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Position |
Professor |
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Research Field |
Nanotechnology/Materials / Bio chemistry, Manufacturing Technology (Mechanical Engineering, Electrical and Electronic Engineering, Chemical Engineering) / Biofunction and bioprocess engineering, Nanotechnology/Materials / Nanomaterials |
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External Link |
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Graduating School 【 display / non-display 】
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Kyoto University Faculty of Science Graduated
- 1979.3
Graduate School 【 display / non-display 】
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Kyoto University Graduate School, Division of Natural Science Doctor's Course Completed
- 1985.3
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Kyoto University Graduate School, Division of Natural Science Master's Course Completed
- 1982.3
Campus Career 【 display / non-display 】
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KONAN UNIVERSITY Frontier Institute for Biomolecular Engineering Research, Konan University Distinguished Professor
2024.4
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KONAN UNIVERSITY Faculty of Frontiers of Innovative Research in Science and Technology Faculty of Frontiers of Innovative Research in Science and Technology Department of Nanobiochemistry Professor
2009.4 - 2024.3
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KONAN UNIVERSITY Frontier of Institute for Biomolecular Engineering Research in Science and Technology Department of Nanobiochemistry Director in General
2004.4 - 2024.3
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ハイテクリサーチセンター 所長
2001.4 - 2004.3
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KONAN UNIVERSITY Faculty of Science Professor
1994.4 - 2009.3
External Career 【 display / non-display 】
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学校法人 甲南学園
2012.8
Country：Japan
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ロチェスター大学
1985.4 - 1988.3
Country：United States
Papers 【 display / non-display 】
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Contrasting effect of different crowding agents on pseudoknot RNA stability Reviewed
S. Satpathi, T. Endoh and N. Sugimoto
Med. Chem. Res 48 2024.8
Pseudoknot (PK) is one of the prevalent and potential targets for drug discovery. It is still difficult to predict PK-forming regions within endogenous RNA transcripts because the intracellular environment consisting of various cellular agents has diverse effects on the structure and stability of nucleic acids. In this study, we have demonstrated the impact of the varied crowding conditions on the structural stability of pseudoknot RNA, emphasizing the distinct stabilities of PK structures depending on the crowding environment.
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Guanidine modification improves functions of natural RNA-targeting alkaloids Reviewed International coauthorship
Tamaki Endoh, Sagar Satpathi, Yutong Chen, Saki Matsumoto, Tatsuya Ohyama, Peter Podbevšek, Janez Plavec, Kazumitsu Onizuka, Fumi Nagatsugi, Naoki Sugimoto
New Journal of Chemistry 48 ( 19 ) 8529 - 8533 2024.4
Publisher：Royal Society of Chemistry (RSC)
Guanidine modification on berberine improved RNA binding affinity and enhanced suppression of protein expression.
DOI： 10.1039/d3nj05833f
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Development of a Pseudocellular System to Quantify Specific Interactions Determining the G-Quadruplex Function in Cells Reviewed International journal
Hisae Tateishi-Karimata, Keiko Kawauchi, Shuntaro Takahashi, and Naoki Sugimoto
J. Am. Chem. Soc., 146 ( 12 ) 8005 - 8015 2024.3
Joint Work
Publisher：American Chemical Society (ACS)
Intracellular chemical microenvironments, including ion concentrations and molecular crowding, play pivotal roles in cell behaviors, such as proliferation, differentiation, and cell death via regulation of gene expression. However, there is no method for quantitative analysis of intracellular environments due to their complexity. Here, we have developed a system for highlighting the environment inside of the cell (SHELL). SHELL is a pseudocellular system, wherein small molecules are removed from the cell and a crowded intracellular environment is maintained. SHELL offers two prominent advantages: (1) It allows for precise quantitative biochemical analysis of a specific factor, and (2) it enables the study of any cell, thereby facilitating the study of target molecule effects in various cellular environments. Here, we used SHELL to study G-quadruplex formation, an event that implicated cancer. We show that G-quadruplexes are more stable in SHELL compared with in vitro conditions. Although malignant transformation perturbs cellular K+ concentrations, environments in SHELL act as buffers against G-quadruplex destabilization at lower K+ concentrations. Notably, the buffering effect was most pronounced in SHELL derived from nonaggressive cancer cells. Stable G-quadruplexes form due to the binding of the G-quadruplex with K+ in different cancer cells. Furthermore, the observed pattern of G-quadruplex-induced transcriptional inhibition in SHELL is consistent with that in living cells at different cancer stages. Our results indicate that ion binding to G-quadruplexes regulates gene expression during pathogenesis.
