Papers - SUGIMOTO Naoki
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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. -
Predictability of environment-dependent formation of G-quadruplex DNAs in human mitochondria Reviewed
Lutan Liu;Shuntaro Takahashi;Sarptarshi Ghosh;Tamaki Endoh;Naoto Yoshinaga;Keiji Numata;Naoki Sugimoto
Communications Chemistry 8 ( 1 ) 135 - 135 2025.5
Authorship：Corresponding author
Abstract
Molecular crowding affects the stability of nucleic acids (DNA and RNA) and induces their non-canonical structures. As the level of molecular crowding varies spatio-temporally in cells, it would be beneficial to predict the behaviour of DNA and RNA structures depending on the local cellular environments. This has applications in human mitochondria, which possess an especially crowded condition. In this study, the predictability of guanine-quadruplex (G4) DNA formation in the environment specific to human mitochondria was investigated. In accordance with the stability of duplexes predicted by our nearest-neighbour parameters, the G-rich duplex stability was found to effectively decrease and G4 formation was induced in mitochondrion-like conditions compared to the nucleus-like conditions. Using a peptide-based mitochondrial targeting system, a G4 reporter assay performed in mitochondria indicated that G4 formation were more favoured in mitochondria more than in the nucleus. These findings provide insights useful for the prediction of the behaviour of nucleic acids in mitochondria. -
Imperfect G-quadruplex as an emerging candidate for transcriptional regulation Reviewed
Sunipa Sarkar, Hisae Tateishi-Karimata, Tatsuya Ohyama, Naoki Sugimoto
Nucleic Acids Res. 53 ( 5 ) gkaf164 - gkaf164 2025.2
Authorship：Corresponding author
Abstract
G-quadruplexes (G4s) with continuous G-tracts are well-established regulators of gene expression and important therapeutic targets for various diseases. However, bioinformatics analyses have identified G4-like sequences containing interrupted G-tracts, incorporating non-G nucleotides as bulges (buG4s). Our findings show that the stability of buG4s is significantly influenced by the bulge position and size within the G-tract, with bulges at the 5' end exhibiting the highest stability. Moreover, a molecular crowding condition inducing by poly (ethylene glycol), providing a suitable intracellular environment, stabilizes buG4s, especially those with longer bulges, making their formation more pronounced. A transcription assay performed under crowding conditions revealed that the transcription arrested efficiency by buG4s is affected not only by stability but also by the position and size of the bulge. Based on these findings, we propose a model for the preliminary screening of buG4 sequences according to their stability, distinguishing functional sequences capable of transcriptional arrest (ΔG°37 ≤ -3.3 kcal·mol-1) from nonfunctional sequences (ΔG°37 > -3.3 kcal·mol-1). This provides valuable insight into estimating the efficiency of target buG4 sequences in either arresting or facilitating transcription, presenting a novel approach and emphasizing buG4s as emerging therapeutic targets.DOI： 10.1093/nar/gkaf164
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Fitness landscapes and thermodynamic approaches to development of nucleic acids enzymes: From classical methods to AI integration Reviewed
Shuntaro Takahashi, Michiaki Hamada, Hisae Tateishi-Karimata, Naoki Sugimoto
RSC Chem. Biol. 2025
Authorship：Corresponding author
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Saptarshi Ghosh, Shuntaro Takahashi, Tatsuya Ohyama, Lutan Liu, Naoki Sugimoto
Journal of the American Chemical Society 146 ( 47 ) 32479 - 32497 2024.11
Authorship：Corresponding author
Abstract
Hydration plays a key role in the structure-specific stabilization of biomolecules such as nucleic acids. The hydration patterns of biased DNA sequences in the genome, such as GC-repetitive and AT-repetitive regions, are unique to their duplex grooves. As these regions are crucial for maintaining genomic homeostasis and preventing diseases such as cancer and neurodegenerative disorders, the effects of hydration on their stability and functions must be quantitatively analyzed in chemical environments that resemble intracellular conditions. In this study, we systematically investigated duplex formation of biased sequences in cell-like molecularly crowded environments to quantify the effects of groove hydration on their thermodynamics. The interaction of crowders with water molecules in the grooves was found to provide excess stabilization to biased DNAs than to unbiased DNAs, as estimated from the nearest-neighbor prediction model. These hydration effects are sequence-specific and depend on the cation type and cosolute size. Introduction of the "hydration parameters" into the nearest-neighbor model quantifying the effect of groove hydration remarkably enhanced the prediction accuracy for biased DNA stability in crowded environments. Hydration parameters can aid in elucidating the roles of biased sequences in cells such as cation-dependent quadruplex formation in cancer-related genes and regulation of replication initiation by intracellular crowding fluctuations. Additionally, these parameters can predict the free energy changes during the binding of protein to DNA grooves. Overall, our findings can help in realizing and predicting the functions of biased DNAs in cells controlled by variable chemical environments.DOI： 10.1021/jacs.4c09388
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Contrasting effect of different crowding agents on pseudoknot RNA stability Reviewed
S. Satpathi, T. Endoh and N. Sugimoto
Medicinal Chemistry Research 33 2079 - 2084 2024.8
Pseudoknot (PK) is one of the prevalent and potential targets for drug discovery. It is still difficult to predict PK-forming regions within endogenous RNA transcripts because the intracellular environment consisting of various cellular agents has diverse effects on the structure and stability of nucleic acids. In this study, we have demonstrated the impact of the varied crowding conditions on the structural stability of pseudoknot RNA, emphasizing the distinct stabilities of PK structures depending on the crowding environment.
