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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 - 2024.3
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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疾患進行における非二重らせん核酸構造の機能 擬似細胞系SHELLによる機構的理解
建石 寿枝, 杉本 直己
生化学 98 ( 1 ) 132 - 136 2026.2
Publisher：(公社)日本生化学会
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Stability of non-canonical nucleic acid structure as a potential modulator of cell fate. International journal
Shuntaro Takahashi, Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic acids research 54 ( 2 ) 2026.1
Cellular morphological changes occur during cell life and diseases, such as senescence and cancer. Although the cellular conditions should be varied with the morphology changes, there have been no attempts to understand the cellular morphological changes by focusing on the intracellular molecular environment and elucidating the behaviour of nucleic acids. Nucleic acids can form hierarchical secondary and higher-order structures due to intermolecular interactions and other factors. Additionally, a number of important discoveries indicate a link between the effects of intracellular cations, hydration, and metabolic products on the stability of nucleic acid structures and diseases, such as cancer. Thus, changes in gene expression by environments can trigger morphological changes in cells. To elucidate the mechanisms of intracellular gene expression governed by nucleic acid behaviour, it is extremely important to analyse the stability of nucleic acid structures in the whole cell or local cellular spaces by manipulating the actions of small molecules, such as cations, water, and metabolic products. This review article describes the research background and latest progress in controlling senescence and cancer by modulating gene expression based on the prediction of intracellular nucleic acid behaviour, with a focus on the effects of cations, hydration, and metabolites on intracellular nucleic acid structures and their stability.
DOI： 10.1093/nar/gkaf1486
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Conformational Transition of Viral Nucleic Acids in a Capsid‐Like Confined Environment Reviewed International journal
Sunipa Sarkar, Hisae Tateishi‐Karimata, Kazunori Matsuura, Naoki Sugimoto
Chemistry – A European Journal 31 ( 45 ) e01208 - e01208 2025.7
Authorship：Corresponding author Publisher：Wiley
Abstract
Nucleic acid molecules within viral genomes can fold into noncanonical structures, such as G‐quadruplexes (G4s), which play crucial roles in regulating viral gene expression. These genomes are confined within capsid environments that vary in dimensions and ionic compositions. Structural transitions in RNA or DNA within these confined environments are essential for modulating viral biological functions; however, these transitions remain poorly understood. In this study, we demonstrated that an RNA sequence derived from the human immunodeficiency virus (HIV‐1) genome adopts a dynamic equilibrium between G4 and hairpin (Hp) structures modulated by ionic conditions. The equilibrium shifts toward the G4 conformation in the presence of potassium (K⁺) and magnesium (Mg<sup>2</sup>⁺) ions. Using reverse micelles (RMs) as mimetics of the intracapsid environment, we showed that the size of the RM water pool influences significantly this equilibrium: smaller water pools favor G4 formation, whereas larger pools prefer the Hp structure owing to variations in the dielectric constant. Notably, the addition of Mg<sup>2</sup>⁺ ions alters the size‐dependent effects of RMs by stabilizing the G4 structure. These findings highlight the critical roles of environmental confinement and ionic conditions in regulating viral RNA structural dynamics, offering new insights into RNA‐based regulatory mechanisms and their impact on viral gene expression. -
Twisting tetraplex DNA: A strand dynamics regulating i-motif function in diverse molecular crowding environments Reviewed International coauthorship International journal
Shuntaro Takahashi, Saptarshi Ghosh, Marko Trajkovski, Tatsuya Ohyama, Janez Plavec, Naoki Sugimoto
Nucleic Acids Research 53 ( 12 ) gkaf500 - gkaf500 2025.6
Authorship：Corresponding author Publisher：Oxford University Press (OUP)
Abstract
