講演・口頭発表等 - 杉本 直己
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“To B or not to B” in Nucleic Acids Chemistry 招待あり
N. Sugimoto
The Seminar of Beijing Advanced Center of RNA Biology(BEACON) (Beijing Advanced Center of RNA Biology(BEACON), Beijing) 2025年7月 Beijing Advanced Center of RNA Biology(BEACON)
開催年月日： 2025年7月
国名：中華人民共和国
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All about “To B or not to B” in Nucleic Acids Chemistr 招待あり
N. Sugimoto
The Seminar of University of Toronto 2025年7月
開催年月日： 2025年7月
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All About "To B or Not to B" in Nucleic Acids Chemistry 招待あり
N. Sugimoto
Gordon Research Conference (Nucleosides, Nucleotides and Oligonucleotides) (Salve Regina University, Newport) 2025年7月 Gordon Research Conference
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“To B or not to B” in Nanotechnology of Nucleic Acid 招待あり
N. Sugimoto
The 12th Conference on DNA Nanotechnology (Jinniu Hotel, Chengdu ) 2025年6月 Organizing Committee of the12th Conference on DNA Nanotechnology
開催年月日： 2025年6月
国名：中華人民共和国
Nucleic acids (DNA and RNA) are genetic materials in living organisms and formed by a sequence of nucleobases. The stability of nucleic acids 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 nucleic acids 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 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.1-11 I also describe advances in the prediction of non-canonical 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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All about “To B or not to B” in Nucleic Acids Chemistry 招待あり
N. Sugimoto
XIXth Symposium on Chemistry of Nucleic Acid Components (SCNAC2025) (Hotel Ruze, Cesky Krumlov) 2025年6月 Organizing committee of the 2025 SCNAC
開催年月日： 2025年6月
国名：チェコ共和国
Nucleic acids typically form a double helix structure through Watson-Crick base-pairing. In contrast, non-Watson-Crick base pairs can form other three-dimensional structures. Although it is well-known that Watson-Crick base pairs may be more unstable than non-Watson-Crick base pairs under some conditions, the importance of non-Watson-Crick base pairs has not been widely examined. Hoogsteen base pairs, which are one of the typical non-Watson-Crick base pairs, contain important hydrogen-bond patterns that form the helices of nucleic acids, such as in Watson-Crick base pairs, and can also form non-double helix structures such as triplexes and quadruplexes. In recent years, non-double helix structures have been discovered in cells and were reported to considerably influence gene expression. The complex behavior of these nucleic acids in cells is gradually being revealed, but the underlying mechanisms remain almost unknown. Quantitatively analyzing the structural stability of nucleic acids is important for understanding their behavior. A nucleic acid is an anionic biopolymer composed of a sugar, base, and phosphoric acid. The physicochemical factors that determine the stability of nucleic acid structures include those derived from the interactions of nucleic acid structures and those derived from the environments surrounding nucleic acids. The Gibbs free energy change (ΔG) of structure formation is the most commonly used physicochemical parameter for analyzing quantitative stability. Quantitatively understanding the intracellular behavior of nucleic acids involves describing the formation of nucleic acid structures and related reactions as ΔG. Based on this concept, we quantitatively analyzed the stability of double helix and non-double helix structures and found that decreased water activity, one of the important factors in crowded cellular conditions, significantly destabilize the formation of Watson-Crick base pairs but stabilizes Hoogsteen base pairs.
In my presentation, I will describe a physicochemical approach to understand the regulation of gene expressions based on the stability of nucleic acid structures (1). We developed new methods for predicting the stability of double and non-double helices in various molecular environments by mimicking intracellular environments. Furthermore, the physicochemical approach used for analyzing gene expression regulated by non-double helix structures is useful for not only determining how gene expression is controlled by cellular environments but also for developing new technologies to chemically regulate gene expression by targeting non-double helix structures such as G-quadruplexes and i-motifs. I will discuss the roles of Watson-Crick and Hoogsteen base pairs in cells based on our results and why both types of base pairing are required for life. Finally, a new concept in nucleic acid science beyond that of Watson and Crick base pairing is introduced. -
To B or not to B” in Nucleic Acids Chemistry 招待あり
N. Sugimoto
iNANo Minisymposium on Non-canonical Nucleic Acid structures (Aarhus University, Aarhus) 2025年5月 Aarhus University
開催年月日： 2025年5月
国名：デンマーク王国
Nucleic acids (DNA and RNA) are genetic materials in living organisms and formed by a sequence of nucleobases. The stability of nucleic acids 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 nucleic acids 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 nucleic acid structures.1-9 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 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 招待あり
N. Sugimoto
Sungkyunkwan University Nucleic Acid Forum (SKKU NAF 2025) (Sungkyunkwan University, Seoul) 2025年5月 Sungkyunkwan University
開催年月日： 2025年5月
国名：大韓民国
Nucleic acids (DNA and RNA) are genetic materials in living organisms and formed by a sequence of nucleobases. The stability of nucleic acids 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 nucleic acids 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 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 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.