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Guanidine modification improves functions of natural RNA-targeting alkaloids Reviewed International coauthorship
Tamaki Endoh, Sagar Satpathi, Yutong Chen, Saki Matsumoto, Tatsuya Ohyama, Peter Podbevšek, Janez Plavec, Kazumitsu Onizuka, Fumi Nagatsugi, Naoki Sugimoto
New Journal of Chemistry 48 ( 19 ) 8529 - 8533 2024.4
Publisher：Royal Society of Chemistry (RSC)
Guanidine modification on berberine improved RNA binding affinity and enhanced suppression of protein expression.
DOI： 10.1039/d3nj05833f
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Development of a Pseudocellular System to Quantify Specific Interactions Determining the G-Quadruplex Function in Cells Reviewed International journal
Hisae Tateishi-Karimata, Keiko Kawauchi, Shuntaro Takahashi, and Naoki Sugimoto
J. Am. Chem. Soc., 146 ( 12 ) 8005 - 8015 2024.3
Joint Work
Publisher：American Chemical Society (ACS)
Intracellular chemical microenvironments, including ion concentrations and molecular crowding, play pivotal roles in cell behaviors, such as proliferation, differentiation, and cell death via regulation of gene expression. However, there is no method for quantitative analysis of intracellular environments due to their complexity. Here, we have developed a system for highlighting the environment inside of the cell (SHELL). SHELL is a pseudocellular system, wherein small molecules are removed from the cell and a crowded intracellular environment is maintained. SHELL offers two prominent advantages: (1) It allows for precise quantitative biochemical analysis of a specific factor, and (2) it enables the study of any cell, thereby facilitating the study of target molecule effects in various cellular environments. Here, we used SHELL to study G-quadruplex formation, an event that implicated cancer. We show that G-quadruplexes are more stable in SHELL compared with in vitro conditions. Although malignant transformation perturbs cellular K+ concentrations, environments in SHELL act as buffers against G-quadruplex destabilization at lower K+ concentrations. Notably, the buffering effect was most pronounced in SHELL derived from nonaggressive cancer cells. Stable G-quadruplexes form due to the binding of the G-quadruplex with K+ in different cancer cells. Furthermore, the observed pattern of G-quadruplex-induced transcriptional inhibition in SHELL is consistent with that in living cells at different cancer stages. Our results indicate that ion binding to G-quadruplexes regulates gene expression during pathogenesis.
DOI： 10.1021/jacs.3c11160
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Hisae Tateishi-Karimata, Naoki Sugimoto
ACS Omega 9 ( 5 ) 5675 - 5682 2024.1
G-quadruplexes in disease-related genes are associated with various biological processes and regulate disease progression. Although methods involving ligands and other techniques are available to stabilize G-quadruplexes, approaches for destabilizing G-quadruplexes remain limited. Here, we evaluated whether G-quadruplexes can be destabilized using choline dihydrogen phosphate (choline dhp), a highly biocompatible hydrated ionic liquid. Circular dichroism spectral measurements at increasing temperatures revealed that choline dhp destabilized G-quadruplexes more effectively than did KCl-containing solutions. Thermodynamic analysis indicated that destabilization occurred via an entropic contribution, suggesting that choline ions did not coordinate with the G-quartets, because of their large radii. Subsequently, plasmid DNAs containing G-quadruplexes were constructed, and transcription reactions were performed in nuclear extracts from living cells. G-quadruplexes repressed transcription, whereas the addition of choline dhp increased transcription. Although ionic liquids often inactivate biomolecules, choline dhp can be used to culture various cells. Furthermore, the transcription of template DNA containing the G-quadruplex was greatly enhanced in living MDA-MD-231 cells (aggressive human breast cancer cells) cultured with choline dhp. Our results show that choline dhp destabilizes G-quadruplexes in cells, indicating that choline dhp can regulate gene expression. Thus, choline dhp may be useful for regulating target disease-related genes.
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In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics. Reviewed International coauthorship International journal
Dipanwita Banerjee, Hisae Tateishi-Karimata, Maria Toplishek, Tatsuya Ohyama, Saptarshi Ghosh, Shuntaro Takahashi, Marko Trajkovski, Janez Plavec, Naoki Sugimoto
Journal of the American Chemical Society 145 ( 43 ) 23503 - 23518 2023.11
In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear. Therefore, the mechanistic details of the effect of such molecular crowding were investigated at the molecular level by using thermodynamic and nuclear magnetic resonance analyses, revealing structure-dependent destabilization of the duplexes under crowded conditions. The transition from B- to A-like hybrid duplexes due to a change in conformation of the DNA strand guided by purine-pyrimidine asymmetry significantly increased the hydration number, which resulted in greater destabilization by the addition of cosolutes. By quantifying the individual contributions of environmental factors and the bulk structure of the duplex, we developed a set of parameters that predict the stability of hybrid duplexes with conformational dissimilarities under diverse crowding conditions. A comparison of the effects of environmental conditions in living cells and in vitro crowded solutions on hybrid duplex formation using the Förster resonance energy transfer technique established the applicability of our parameters to living cells. Moreover, our derived parameters can be used to estimate the efficiency of transcriptional inhibition, genome editing, and silencing techniques in cells. This supports the usefulness of our parameters for the visualization of cellular mechanisms of gene expression and the development of nucleic acid-based therapeutics targeting different cells.