Intercalated motif (i-motif) tetraplex DNA plays a crucial role in gene expression and diseases. However, due to the limited number of i-motif binding proteins in human cells, the chemical mechanisms regulating i-motifs within cell remain currently unknown. Thus, molecular environment should have a main factor to control i-motif formation and functions in cells. Here, we systematically investigated the stability and functions of i-motif DNAs by using various polyethylene glycols (PEGs) and oligoethylene glycols (OEGs) that mimicked diverse cellular crowding environments. We found that the human telomere i-motif was significantly stabilized by PEGs and OEGs having six or more ethylene glycol units, whereas it was destabilized by those having less than six units. As these stabilization effects coincided with the drastic changes in hypochromicity by i-motif helixes, we quantitatively validated these effects through changes in solution properties and by assessing the twisting of the tetraplex structure using nuclear magnetic resonance (NMR) and molecular dynamics simulations. Furthermore, cosolute-induced twisting dynamics controlled by different cosolutes changed the activation energy barrier of replication by a twofold magnitude along the i-motif-forming DNAs. Our findings indicate that regulatory mechanisms underlying the biological roles of i-motifs across different cellular phases may exist by molecular environments.DOI： 10.1093/nar/gkaf500
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Controlling the local conformation of RNA G-quadruplex results in reduced RNA/peptide cytotoxic accumulation associated with C9orf72 ALS/FTD Reviewed International journal
Saki Matsumoto, Hisae Tateishi-Karimata, Tatsuya Ohyama, Naoki Sugimoto
Small Methods 9 ( 6 ) 2401630 - 2401630 2025.6
Authorship：Corresponding author
Abstract
Repeat expansion of d(G4C2) in the noncoding region of the C9orf72 gene contributes to neurodegenerative diseases. The repeat expansion transcript r(G4C2) induces RNA/peptide accumulation, which, in turn, induces cytotoxicity and accelerates the development of neurodegenerative diseases. Such cytotoxic accumulation is triggered by peptide aggregation. Here, a technique is developed to prevent accumulation by regulating RNA interactions, assuming that RNA structure is important for peptide interactions. A screening method is used to identify compounds that suppress RNA accumulation of r(G4C2) repeats. The four compounds are identified with wide π-planes containing hydroxyl, methoxy, and cyclic ether groups that suppressed RNA accumulation. Interestingly, these compounds also suppressed RNA/peptide accumulation in neuroblastoma cells, indicating that RNA accumulation is a key regulator of RNA/peptide cytotoxic aggregate formation. In vitro and in silico physicochemical analyses reveal that these compounds bind to the loop region of the G-quadruplex via hydrogen bonds or CH-π interactions, resulting in an altered loop conformation. Importantly, these conformational changes inhibited RNA G-quadruplex associations. These results show that conformational changes are promising for controlling the interactions between G-quadruplexes and further RNA accumulation. These findings may be useful in the development of therapeutic strategies for the treatment of neurodegenerative diseases.
Keywords: G‐quadruplex; RNA gelation; compound screening; liquid–liquid phase separation; neurodegenerative diseases.
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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Cell-Specific Nearest-Neighbor Parameters for Developing Functional DNA Devices Working in Cancer Cells
CHEN Kun, TATEISHI-KARIMATA Hisae, TAKAHASHI Shuntaro, OHYAMA Tatsuya, SUGIMOTO Naoki
Program & Abstracts. International Symposium on Nucleic Acids Chemistry 52nd 2025
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New Data Science in Nucleic Acids Chemistry (17): Development of a pseudo-cellular system with different molecular crowding environments
TAKATSU Masako, TATEISHI-KARIMATA Hisae, SUGIMOTO Naoki
日本化学会春季年会講演予稿集(Web) 105th 2025
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New Data Science in Nucleic Acids Chemistry (14): Development of methods to predict RNA secondary structures in cells
TATEISHI-KARIMATA Hisae, TATEISHI-KARIMATA Hisae, DIPANWITA Banerjee, TAKAHASHI Shuntaro, NISHIMURA Tomohiro, FUKUNAGA Tsukasa, HAMADA Michiaki, SUGIMOTO Naoki
日本化学会春季年会講演予稿集(Web) 105th 2025
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Stability prediction of RNA structures using nearest neighbor parameters developed in pseudo-cellular systems
TATEISHI-KARIMATA Hisae, DIPANWITA Banerjee, KUN Chen, TAKAHASHI Shuntaro, NISHIMURA Tomohiro, FUKUNAGA Tsukasa, HAMADA Michiaki, HAMADA Michiaki, SUGIMOTO Naoki
Program & Abstracts. International Symposium on Nucleic Acids Chemistry 52nd 2025
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New Data Science in Nucleic Acids Chemistry (8): Real-time monitoring of nucleic acids conformational change in living cells using high-speed confocal imaging system
ENDOH Tamaki, TATEISHI-KARIMATA Hisae, TSUTSUI Keita, FUKAYA Yoko, TSUKIJI Shinya, SUGIMOTO Naoki, SUGIMOTO Naoki
日本化学会春季年会講演予稿集(Web) 104th 2024
Presentations 【 display / non-display 】
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Italian Meeting on G-quadruplexes (G4) and other non-canonical nucleic acid structure (G4ME Ancona 2026) (Ancona) 2026.7 Organizing Committee of the Italian Meeting on G-quadruplexes (G4) and other non-canonical nucleic acid structure (G4ME Ancona 2026)
