, 杉本直己
    • Organizer
      第16回バイオ関連化学シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] RNAシュードノット構造の安定性予測のための最近接塩基対モデルの検証2022

    • Author(s)
      遠藤玉樹, Sagar Satpathi, 杉本直己
    • Organizer
      第16回バイオ関連化学シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] Beyond "To B or not to B" in Nucleic Acids Chemistry2022

    • Author(s)
      N. Sugimoto
    • Organizer
      Advances in Noncanonical Nucleic Acids 2022 “ANNA2022”
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] DNA methylation depending on stability and topology of G-quadruplex2022

    • Author(s)
      S. Matsumoto, H. Tateishi-Karimata, N. Sugimoto
    • Organizer
      Advances in Noncanonical Nucleic Acids 2022 “ANNA2022”
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Analysis of dynamic behaviors of G-quadruplexes using molecular simulations2022

    • Author(s)
      T. Ohyama, H. Tateishi-Karimata, S. Takahashi, S. Tanaka, N. Sugimoto
    • Organizer
      Advances in Noncanonical Nucleic Acids 2022 “ANNA2022”
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Design of artificial viral capsid encapsulating mRNA to endow self-replicability2022

    • Author(s)
      Kentarou Sakamoto,Hiroshi Inaba,Takashi Iwasaki,Kazunori Matsuura
    • Organizer
      第59回ペプチド討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Analysis of the effect of high-pressure on the stability of nucleic acids using molecular dynamics simulations2022

    • Author(s)
      T. Ohyama, S. Takahashi, H. Tateishi-Karimata, S. Tanaka, N. Sugimoto
    • 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] Thermodynamics approach for the fidelity of RNA-dependent RNA polymerase of SARS- CoV-2 under molecular crowdings2022

    • Author(s)
      S. Takahashi, N. Sugimoto
    • 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] Prediction of RNA duplex stability in physiological crowding conditions based on the nearest-neighbor model2022

    • Author(s)
      S. Ghosh, S. Takahashi, D. Banerjee, T. Ohyama, T. Endoh, H. Tateishi-Karimata, N. Sugimoto
    • 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] New parameters for accurate prediction of RNA/DNA hybrid duplex stability and their advantage in CRISPR- Cas9 technique2022

    • Author(s)
      D. Banerjee, H. Tateishi-Karimata, T. Ohyama, S. Ghosh, T. Endoh, S. Takahashi, N. Sugimoto
    • 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] Crystallographic studies of ruthenium polypyridyl complexes bound to G-quadruplexes: Towards design, specificity, and function2022

    • Author(s)
      K. McQuaid, D. Cardin, J. Hall, N. Paterson, S. Takahashi, N. Sugimoto, C. Cardin
    • 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] The effect of stability and topology of G-quadruplex on DNA methylation2022

    • Author(s)
      S. Matsumoto, H. Tateishi-Karimata, N. Sugimoto
    • 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] Quantitative analysis for G-quadruplex and i-motif formations in malignant cancers2022

    • Author(s)
      H. Tateishi-Karimata, N. Sugimoto
    • 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] 分子シミュレーションを用いた高圧環境における核酸の安定性の解析2022

    • Author(s)
      大山達也、高橋俊太郎、建石寿枝、田中成典、杉本直己
    • Organizer
      核酸化学若手フォーラム2022
    • Related Report
      2022 Annual Research Report
  • [Presentation] 化学でウイルスレプリカを合成する2022

    • Author(s)
      松浦和則
    • Organizer
      2022年 繊維学会秋季研究発表会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Book] Liquid-Liquid Phase Separation and Nucleic Acids. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids2023

    • Author(s)
      Tateishi-Karimata Hisae、Matsumoto Saki、Sugimoto Naoki
    • Total Pages
      40
    • Publisher
      Springer, Singapore
    • Related Report
      2023 Annual Research Report
  • [Book] Effects of Molecular Crowding on Structures and Functions of Nucleic Acids. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids.2023

    • Author(s)
      Endoh, T., Tateishi-Karimata, H., Sugimoto, N.
    • Total Pages
      45
    • Publisher
      Springer, Singapore
    • ISBN
      9789811613135
    • Related Report
      2022 Annual Research Report
  • [Book] Stability Prediction of Canonical and Noncanonical Structures of Nucleic Acids. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids.2022

    • Author(s)
      Takahashi, S., Tateishi-Karimata, H., Sugimoto, N.
    • Total Pages
      44
    • Publisher
      Springer, Singapore
    • ISBN
      9789811613135
    • Related Report
      2022 Annual Research Report
  • [Remarks] 甲南大学先端生命工学研究所ホームページ

    • URL

      https://konan-fiber.jp/indexb

    • Related Report
      2023 Annual Research Report
  • [Remarks] 甲南大学先端生命工学研究所ホームページ

    • URL

      https://www.konan-fiber.jp/index.php

    • Related Report
      2022 Annual Research Report

URL: 

Published: 2022-04-28   Modified: 2025-04-17  

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