DOI： 10.1021/jacs.3c06706
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Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet Reviewed International coauthorship International journal
Sinjan Das , Shuntaro Takahashi , Tatsuya Ohyama, Sudipta Bhowmik , Naoki Sugimoto
Scientific Reports 13 2023.9
Ligands that recognise specific i-motif DNAs are helpful in cancer diagnostics and therapeutics, as i-motif formation can cause cancer. Although the loop regions of i-motifs are promising targets for ligands, the interaction between a ligand and the loop regions based on sequence information remains unexplored. Herein, we investigated the loop regions of various i-motif DNAs to determine whether these regions specifically interact with fluorescent ligands. Crystal violet (CV), a triphenylmethane dye, exhibited strong fluorescence with the i-motif derived from the promoter region of the human BCL2 gene in a sequence- and structure-specific manner. Our systematic sequence analysis indicated that CV was bound to the site formed by the first and third loops through inter-loop interactions between the guanine bases present in these loops. As the structural stability of the BCL2 i-motif was unaffected by CV, the local stabilisation of the loops by CV could inhibit the interaction of transcription factors with these loops, repressing the BCL2 expression of MCF-7 cells. Our finding suggests that the loops of the i-motif can act as a novel platform for the specific binding of small molecules; thus, they could be utilised for the theranostics of diseases associated with i-motif DNAs.
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Kohei Yokosawa, Mitsuki Tsuruta, Shinji Kajimoto, Naoki Sugimoto, Daisuke Miyoshi, Takakazu Nakabayashi
Chemical Physics Letters 826 140634 2023.9
Publisher：Elsevier BV
Liquid–liquid phase separation (LLPS), which results in the formation of highly concentrated droplets of biomolecules, is involved in various physiological phenomena. We have performed a label-free quantification of the concentration of a G-quadruplex-forming RNA and an RGG peptide in a single droplet using Raman microscopy. The concentration ratio of the RNA to the peptide within the droplet was found to maintain even when the prepared concentration ratio of these two species was varied. This result indicates that electrostatic interactions between the RNA and the peptide induced the droplet formation. It was also shown that the RNA maintains its G-quadruplex structure inside the droplets.
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Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions Reviewed International journal
S. Ghosh, S. Takahashi, D. Banerjee, T. Ohyama, T. Endoh, H. Tateishi-Karimata, and N. Sugimoto
Nucleic Acids Res. 51 4101 - 4111 2023.5
RNA performs various spatiotemporal functions in living cells. As the solution environments significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in diverse crowded conditions is required to understand and modulate gene expression in heterogeneously crowded intracellular conditions. Herein, we determined the nearest-neighbor (NN) parameters for RNA duplex formation when subjected to crowding conditions with an ionic concentration relevant to that found in cells. Determination of the individual contributions of excluded volume effect and water activity to each of the NN parameters in crowded environments enabled prediction of the thermodynamic parameters and their melting temperatures for plenty of tested RNA duplex formation in vitro and in cell with significant accuracy. The parameters reported herein will help predicting RNA duplex stability in different crowded environments, which will lead to an improved understanding of the stability-function relationship for RNAs in various cellular organelles with different molecular environments.
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Simple and fast screening for structure-selective G-quadruplex ligands Reviewed International journal
Y. Hashimoto, Y. Imagawa, K. Nagano, R. Maeda, N. N.agahama, T. Torii, N. Kinoshita, N. Takamiya, K. Kawauchi, H. Tateishi-Karimata, N. Sugimoto and D. Miyoshi
Chem. Commun. 59 4891 - 4894 2023.4
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Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase Reviewed International journal
T. Endoh, S. Takahashi, and N. Sugimoto
Chem. Commun. 59 872 - 875 2023.1
Replication of RNA viruses is catalysed by virus-specific polymerases, which can be targets of therapeutic strategies. In this study, we used a selection strategy to identify endogenous RNAs from a transcriptome library derived from lung cells that interact with the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Some of the selected RNAs weakened the activity of RdRp by forming G-quadruplexes. These results suggest that certain endogenous RNAs, which potentially form G-quadruplexes, can reduce the replication of viral RNAs.
DOI： 10.1039/d2cc05858h
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Pressure-temperature control of activity of RNA polymerase ribozyme Reviewed International journal
S. Takahashi and N. Sugimoto
Biophys. Chem. 292 106914 2023.1
A representative role of nucleic acids (DNA and RNA) is in the storage of genetic information. In contrast, RNAs act as ribozymes that catalyze various biochemical reactions. The “RNA world” hypothesis suggests that the origin of life was RNA because a ribozyme that shows RNA replication activity has been identified. However, prebiotic conditions in the RNA world remain unknown. In this study, we investigated the effect of high pressure and temperature on RNA replication using an RNA polymerase ribozyme tC9Y. We found that pressure accelerated the RNA replication activity of tC9Y ribozyme at higher temperatures than physiological conditions. Furthermore, molecular crowding by concentrated polyethylene glycol 200 (average molecular weight 200) synergistically enhanced the replication activity at higher pressure and temperature because the negative effect of a volumetric contribution of hydration on the tC9Y ribozyme activity decreased under crowding conditions. As a comparison, proteinaceous RNA polymerase that exists in the modern era did not show accelerated activity under high pressure and temperature. Thus, these results imply that the prebiotic conditions for the RNA world were at high pressure and temperatures under crowding conditions.
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Liquid-Liquid Phase Separation and Nucleic Acids
Hisae Tateishi-Karimata, Saki Matsumoto, Naoki Sugimoto
Handbook of Chemical Biology of Nucleic Acids 1 - 40 2023
Publisher：Springer Nature Singapore
DOI： 10.1007/978-981-16-1313-5_90-1
Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K14742/
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Cladogenetic Orthogonal Light-Up Aptamers for Simultaneous Detection of Multiple Small Molecules in Cells Reviewed International coauthorship International journal
T. Endoh, J. H. Tan, S. B. Chen, and N. Sugimoto
Anal. Chem. 95 976 - 985 2022.12
Recent successes in construction of light-up RNA aptamers allowed fluorescence-based live-cell imaging of RNAs. In addition, light-up aptamers have been converted into signaling aptamers that enable fluorometric detection of small chemicals. To date, only a single target chemical has been detected at a time in cells. In this study, we selected cladogenetic orthogonal light-up aptamers that output three different colors from the RNA library having the same ligand binding core. Two of the three functioned in mammalian cells. These two aptamers, which fluoresce blue and green upon binding of cognate fluorogen, were converted into signaling aptamers. Using these signaling aptamers in combination with a previously described light-up aptamer with red fluorescence, we demonstrated simultaneous detection of multiple chemicals in living cells. The cladogenetic orthogonal light-up aptamers developed in this study and the simple strategy for rational designing of the signaling aptamers will provide innovative advances in the field of RNA-based bioimaging.
