Presentations -
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New Data Science in Nucleic Acids Chemistry (25): Analysis and prediction of DNA behavior within mitochondria during stress responses
L. Liu, S. Takahashi, N. Yoshinaga, K. Numata, N. Sugimoto
日本化学会第106回春季年会 (船橋) 2026.3 日本化学会
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New Data Science in Nucleic Acids Chemistry (21): In-cell stability prediction of DNA duplexes for designing functional DNAs working in cells
Funabashi city, Chiba Prefecture 2026.3
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New Data Science in Nucleic Acids Chemistry (24): Optimization of DNAzyme activity using the improved nearest-neighbor parameters
2026.3
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New Data Science in Nucleic Acids Chemistry (22): Quantitative approaches for RNA structure prediction in cells to enable high-impact nucleic acid therapeutics
2026.3
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New Data Science in Nucleic Acids Chemistry (23) : Nearest-neighbour parameters for stability prediction of 2′-MOE RNA duplex in cancer cells
K. Chen, H. Tateishi-Karimata, S. Takahashi, S. Matsumoto, N. Sugimoto
日本化学会第106回春季年会 (船橋) 2026.3 日本化学会
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"To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Pure and Applied Chemistry Conference 2026 (PACCON 2026) (Phitsanulok) 2026.2 Organizing Committee of PACCON 2026
Event date： 2026.2
Country：Thailand
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 Department of Chemistry, Faculty of Science of Chulalongkorn University (Bangkok) 2026.2 Chulalongkorn University
Event date： 2026.2
Country：Thailand
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 the Korea Advanced Institute of Science and Technology (KAIST) (Daejeon) 2026.1 Department of Chemistry at the Korea Advanced Institute of Science and Technology (KAIST)
Event date： 2026.1
Country：Korea, Republic of
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 analyzed quantitatively 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 destabilizes 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 Invited
N.Sugimoto
2025 G-LAMP International Seminar (Cheongju) 2026.1 G-LAMP Project Group at Chungbuk National University
Event date： 2026.1
Country：Korea, Republic of
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 analyzed quantitatively 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 destabilizes 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 and Aptamers Chemistry Invited
N. Sugimoto
The International Chemical Congress of Pacific Basin Societies 2025 (Pacifichem2025) (Hawaii) 2025.12 Pacifichem 2025 Organizing Committee
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“Beyond the Watson-Crick Double Helix: Make New History of Nucleic Acids (10)” Invited
N. Sugimoto
Asia 3 Roundtable on Nucleic Acids 2025 (A3RONA2025) (Sapporo) 2025.11 Organizing Committee of Asia 3 Roundtable on Nucleic Acids 2025 (A3RONA2025)
Event date： 2025.11 - 2025.12
Country：Japan
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.
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“To B or Not to B” in Nucleic Acids Chemistry Invited
N.Sugimoto
Italian Meeting on G-quadruplexes (G4) and other non-canonical nucleic acid structure (G4ME Catanzaro 2025) (Catanzaro) 2025.10 Organizing Committee of G4ME Catanzaro 2025
Event date： 2025.10
Country：Italy
In this lecture, I will provide an overview of the basic concepts, methods, and recent 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 versatility 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. The new physicochemical approach will be introduced to apply the analysis of nucleic acids behaviors in cell. 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
Adriatic NMR Conference (Vodice) 2025.9 Organizing Committee of Adriatic NMR Conference
Event date： 2025.9
Country：Croatia
In this lecture, I will provide an overview of the basic concepts, methods, and recent 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.
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
13th International Conference Structure and Stability of Biomacromolecules (SSB 2025) (Kosice) 2025.9 Organizing Committee of 13th International Conference Structure and Stability of Biomacromolecules (SSB 2025)
Event date： 2025.9
Country：Slovakia
In this lecture, I will provide an overview of the basic concepts, methods, and recent 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.
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Seminar of Beijing Advanced Center of RNA Biology(BEACON) (Beijing Advanced Center of RNA Biology(BEACON), Beijing) 2025.7 Beijing Advanced Center of RNA Biology(BEACON)
Event date： 2025.7
Country：China
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All about “To B or not to B” in Nucleic Acids Chemistr Invited
N. Sugimoto
The Seminar of University of Toronto 2025.7
Event date： 2025.7
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All About "To B or Not to B" in Nucleic Acids Chemistry Invited
N. Sugimoto
Gordon Research Conference (Nucleosides, Nucleotides and Oligonucleotides) (Salve Regina University, Newport) 2025.7 Gordon Research Conference
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“To B or not to B” in Nanotechnology of Nucleic Acid Invited
N. Sugimoto
The 12th Conference on DNA Nanotechnology (Jinniu Hotel, Chengdu ) 2025.6 Organizing Committee of the12th Conference on DNA Nanotechnology
Event date： 2025.6
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.1-11 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 Invited
N. Sugimoto
XIXth Symposium on Chemistry of Nucleic Acid Components (SCNAC2025) (Hotel Ruze, Cesky Krumlov) 2025.6 Organizing committee of the 2025 SCNAC
Event date： 2025.6
Country：Czech Republic
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 Invited
N. Sugimoto
iNANo Minisymposium on Non-canonical Nucleic Acid structures (Aarhus University, Aarhus) 2025.5 Aarhus University
Event date： 2025.5
Country：Denmark
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.