Acknowledgements：The author is grateful to the colleagues named in the cited papers from my laboratory, institute (FIBER), and others. This work was supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and the Japan Society for the Promotion of Science (JSPS) (Grant No. JP17H06351, 18KK0164, 19H00928, and 20K21258), especially for Grant-in-Aid for Scientific Research (S) (22H04975), JSPS Core-to-Core Program (JPJSCCA20220005), The Hirao Taro Foundation of Konan Gakuen for Academic Research, and The Chubei Itoh Foundation. -
“To B or not to B” in Nucleic Acids Chemistry 招待あり
N. Sugimoto
International Workshop “Trends in Nucleic Acid (TINA) 2025” (Nankai University, Tianjin) 2025年4月 Nakai University
開催年月日： 2025年4月
国名：中華人民共和国
Nucleic acids are genetic materials in living organisms and formed by a sequence of nucleobases. The stability of nucleic acids structures cannot be determined from only the sequence composition, because 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 biomaterials with nucleic acids 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 nucleic acid structures.1-10 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 structures such as 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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All about “To B or not to B” in Nucleic Acids Chemistry 招待あり
N. Sugimoto
The Seminar of School of Chemistry and Chemical Engineering, Nanjing University (Nanjing University, Nanjing) 2025年4月 Nanjing University
開催年月日： 2025年4月
国名：中華人民共和国
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Construction of artificial viral capsid encapsulating quadruplex DNA and its intracellular delivery
K. Matsuura, M. Ishii, H. Inaba, T. Endoh, H. Tateshi-Karimata, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (20) : G-quadruplex DNA formations depending on the environments in the mitochondrial matrix
L. Liu, S. Takahashi, G. Sarptarshi, T. Endoh, N. Yoshinaga, K. Numata, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (19): ATP regulates the DNA stability through structure-dependent cation exchange
S. Das, S. Takahashi, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (18) : Comparison of the stability of DNA duplexes among normal and cancer cells
K. Chen, H. Tateishi-Karimata, S. Takahashi, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids (17): Development of a pseudo-cellular system with different molecular crowding environments
M. Takatsu, H. Tateishi-Karimata, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (16) : Cellular compartment size as a critical factor in the stability and function of nucleic acids
S. Sarkar, H. Tateishi-Karimata, K. Matsuura, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (15): Universal prediction of DNAzyme activity using new nearest neighbor parameters and AI
S.Takahashi, T. Nishimura, S. Ghosh, H. Tateishi-Karimata, T. Fukunaga, M. Hamada, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (14), Development of methods to predict RNA secondary structures in cells
H. Tateishi-Karimata, D. Banerjee, S. Takahashi, T. Nishimura, T. Fukunaga, M. Hamada, M. Orehova, J. Plavec, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (13): Global and local molecular crowding effects depending on the size of crowding cosolute on stability of pseudoknot RNA
T. Endoh, S. Satpathi, N. Sugimoto
日本化学会第105回春季年会
開催年月日： 2025年3月
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New Data Science in Nucleic Acids Chemistry (12) : Role of groove hydration on stability and functions of biased DNA duplexes
N. Sugimoto, S. Ghosh, S. Takahashi, T. Ohyama, L. Liu
日本化学会第105回春季年会
開催年月日： 2025年3月
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Predictability of environment-dependent formation of the behavior of DNAs in human mitochondria
S. Takahashi, L. Liu, S. Ghosh, T. Endoh, N. Yoshinaga, K. Numata and N. Sugimoto
To B or Not to B Symposium 2025
開催年月日： 2025年3月