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High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs Reviewed International coauthorship International journal
Y. Zhang, H. Tateishi-Karimata, T. Endoh, Q. J., Kexin Li, X. Fan, Y. Ma, L. Gao, H. Lu, Z. Wang, A. E. Cho, X. Yao, Ch. Liu, N. Sugimoto, S. Guo, X. Fu, Q. Shen, G. Xu, L. R. Herrera-Estrella, X. Fan
Science Advances 8 9785 2022.11
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Controlling liquid-liquid phase separation of G-quadruplex-forming RNAs in a sequence-specific manner. Reviewed International journal
Mitsuki Tsuruta, Takeru Torii, Kazuki Kohata, Keiko Kawauchi, Hisae Tateishi-Karimata, Naoki Sugimoto, Daisuke Miyoshi
Chemical communications (Cambridge, England) 58 ( 93 ) 12931 - 12934 2022.11
We constructed a minimum liquid-liquid phase separation model system to form liquid droplets using only G-quadruplex-forming oligonucleotides and R- and G-rich oligopeptides. We found that the G-quadruplex structure is an essential component for RNA to form droplets with the peptide. Based on this model system and our findings, droplet redissolution via structure transition from a G-quadruplex to a duplex was achieved in a sequence-specific manner.
Liquid–liquid phase separation (LLPS) of biomacromolecules has been attracting attention as a novel phenomenon and a new phase in living cells.1 It is now evident that LLPS involving nucleic acids participates in the regulation of gene expression at various levels, including replication, transcription, RNA processing, localization, and translation.2 Dysfunction of LLPS is linked to the onset of viral infection,3 cancer,4 and neurodegenerative diseases.2 Although LLPS is induced by different molecular compositions, it is considered that LLPS of different molecular compositions has common assembly and disassembly mechanisms.5 Many of the protein motifs essential for LLPS are intrinsically disordered regions (IDRs) such as RGG motifs.6 Moreover, databases and prediction models of proteins undergoing LLPS have been established.7 Furthermore, fundamental properties of RNAs for inducing LLPS is becoming clear.8–11 RNA secondary structure-dependent LLPS has also been reported.12
Of note, the RGG domain derived from various RNA binding proteins (RBPs) selectively binds with G-quadruplexes (G4s), a non-canonical secondary structure of nucleic acids.13 G4 formed by guanine-rich sequences have been reported to induce LLPS in a structure-specific manner. Fragile X mental retardation protein (FMRP),14 SERPINE1 mRNA-binding protein 1 (SERBP1),15 and Histone H116 all induce LLPS with G4. The repetitive GGGGCC sequence, found within the C9orf72 gene, undergoes pathogenic expansion responsible for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD).17 Repetitive expansion of GGC repeats on the FMR1 gene is considered as an onset mechanism of neurodegenerative diseases such as fragile X syndrome (FXS) and fragile X-associated tremor/ataxia syndrome (FXTAS).18 These sequences can fold to form G4 structures and induce aberrant RNA foci in the nucleus through sequestration of various RBPs.19 Although the characteristics of the various protein and nucleic acid sequences of droplets are becoming clearer, methods for regulating droplets have not yet been developed. Here, we developed a model system of LLPS based on oligonucleotides and oligopeptides to investigate the essential properties of RNA that directly induce and control LLPS.
A series of RNA oligonucleotides were designed to study their ability to undergo LLPS with a cationic peptide containing the RGG motif derived from FMRP (Table 1).13 FMR1 RNA and C9orf72 RNA are four repeats of GGC and GGGGCC, respectively, which may form a G4. sFMR1 RNA is a scrambled sequence of FMR1 RNA that does not form a G4. Comp-RNA is complementary to FMR1 RNA. dsRNA was designed to form an intramolecular duplex (a hairpin loop structure). The structure of the RNA oligonucleotides was studied by CD spectroscopy and UV melting curves (Fig. S1, ESI†). These results are consistent with each other and show that FMR1 RNA and c9orf72 RNA fold into parallel G4s, and the 1 : 1 mixture and dsRNA forms A-form duplexes in the experimental conditions. (See Fig. S1, ESI† for explanations of the CD spectra and UV melting curves).DOI： 10.1039/d2cc04366a
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DNA methylation is regulated by both the stability and topology of G-quadruplex Reviewed International journal
S. Matsumoto, H. Tateishi-Karimata, N. Sugimoto
Chem. Commun., 58 12459 - 12462 2022.10
DOI： 10.1039/d2cc04383a
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Volumetric strategy for quantitatively elucidating local hydration network around a G-quadruplex Reviewed International coauthorship International journal
S. Matsumoto, S. Takahashi, S. Bhowmik, T. Ohyama, and N. Sugimoto
Anal. Chem 94 ( Selected as a Supplemental Cover ) 7400 - 7407 2022.5
Authorship：Last author
Hydration around nucleic acids, such as DNA and RNA, is an important factor not only for the stability of nucleic acids but also for their interaction with binding molecules. Thus, it is necessary to quantitatively elucidate the hydration properties of nucleic acids around a certain structure. In this study, volumetric changes in G-quadruplex (G4) RNA formation were investigated by systematically changing the number of G-quartet stacks under high pressure. The volumetric contribution at the level of each G4 structural unit revealed that the core G4 helix was significantly more dehydrated than the other parts, including the edges of G-quartets and loops. These findings will help in predicting the binding of G4 ligands on the surface of G4, depending on the chemical structure of the ligand and solution environment. Therefore, the preset volumetric parameter provides information that can predict molecular interactions in G4 formations during molecular crowding in cells.