DOI： 10.1021/jacs.3c11160
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Hisae Tateishi-Karimata, Naoki Sugimoto
ACS Omega 9 ( 5 ) 5675 - 5682 2024.1
G-quadruplexes in disease-related genes are associated with various biological processes and regulate disease progression. Although methods involving ligands and other techniques are available to stabilize G-quadruplexes, approaches for destabilizing G-quadruplexes remain limited. Here, we evaluated whether G-quadruplexes can be destabilized using choline dihydrogen phosphate (choline dhp), a highly biocompatible hydrated ionic liquid. Circular dichroism spectral measurements at increasing temperatures revealed that choline dhp destabilized G-quadruplexes more effectively than did KCl-containing solutions. Thermodynamic analysis indicated that destabilization occurred via an entropic contribution, suggesting that choline ions did not coordinate with the G-quartets, because of their large radii. Subsequently, plasmid DNAs containing G-quadruplexes were constructed, and transcription reactions were performed in nuclear extracts from living cells. G-quadruplexes repressed transcription, whereas the addition of choline dhp increased transcription. Although ionic liquids often inactivate biomolecules, choline dhp can be used to culture various cells. Furthermore, the transcription of template DNA containing the G-quadruplex was greatly enhanced in living MDA-MD-231 cells (aggressive human breast cancer cells) cultured with choline dhp. Our results show that choline dhp destabilizes G-quadruplexes in cells, indicating that choline dhp can regulate gene expression. Thus, choline dhp may be useful for regulating target disease-related genes.
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In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics. Reviewed International coauthorship International journal
Dipanwita Banerjee, Hisae Tateishi-Karimata, Maria Toplishek, Tatsuya Ohyama, Saptarshi Ghosh, Shuntaro Takahashi, Marko Trajkovski, Janez Plavec, Naoki Sugimoto
Journal of the American Chemical Society 145 ( 43 ) 23503 - 23518 2023.11
In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear. Therefore, the mechanistic details of the effect of such molecular crowding were investigated at the molecular level by using thermodynamic and nuclear magnetic resonance analyses, revealing structure-dependent destabilization of the duplexes under crowded conditions. The transition from B- to A-like hybrid duplexes due to a change in conformation of the DNA strand guided by purine-pyrimidine asymmetry significantly increased the hydration number, which resulted in greater destabilization by the addition of cosolutes. By quantifying the individual contributions of environmental factors and the bulk structure of the duplex, we developed a set of parameters that predict the stability of hybrid duplexes with conformational dissimilarities under diverse crowding conditions. A comparison of the effects of environmental conditions in living cells and in vitro crowded solutions on hybrid duplex formation using the Förster resonance energy transfer technique established the applicability of our parameters to living cells. Moreover, our derived parameters can be used to estimate the efficiency of transcriptional inhibition, genome editing, and silencing techniques in cells. This supports the usefulness of our parameters for the visualization of cellular mechanisms of gene expression and the development of nucleic acid-based therapeutics targeting different cells.
DOI： 10.1021/jacs.3c06706
Books and Other Publications 【 display / non-display 】
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Stability Prediction of Canonical and Noncanonical Structures of Nucleic Acids.
S. Takahashi, H. Tateishi-Karimata, N. Sugimoto（ Role： Joint author）
Handbook of Chemical Biology of Nucleic Acids.Springer 2023
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Liquid Phase Separation and Nucleic Acids
H. Tateishi-Karimata, S. Matsumoto, N. Sugimoto（ Role： Joint author）
Handbook of Chemical Biology of Nucleic Acids.Springer 2023
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Effects of Molecular Crowding on Structures and Functions of Nucleic Acids.
