Presentations -
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“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The XIV Meeting on Nucleic Acids and Nucleosides (RANN XIV) , Post-symposium of XXVI International Roundtable on Nucleosides, Nucleotides and Nucleic Acids (IRT2026) (Hotel Barcelo Sants) 2026.8 Organizing Committee of RANN XIV
Event date： 2026.8
Country：Spain
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 structures1-16. 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 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.
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"To B or not to B" in Nucleic Acids Chemistry Invited
N. Sugimoto
University of Wurzburg, GDCh colloquium series (Wurzburg) 2026.5 University of Wurzburg
Event date： 2026.5
Country：Germany
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. -
“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Seminar of University of Cologne, GDCh colloquium series (Cologne) 2026.5 University of Cologne
Event date： 2026.5
Country：Germany
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. -
“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
The Seminar of Hangzhou Institute of Medicine (Hangzhou) 2026.4 Hangzhou Institute of Medicine
Event date： 2026.4
Country：China
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. -
“To B or not to B” in Nucleic Acids Chemistry Invited
N. Sugimoto
International Workshop “Trends in Nucleic Acid (TINA) 2026” (Nankai University, Tianjin) 2026.4 Nankai University
Event date： 2026.4
Country：China
We have determined new nearest neighbor parameters to predict stability of the canonical duplex structures of nucleic acids1 and elucidated roles of their non-canonical structures.2 we recently developed a pseudo-cellular system called SHELL (System for Highlighting the Environments Inside the Cell),3 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.
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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