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Applicability of Nearest-neighbour Model for Pseudoknot RNAs Reviewed International journal
S. Satpathi, T. Endoh, and N. Sugimoto
Chem. Commun 58 ( [Selected as an Inside Back Cover] ) 5952 - 5955 2022.4
Authorship：Last author
DOI： 10.1039/d1cc07094k
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Replication Control of Human Telomere G-Quadruplex DNA by G-Quadruplex Ligands Dependent on Solution Environment Reviewed International journal
S. Takahashi, S. Bhowmik, S. Sato, S. Takenaka, and N. Sugimoto
Life 12 ( 4 ) 553 2022.4
Authorship：Last author
The human telomere region is known to contain guanine-rich repeats and form a guanine-quadruplex (G4) structure. As telomeres play a role in the regulation of cancer progression, ligands that specifically bind and stabilize G4 have potential therapeutic applications. However, as the human telomere sequence can form G4 with various topologies due to direct interaction by ligands and indirect interaction by the solution environment, it is of great interest to study the topology-dependent control of replication by ligands. In the present study, a DNA replication assay of a template with a human telomere G4 sequence in the presence of various ligands was performed. Cyclic naphthalene diimides (cNDI1 and cNDI2) efficiently increased the replication stall of the template DNA at G4 with an anti-parallel topology. This inhibition was stability-dependent and topology-selective, as the replication of templates with hybrid or parallel G4 structures was not affected by the cNDI and cNDI2. Moreover, the G4 ligand fisetin repressed replication with selectivity for anti-parallel and hybrid G4 structures without stabilization. Finally, the method used, referred to as quantitative study of topology-dependent replication (QSTR), was adopted to evaluate the correlation between the replication kinetics and the stability of G4. Compared to previous results obtained using a modified human telomere sequence, the relationship between the stability of G4 and the effect on the topology-dependent replication varied. Our results suggest that native human telomere G4 is more flexible than the modified sequence for interacting with ligands. These findings indicate that the modification of the human telomeric sequence forces G4 to rigidly form a specific structure of G4, which can restrict the change in topology-dependent replication by some ligands.
DOI： 10.3390/life12040553
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Ruthenium Polypyridyl Complex Bound to a Unimolecular Chair-Form G-Quadruplex Reviewed International coauthorship International journal
Kane T. McQuaid, Shuntaro Takahashi, Lena Baumgaertner, David J. Cardin, Neil G. Paterson, James P. Hall, Naoki Sugimoto, and Christine J. Cardin
Journal of the American Chemical Society 144 ( 13 ) 5956 - 5964 2022.4
The DNA G-quadruplex is known for forming a range of topologies and for the observed lability of the assembly, consistent with its transient formation in live cells. The stabilization of a particular topology by a small molecule is of great importance for therapeutic applications. Here, we show that the ruthenium complex Λ-[Ru(phen)2(qdppz)]2+ displays enantiospecific G-quadruplex binding. It crystallized in 1:1 stoichiometry with a modified human telomeric G-quadruplex sequence, GGGTTAGGGTTAGGGTTTGGG (htel21T18), in an antiparallel chair topology, the first structurally characterized example of ligand binding to this topology. The lambda complex is bound in an intercalation cavity created by a terminal G-quartet and the central narrow lateral loop formed by T10–T11–A12. The two remaining wide lateral loops are linked through a third K+ ion at the other end of the G-quartet stack, which also coordinates three thymine residues. In a comparative ligand-binding study, we showed, using a Klenow fragment assay, that this complex is the strongest observed inhibitor of replication, both using the native human telomeric sequence and the modified sequence used in this work.
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Thermodynamic Analysis to Elucidate the Behaviors Reviewed International journal
S. Takahashi, N.Sugimoto
49 14 - 19 2022.1
Joint Work
The folding and unfolding of nucleic acids (DNA and RNA) are essential for these functions in cells.
These behaviours are also widely used for various technical applications using nucleic acids. To understand the biological mechanism of nucleic acids function and design materials of nucleic acids, the biophysical approach using thermodynamics is highly useful and important. The stability prediction of duplexes of nucleic acids have been developed and widely used. However, it has been also noted that such predictions cannot be always adopted to prediction in various solution conditions, especially the cellular conditions, because the concentrations of cations and cosolutes in the intracellular condition termed molecular crowding are different from those in the standard experimental condition.
Moreover, the crowding condition in cells is spatiotemporally variable. Therefore, it is highly demanded to establish the prediction method available in cellular conditions for the stability of various structures of nuclei acids. This article reviews the biophysicochemical background predicting nucleic acids stability and our recent studies for the prediction of these stability in the cellular conditions.