Event date： 2026.7
Country：Italy
Various nucleic acid structures other than just the duplex structure, for example, G-quadruplex, play important roles in cellular systems. Before the formation of these structures, the duplex has to unfold, thus the stability information about the duplex is very useful in chemical biology. We have determined new nearest neighbor parameters to predict stability of the canonical duplex structures of nucleic acids1-5 and elucidated roles of their non-canonical structures.6-14 We recently developed a pseudo-cellular system called SHELL (System for Highlighting the Environments Inside the Cell),15 which integrates compartmental heterogeneity and dynamic molecular behavior into a unified system. The SHELL model mimics more closely the compartmentalized and dynamic nature of intracellular environments. As a result, SHELL captures the cumulative thermodynamic effects of spatial heterogeneity, offering a practical alternative to conventional homogeneous polyethylene glycol (PEG)-induced systems. In this study, we applied the SHELL system to evaluate the NN model in three representative mammalian cells, NIH3T3 (normal), MCF-7 (mild cancer), and MDA-MB-231 (aggressive cancer). We assessed both the thermodynamic stability of DNA duplexes and the catalytic activity of DNAzymes in these cell-type-specific environments. The resulting NN parameters reflected clear and consistent differences in intracellular thermodynamic parameters, revealing a gradient of DNA duplex stability correlating with malignancy. We will further demonstrate that these parameters enable predictive control over nucleic acid function. Finally, studies of intracellular analysis and stability prediction are discussed for the application of NN parameters for human health and diseases.
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“To B or not to B” in Nanotechnology of Nucleic Acids: Part III Invited
N. Sugimoto
The 13th International Conference on DNA Nanotechnology (Beijing) 2026.6 Polymer Discipline Committee, Chinese Chemical Society
Event date： 2026.6
Country：China
Nucleic acids (NAs; DNA and RNA) are genetic materials in living organisms and formed by a sequence of nucleobases. The stability of NA structures cannot be determined from only the sequence composition, as this property critically depends on the surrounding environment of the solution. The intracellular condition is greatly different from that of the diluted buffer typically used for standard experiments and is not constant in each local area of the cell. Thus, to make excellent nanomaterials with NAs working in cells, stability predictions should reflect the situation under intracellular conditions and are required importantly.
In this lecture, I will provide an overview of the basic concepts, methods, and applications of predicting the stabilities of NA structures. I explain the theory of the most successful prediction method based on a nearest-neighbor (NN) model. I also describe advances in the prediction of non-canonical structures of G-quadruplexes and i-motifs of NAs. Finally, studies of intracellular analysis and stability prediction are discussed for the application of NN parameters for designing DNA nanomaterials. As computational structural predictions advance in the field of NAs, an accurate prediction model for NAs, similar to AlphaFold, may be established in the near future. However, two key issues remain, which the alphaFold algorithm does not account for: (1) Prediction of the de novo structure from primary sequence information and, more importantly, (2) effect of the molecular environment on structure formation. Since NAs fold dynamically to form tertiary structures from single strands and are more sensitive to the environment than proteins, basic energetic information on how the environment affects their base pairing will be required for accurately predicting the structure and activity of functional Nas in the bionanotechnology. -
“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
RNA Salon Poznan (Poznan) 2026.6 Department of Biology, Adam Mickiewicz University
Event date： 2026.6
Country：Poland
In this lecture, I will provide an overview of the basic concepts, methods, and recent applications of predicting the stabilities and functions of nucleic acid structures. I explain the theory of the most successful prediction method based on a nearest-neighbor (NN) model. To improve the versality of prediction, corrections for various solution conditions considered hydration have been investigated. I also describe advances in the prediction of non-canonical nucleic acids structures of G-quadruplexes and i-motifs. Finally, studies of intracellular analysis and stability prediction are discussed for the application of NN parameters for human health and diseases.
