Presentations -
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
Sungkyunkwan University Nucleic Acid Forum (SKKU NAF 2025) (Sungkyunkwan University, Seoul) 2025.5 Sungkyunkwan University
Event date： 2025.5
Country：Korea, Republic of
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 Invited
N. Sugimoto
International Workshop “Trends in Nucleic Acid (TINA) 2025” (Nankai University, Tianjin) 2025.4 Nakai University
Event date： 2025.4
Country：China
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 Invited
N. Sugimoto
The Seminar of School of Chemistry and Chemical Engineering, Nanjing University (Nanjing University, Nanjing) 2025.4 Nanjing University
Event date： 2025.4
Country：China
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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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
Event date： 2025.3
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Quantify specific interactions determining G-quadruplex and i-motif formation during cancer progression
H. Tateishi-Karimata, K. Kawauchi, S. Takahashi, and N. Sugimoto
To B or Not to B Symposium 2025
Event date： 2025.3
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Seminar of Department of Pharmacy, University of Naples Federico II (Naples) 2025.2 University of Naples “Federico II”
Event date： 2025.2
Country：Italy
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.1-12 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 Invited
N. Sugimoto
The Seminar of Department of Molecular Medicine of the University of Padua (Padua) 2025.1 University of Padua
Event date： 2025.1
Country：Italy
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 pplications of predicting the stabilities of nucleic acid structures.1-12 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 ntracellular 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 Invited
N. Sugimoto
The 7th Asian Chemical Biology Conference 2025 (ACBC) (Kowloon) 2025.1 The Hong Kong University of Science and Technology
Event date： 2025.1
Country：Hong Kong
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.1-11 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 Invited
N. Sugimoto
Special Departmental Seminar of Chemistry Department of City University of Hong Kong (Kowloon) 2025.1 City University of Hong Kong
Event date： 2025.1
Country：Hong Kong
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.1-11 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 Invited
N. Sugimoto
the 11th Asian Biological Inorganic Chemistry Conference (Guilin) 2024.12 Asian Bioinorganic Chemistry Steering Committee
Event date： 2024.12
Country：China
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.1-6 I also describe advances in the prediction of non-canonical structures of G-quadruplexes and i-motifs. Finally, studies of ligands binding to canonical and non-canonical structures of nucleic acids are discussed for human health and diseases.