Keywords: nucleic acids, thermodynamics, duplex, stability prediction, molecular crowding, intracellular condition. -
Dielectricity of a molecularly crowded solution accelerates NTP misincorporation during RNA-dependent RNA polymerization by T7 RNA polymerase Reviewed International journal
S. Takahashi, S. Matsumoto, P. Chilka, S. Ghosh, H. Okura, and N. Sugimoto
Scientific reports 12 1149 2022.1
Authorship：Last author
In biological systems, the synthesis of nucleic acids, such as DNA and RNA, is catalyzed by enzymes in various aqueous solutions. However, substrate specificity is derived from the chemical properties of the residues, which implies that perturbations of the solution environment may cause changes in the fidelity of the reaction. Here, we investigated non-promoter-based synthesis of RNA using T7 RNA polymerase (T7 RNAP) directed by an RNA template in the presence of polyethylene glycol (PEG) of various molecular weights, which can affect polymerization fidelity by altering the solution properties. We found that the mismatch extensions of RNA propagated downstream polymerization. Furthermore, PEG promoted the polymerization of non-complementary ribonucleoside triphosphates, mainly due to the decrease in the dielectric constant of the solution. These results indicate that the mismatch extension of RNA-dependent RNA polymerization by T7 RNAP is driven by the stacking interaction of bases of the primer end and the incorporated nucleotide triphosphates (NTP) rather than base pairing between them. Thus, proteinaceous RNA polymerase may display different substrate specificity with changes in dielectricity caused by molecular crowding conditions, which can result in increased genetic diversity without proteinaceous modification.
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Effect of DNA modifications on the transition bet and non-canoncial DNA stransures in CpG islands during senescence Reviewed International journal
S.Matsumoto, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto
RSC Advances 11 37205 - 37217 2021.12
Joint Work
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Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gen Reviewed International journal
W. Sugimoto, N. Kinoshita, M. Nakata, T. Ohyama, H. Tateishi-Karimata, T. Nishikata, N. Sugimoto, D. Miyoshi, and K. Kawauchi
Chem. Commun. 58 48 - 51 2021.11
Joint Work
DOI： 10.1039/d1cc05523b
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Correction to 'Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition'. Reviewed International journal
Dipanwita Banerjee, Hisae Tateishi-Karimata, Tatsuya Ohyama, Saptarshi Ghosh, Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids research 49 ( 18 ) 10796 - 10799 2021.10
The stability of Watson–Crick paired RNA/DNA hybrids is important for designing optimal oligonucleotides for ASO (Antisense Oligonucleotide) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)–Cas9 techniques. Previous nearest-neighbour (NN) parameters for predicting hybrid stability in a 1 M NaCl solution, however, may not be applicable for predicting stability at salt concentrations closer to physiological condition (e.g. ∼100 mM Na+ or K+ in the presence or absence of Mg2+). Herein, we report measured thermodynamic parameters of 38 RNA/DNA hybrids at 100 mM NaCl and derive new NN parameters to predict duplex stability. Predicted ΔG°37 and Tm values based on the established NN parameters agreed well with the measured values with 2.9% and 1.1°C deviations, respectively. The new results can also be used to make precise predictions for duplexes formed in 100 mM KCl or 100 mM NaCl in the presence of 1 mM Mg2+, which can mimic an intracellular and extracellular salt condition, respectively. Comparisons of the predicted thermodynamic parameters with published data using ASO and CRISPR–Cas9 may allow designing shorter oligonucleotides for these techniques that will diminish the probability of non-specific binding and also improve the efficiency of target gene regulation.
DOI： 10.1093/nar/gkab780
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Chemical Modulation of DNA Replication along G-Quadruplex Based on Topology-Dependent Ligand Binding Reviewed International journal
高橋 俊太郎, 建石 寿枝, 杉本 直己
Journal of the American Chemical Society 143 16458 - 16469 2021.9
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Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity Reviewed International coauthorship International journal
S.Satopathi, T.Endoh, Peter Podbevˇsek, Janez Plavec, N. Sugimoto
Nucleic acids research 49 8449 - 8461 2021.9
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Triple-Helical Binding of Peptide Nucleic Acid Inhibits Maturation of Endogenous MicroRNA-197 Reviewed International coauthorship International journal
遠藤 玉樹, 杉本 直己
ACS Chemical biology 16 1147 - 1151 2021.7
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Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question” Reviewed International journal
N. Sugimoto, T. Endoh, S. Takahashi, H. Tateishi-Karimata
Bulletin of the Chemical Society of Japan 94 1970 - 1998 2021.7
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Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations. Reviewed International journal
Shu-Ichi Nakano, Hirofumi Yamashita, Naoki Sugimoto
Chembiochem : a European journal of chemical biology 2021.7
Catalytic turnover is important for the application of ribozymes to biotechnology. However, the turnover is often impaired because of the intrinsic high stability of base pairs with cleaved RNA products. Here, organic cations were used as additives to improve the catalytic performance of hammerhead ribozyme constructs that exhibit different kinetic behaviors. Kinetic analysis of substrate cleavage demonstrated that bulky cations, specifically tetra-substituted ammonium ions containing pentyl groups or a benzyl group, have the ability to greatly increase the turnover rate of the ribozymes. Thermal stability analysis of RNA structures revealed that the bulky cations promote the dissociation of cleaved products and refolding of incorrectly folded structures with small disruption of the catalytic structure. The use of bulky cations is a convenient method for enhancing the catalytic activity of hammerhead ribozymes, and the approach may be useful for advancing ribozyme technologies.