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Seminar of Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCH PAS) (Poznan) 2026.6 Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCH PAS)
Event date： 2026.6
Country：Poland
In this lecture, I will provide an overview of the basic concepts, methods, and recent applications of predicting the stabilities and functions of nucleic acid structures. I explain the theory of the most successful prediction method based on a nearest-neighbor (NN) model. To improve the versality of prediction, corrections for various solution conditions considered hydration have been investigated. I also describe advances in the prediction of non-canonical nucleic acids structures of G-quadruplexes and i-motifs. Finally, studies of intracellular analysis and stability prediction are discussed for the application of NN parameters for human health and diseases.
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Seminar of Centre of Molecular and Macromolecular Studies, the Polish Academy of Sciences （CBMM PAS） (Lodz) 2026.6 Centre of Molecular and Macromolecular Studies, the Polish Academy of Sciences （CBMM PAS）
Event date： 2026.6
Country：Poland
In this lecture, I will provide an overview of the basic concepts, methods, and recent applications of predicting the stabilities and functions of nucleic acid structures. I explain the theory of the most successful prediction method based on a nearest-neighbor (NN) model. To improve the versality of prediction, corrections for various solution conditions considered hydration have been investigated. I also describe advances in the prediction of non-canonical nucleic acids structures of G-quadruplexes and i-motifs. Finally, studies of intracellular analysis and stability prediction are discussed for the application of NN parameters for human health and diseases.
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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Frantisek Sorm Memorial Medal
2025.6 Academy of Sciences of the Czech Republic
Naoki Sugimoto
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The Ikehara Award (Top Award)
2024.9 Japan Society of Nucleic Acids Chemistry (JSNAC)
Naoki Sugimoto
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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
Grant-in-Aid for Scientific Research 【 display / non-display 】
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核酸二重らせんの塩基対形性を支配する構造エントロピーの定量的解析
2025.11 - 2027.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows
杉本 直己
本研究では、各種二重鎖の構造エントロピーを決定する新規手法を確立するため、まずRNA/RNA、DNA/DNA、RNA/DNA二量体の末端塩基対における水素結合の自由エネルギーと塩基スタッキングの自由エネルギーを定量化する。続いて、それらがDNA鎖とRNA鎖の結合・解離速度に及ぼす影響を評価する。DNAやRNAといった核酸の種類が決定する化学的および生物学的な意義を理解するため、GあるいはCの連続配列、またはGCが交互に配列する鋳型鎖を用いて、ポリメラーゼによるプライマー伸長アッセイを実施する。さらに、細胞抽出液や細胞内で同様のアッセイを行い、二重鎖の構造エントロピーが有する生物学的な意義を解明する。
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細胞内局所環境での核酸集団の機能解明を目指した次世代の統計熱力学の開拓
2025.6 - 2028.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Pioneering)
杉本 直己
中分子数での振る舞いは、ボルツマンの原理にある状態数Wを減少させ、局所環境の生体分子のエントロピーを少なくする。つまり、局所環境では分子挙動の状態数を小さくすることで、その安定性が大きく制御されうると考えられる。それ故、細胞内の特定のStateや時間においては、準安定な構造がかなり形成され、それらの構造が生命現象を制御する役割を担っている可能性がある。つまり、生命現象を理解するためには、これまでの物理化学の常識であるモル集団(N)の考え方以外の概念が必要である。そこで本研究では、細胞内の異なる時空間における核酸の機能解明を目指した「細胞内局在化核酸の次世代統計熱力学」を開拓する。
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Quantitative analysis and regulation of the tetraplexes of nucleic acids controlling cell cycle
2024.7 - 2026.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows
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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
Other External funds procured 【 display / non-display 】
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非二重らせん核酸を活用した遺伝子発現の制御法を開発する核酸化学
2022.4 - 2027.3
日本学術振興会 研究拠点形成事業 学術国際交流事業
杉本 直己
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ヒトがん遺伝子およびウイルス遺伝子を標的とした先制核酸医工学の開発～がん遺伝子の構造予測パラメータの開発～
2022.4 - 2026.3
公益財団法人 伊藤忠兵衛基金 医療研究助成金 公益財団法人伊藤忠兵衛基金医療研究助成金
杉本 直己
Authorship：principal_investigator
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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
Joint and Contract research activities (Public) 【 display / non-display 】
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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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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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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)の立体構造の解明
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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