T. Endoh, H. Tateishi-Karimata, N. Sugimoto（ Role： Joint author）
Handbook of Chemical Biology of Nucleic Acids.Springer 2023
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Chemistry and Biology of Non-canonical Nucleic Acids
N. Sugimoto（ Role： Sole author）
WILEY 2021.4
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相分離生物学の全貌（現代化学増刊46）
建石寿枝, 杉本直己（ Role： Joint author , 第Ⅳ部 生物学的相分離の理論）
東京化学同人 2021
Review Papers (Misc) 【 display / non-display 】
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分子夾雑系での核酸挙動
建石寿枝、三好大輔、杉本直己
CSJカレントレビュー「生体分環境の化学―分子夾雑と1分子で解き明かす生体の挙動―」化学同人 45 36 - 41 2023.2
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遺伝子発現における核酸の新機能 Reviewed
松本咲, 杉本直己
CSJカレントレビュー「進化を続ける核酸化学―ゲノム編集、非二重らせん、核酸医薬―」 41 146 - 154 2021.10
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細胞内の核酸物理化学 Reviewed
高橋俊太郎, 杉本直己
CSJカレントレビュー「進化を続ける核酸化学―ゲノム編集、非二重らせん、核酸医薬―」 41 14 - 21 2021.10
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フロントランナーに聞く「令和の時代も進化を続ける核酸化学」
神谷真子, 建石寿枝, 永次史, 山吉麻子, 杉本直己
CSJカレントレビュー「進化を続ける核酸化学―ゲノム編集、非二重らせん、核酸医薬―」 41 2 - 13 2021.10
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がん関連mRNAと光線力学療法
三好大輔, 杉本直己
CSJカレントレビュー「生体分子と疾患」 39 75 - 83 2021.8
Publisher：化学同人
Presentations 【 display / non-display 】
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In Cell Statistical Thermodynamics for Analyzing and Controlling Functions of Nucleic Acids Invited
N. Sugimoto
2024.9
Event date： 2024.9
Country：Japan
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
2024.9 The Japan Society of Nucleic Acids Chemistry
Event date： 2024.9
Country：Japan
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“To B or not to B” in Nanotechnology of Nucleic Acids Invited
N. Sugimoto
Lecture at UCL School of Pharmacy (London) 2024.7 UCL School of Pharmacy
Event date： 2024.7
Country：United Kingdom
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“To B or not to B" in Nucleic Acids Chemistry Invited
N. Sugimoto
Lecture at Nankai University (Tianjin) 2024.7 The State Key Laboratory of Elemento-organic Chemistry of Nankai University
Event date： 2024.7
Country：China
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“To B or not to B”in Nanotechnology of Nucleic Acids Invited
N. Sugimoto
11th International Conference on DNA Nanotechnology (Sainan) 2024.7 The School of Chemistry & Chemical Engineering and Materials Science at Shandong Normal University
Event date： 2024.7
Country：China
Industrial property rights 【 display / non-display 】
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核酸の立体構造を制御する方法及びその用途、並びに、細胞内分子クラウディング環境を再現するための組成物
建石 寿枝、高橋 俊太郎、川内 敬子、杉本 直己
Application no：特願2022-189538
Other Research Activities 【 display / non-display 】
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私の自慢「知の系譜：挑戦するオストワルト・ギブスの末裔たち－物理化学は細胞の中へ，極限状態の生命へ」
2013.2
Book Review
Academic Awards Received 【 display / non-display 】
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第72回日本化学会賞
2020.3 公益社団法人日本化学会 分子クラウディング環境における非二重らせん核酸の化学
杉本直己
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The Imbach-Townsend Award
2018.8 IS3NA（International Society for Nucleosides, Nucleotides, and Nucleic Acids）
N. Sugimoto
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Keynote Lecture賞
2016.6 European Chemistry Congress (Euro Chemistry2016)
Naoki Sugimoto
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第39回井植文化賞（科学技術部門）
2015.10 公益財団法人 井植記念会
杉本直己
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平成26年度 錯体化学会 貢献賞
2014.9 錯体化学会
杉本 直己
Grant-in-Aid for Scientific Research 【 display / non-display 】
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Quantitative prediction of nucleic acid structures and functions affected by spaciotemporal environmental factors in cells