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New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments Topics in Current Chemistry Reviewed International journal
S.Matsumoto, N.Sugimoto
Topics in Current Chemistry 379 2021.6
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Artificial turn-on riboswitch to control target gene expression using a wild-type riboswitch splicing mechanism Reviewed International journal
T. Yamauchi, T. Kubodera, D. Miyoshi, N. Sugimoto, and S. Hirohata
Journal of Bioscience and Bioengineering 131 115 - 123 2021.2
Joint Work
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Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes Reviewed International journal
M. Tsuruta, Y. Sugitani, N. Sugimoto, D. Miyoshi
Int. J. Mol. Sci., 22 947 2021.1
Joint Work
DOI： 10.3390/ijms22020947
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Engineering exosome polymer hybrids by atom transfer radical polymerization Reviewed International coauthorship International journal
S. Lathwal, S. S. Yerneni, S. Boye, U. L. Muza, S. Takahashi, N. Sugimoto, A. Lederer, S. R. Das, P. G. Campbell, K. Matyjaszewski
Proc. Natl. Acad. Sci. U. S. A., 118 e2020241118 2021.1
Joint Work
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Effects of Modifying Thioflavin T at the N3-Position on Its G4 Binding and Fluorescence Emission Reviewed International journal
Y. Kataoka, H. Fujita, T. Endoh, N. Sugimoto, and M. Kuwahara
Molecules 25 ( 21 ) 4936 2020.10
Joint Work
Publisher：MDPI
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Effect of Molecular Crowding on DNA Polymerase Reactions along Unnatural DNA Templates Reviewed International coauthorship International journal
S. Takahashi, P. Herdwijn, and N. Sugimoto
Molecules 25 ( 18 ) 4120 2020.9
Joint Work
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Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson–Crick rules Reviewed International journal
S. Takahashi, H. Okura, P. Chilika, S. Ghosh, and N. Sugimoto
RSC Advances 10 33052 - 33058 2020.9
Joint Work
[Selected as a HOT Article]
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Effect of molecular crowding on the stability of RNA G-quadruplexes with various numbers of quartets and lengths of loops Reviewed International journal
S. Matsumoto, H. Takeishi-Karimata, S. Takahashi, T. Ohyama, and N. Sugimoto
Biochemistry 59 ( 28 ) 2640 - 2649 2020.7
Joint Work
[Selected as a Supplemental Cover]
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Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition Reviewed International journal
D. Banerjee, H. Tateishi-Karimata, T. Ohyama, S. Ghosh, T. Endoh, S. Takahashi, and N. Sugimoto
Nucleic Acids Research 48 ( 21 ) 12042 - 12054 2020.7
Joint Work
[Selected as a Cover]
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Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions Reviewed International journal
S. Ghosh, S. Takahashi, T. Ohyama, T. Endoh, H. Tateishi-Karimata, and N. Sugimoto
Proceedings of the National Academy of Sciences of the United States of America 117 ( 25 ) 14194 - 14201 2020.6
Joint Work
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Signaling Aptamer Optimization through Selection Using RNA-Capturing Microsphere Particles Reviewed International journal
T. Endoh and N. Sugimoto
Analytical Chemistry 92 ( 11 ) 7955 - 7963 2020.6
Joint Work
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RNA G-quadruplexes facilitate RNA accumulation in G-rich repeat expansions Reviewed International journal
Y. Teng, H. Tateishi-Karimata, and N. Sugimoto
Biochemistry 59 ( 21 ) 1972 - 1980 2020.6
Joint Work
[Selected as a Front Cover]
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Preferential targeting cancer-related i-motif DNAs by the plant flavonol fisetin for theranostics applications International coauthorship International journal
S. Takahashi, S. Bhattachargee, S. Ghosh, N. Sugimoto, and S. Bhowmik
Sci. Rep. 10 2504 2020
Joint Work
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Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA Reviewed International journal
H. Tateishi-Karimata, D. Banerjiee, T. Ohyama, S. Matsumoto, D. Miyoshi, S. Nakano, and N. Sugimoto
Biochem.Biophys. Res. Commun 525 ( 1 ) 177 - 183 2020
Joint Work
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Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides Reviewed International journal
M. Kovačič, P. Podbevšek, H. Tateishi-Karimata, S. Takahashi, N. Sugimoto , J. Plavec
Nucleic Acids Res 48 ( 7 ) 3975 - 3986 2020
Joint Work
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New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures Reviewed International journal
H. Tateishi-Karimata, T. Ohyama, T. Muraoka, S. Tanaka, K. Kinbara, and N. Sugimoto
Molecules 25 ( 3 ) 705 2020
Joint Work
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Effect of Potassium Concentration on Triplex Stability under Molecular Crowding Conditions Reviewed International journal
Y. Teng, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto
Molecules 25 ( 2 ) 387 2020
Joint Work
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Bulky cations greatly increase the turnover of a native hammerhead ribozyme
S. Nakano, H. Yamashita, K. Tanabe, and N. Sugimoto
Royal Society of Chemistry ９ ( 61 ) 35820 - 35824 2019.11
DOI： 10.1039/c9ra06797c
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Stabilization of DNA Loop Structures by Large Cations Reviewed International journal
S. Nakano, T. Ayusawa, Y. Tanino, and N. Sugimoto
J Phys Chem B. 123 7687 - 7694 2019.9
Joint Work
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Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency Reviewed International journal
T. Endoh and N. Sugimoto
Molecules 24 1613 2019.4
Joint Work
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RNA-capturing microsphere particles (R-CAMPs) for optimization of functional aptamers Reviewed International journal
T. Endoh, T. Ohyama, and N. Sugimoto
Small 15 1805062 2019.4
Joint Work
[Selected as an Inside Back Cover]
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Characterization of intracellular crowding environments with topology-based DNA quadruplex sensors Reviewed International journal