2022.4 - 2027.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(S)
Authorship：Principal investigator
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イオンチャンネルは核酸の非二重らせん構造の形成と遺伝子発現を制御しているのか
2020.7 - 2022.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Exploratory Research
イオンチャンネルは核酸の非二重らせん構造の形成と遺伝子発現を制御しているのか
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核小体内クラウディング環境におけるリボソームRNA形成の定量的解析
2019.11 - 2022.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows
核小体内クラウディング環境におけるリボソームRNA形成の定量的解析
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核酸構造のトポロジーによる遺伝子発現の化学的制御
2019.4 - 2022.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(A)
杉本 直己
核酸構造のトポロジーによる遺伝子発現の化学的制御
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核酸の非二重らせん構造を調節し、がんの発症を制御するのは、カリウムイオンなのか
2018.4 - 2020.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Exploratory Research
核酸の非二重らせん構造を調節し、がんの発症を制御するのは、カリウムイオンなのか
Other External funds procured 【 display / non-display 】
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核酸の非標準構造を標的とした細胞応答の化学的制御技術の構築と先制核酸医
2014.4 - 2019.3
文部科学省 文部科学省私立大学戦略的研究基盤形成支援事業
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特異なmRNA構造を活用した翻訳フレームシフト及び産生タンパク質機能の制御
2013.4 - 2014.3
公益財団法人長瀬科学技術振興財団 長瀬科学技術振興財団助成金
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ひらめき☆ときめき サイエンス～要こそ大学の研究室～ＫＡＫＥＮＨＩ
2011.4 - 2012.3
文部科学省 「ひらめき☆ときめき サイエンス～ようこそ大学の研究室～KAKENHI」研究成果の社会還元・普及事業
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生命化学分野に関する学術動向の調査研究
2011.4 - 2012.3
文部科学省 学術システム研究センター研究員
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ひらめき☆ときめき サイエンス～要こそ大学の研究室～ＫＡＫＥＮＨＩ
2010.4 - 2011.3
文部科学省 「ひらめき☆ときめき サイエンス～ようこそ大学の研究室～KAKENHI」研究成果の社会還元・普及事業
Joint and Contract research activities (Public) 【 display / non-display 】
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フタロシアニンなどのπ共役化合物による細胞毒性検討および癌関連酵素の新規測定技術の開発
Domestic Joint Research
2011.4 - 2012.3
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平成23年度調査研究「生命科学分野に関する学術動向の調査研究」
General funded research
2011.4 - 2012.3
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DNAの高次構造に注目した細胞のがん化機構の解明と化学物質のリスク評価システムの構築
General funded research
2010.9 - 2011.8
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フタロシアニンなどのπ共役化合物の抗腫瘍効果の検討および生体センシングへの応用検討
Joint Research on Campus
2010.4 - 2011.3
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DNAの高次構造に注目した細胞のがん化機構の解明と化学物質のリスク評価システムの構築
General funded research
2009.9 - 2010.8
Preferred joint research theme 【 display / non-display 】
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生命分子(核酸・タンパク質等)の立体構造の解明
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生命分子間相互作用のデータベース化
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生命分子(核酸・タンパク質等)の物性解析
Committee Memberships 【 display / non-display 】
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2017.11 - 2020.8 日本核酸化学会 会長
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2015.5 - 2017.5 日本化学会 理事
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2013.3 - 2015.2 日本化学会 生体機能関連部会監事
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2011.3 - 2013.2 日本化学会 生体機能関連部会部会長
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2010.4 - 2017.3 社団法人 日本学術振興会 学術システム研究センター専門研究員
Social Activities 【 display / non-display 】
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ひょうご経済・雇用活性化プラン策定会議構成員
2018.6 - 2019.3
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ひょうご次世代産業高度化プロジェクト推進協議会委員
2018.4 - 2021.3
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南開大学客座教授
2017.3
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兵庫県ひょうご経済・雇用活性化プラン推進会議構成員
2016.7 - 2017.3