S. Takahashi, J. Yamamoto, A. Kitamura, M. Kinjo, and N. Sugimoto
Anal. Chem. 91 2586 - 2590 2019.2
Joint Work
[Selected as a Supplementary Cover]
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C-rich sequence in a non-template DNA strand regulates structure change of G-quadruplex in a template strand during transcription Reviewed International journal
Y. Teng, H. Tateishi-Karimata, and N. Sugimoto
Bull. Chem. Soc. Jpn. 92 ( 3 ) 527 - 577 2019
Joint Work
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Lighting up of thiazole orange on G-quadruplex DNA by high pressure Reviewed International coauthorship International journal
S. Bhowmik, S. Takahashi, and N. Sugimoto
ACS Omega 4 4325 - 4329 2019
Joint Work
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Bisubstrate function of RNA polymerases triggered by molecular crowding conditions Reviewed International journal
S. Takahashi, H. Okura, and N. Sugimoto
Biochemistry 58 1081 - 1093 2019
Joint Work
[Selected as a Supplementary Cover]
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Validation of the Nearest-neighbor Model for Watson–Crick Self-complementary DNA Duplexes in Molecular Crowding Condition Reviewed International journal
S. Ghosh, S. Takahashi, T. Endoh, H. Tateishi-Karimata, S. Hazra, and N. Sugimoto
Nucleic Acids Res. 47 3284 - 3294 2019
Joint Work
[Selected as a Cover]
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In situ condensation of an anti-cancer drug into fibrin gel enabling effective inhibition of tumor cell growth Reviewed International journal
M. Kuwahara, H. Fujita, Y. Kataoka, Y. Nakajima, M. Yamada, and N. Sugimoto
Chem Commun (Camb) 55 11679 - 11682 2019
Joint Work
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Design and Properties of Ligand-Conjugated Guanine Oligonucleotides for Recovery of Mutated G-Quadruplexes Reviewed International coauthorship International journal
S. Takahashi, B. Chelobanov, K. T. Kim, B. H. Kim, D. Stetsenko, and N. Sugimoto
Molecules 23 3228 2018.12
Joint Work
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Recovery of the formation and function of oxidized G-quadruplexes by a pyrene-modified guanine-tract Reviewed International coauthorship International journal
S. Takahashi, K. T. Kim, P. Podbevšek, J. Plavec, B. H. Kim, and N. Sugimoto
J. Am. Chem. Soc. 140 ( 17 ) 5774 - 5783 2018.4
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Alkylating Probes for G-Quadruplex Structure and Evaluation of the Properties of the Alkylated G-Quadruplex DNA Reviewed International journal
N. Satoa, S. Takahashi, H. Tateishi-Karimata, M. E. Hazemi, T. Chikuni, K. Onizuka, N. Sugimoto and F. Nagatsugi
Org. Biomol. Chem. 16 1436 - 1441 2018.1
Joint Work
DOI： 10.1039/C7OB03179C
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Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins Reviewed International coauthorship International journal
E. Natan, T. Endoh, L. Haim-Vilmovsky, T. Flock, G. Chalancon, J. T. S. Hopper, B. Kintses, P. Horvath, L. Daruka, G. Fekete, C. Pál, B. Papp, E. Oszi, Z. Magyar, J. A. Marsh, A. H. Elcock, M. N. Babu, C. V. Robinson, N. Sugimoto, and S. A. Teichmann
Nat Struct Mol Biol. 25 279 - 288 2018.1
Joint Work
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Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations Reviewed International coauthorship International journal
M. Trajkovski, T, Endoh, H. Tateishi-Karimata, T. Ohyama, S. Tanaka, J. Plavec and N. Sugimoto
Nucleic Acids Res. 46 4301 - 4315 2018
Joint Work
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Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition Reviewed International journal
Y. Teng, S. Pramanik, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto
Biochem. Biophys. Res. Commun. 496 601 - 607 2018
Joint Work
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Destabilization of DNA G-quadruplexes by chemical environment changes during tumor progression facilitates transcription Reviewed International journal
H. Tateishi-Karimata, K. Kawauchi, and N. Sugimoto
J. Am. Chem. Soc. 140 642 - 651 2018
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Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit Reviewed International journal
A. B. Rode, T. Endoh, and N. Sugimoto
Angew. Chem. Int. Ed. 57 6868 - 6872 2018
Joint Work
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Co-Transcriptional Molecular Assembly Results in a Kinetically Controlled Irreversible RNA Conformational Switch Reviewed International journal
T. Endoh and N. Sugimoto
Anal. Chem. 90 11193 - 11197 2018
Joint Work
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テトラエチレングリコールで修飾されたグアニン四重鎖の安定性の分子動力学計算による解析 Reviewed
大山達也, 建石寿枝, 田中成典, 杉本直己
日本核酸化学会誌 2 3 - 10 2018
Joint Work
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A Turn-On Detection of DNA Sequences by Means of Fluorescence of DNA-Templated Silver Nanoclusters via Unique Interactions of a Hydrated Ionic Liquid Reviewed International journal
Y. Teng, H. Tateishi-Karimata, T. Tsuruoka, and N. Sugimoto
Molecules 23 2889 2018
Joint Work
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Mirror-image Dependence: Targeting Enantiomeric G-quadruplex DNA by 10 Pairs of Triplex Metallohelices Reviewed International coauthorship International journal
C. Zhao, H. Song, P. Scott, A. Zhao, H. Tateishi-Karimata, N.Sugimoto, J. Ren, and X. Qu
Angew. Chem. Int. Ed. 57 15723 - 15727 2018
Joint Work
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An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex Reviewed International journal
K. Kawauchi, W. Sugimoto, T. Yasui, K. Murata, K. Itoh, K. Takagi, T. Tsuruoka, K. Akamatsu, H. Tateishi-Karimata, N. Sugimoto, and D. Miyoshi
Nat. Commun. 9 2271 2018
Joint Work
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Modulation of Ribozyme and Deoxyribozyme Activities Using Tetraalkylammonium Ions Reviewed International journal
S. Nakano, T. Watabe, and N. Sugimoto
Chem. Phys. Chem. 18 3614 - 3619 2017.11
Joint Work
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Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure Reviewed International journal
S. Takahashi, S. Bhowmik and N. Sugimoto
Journal of Inorganic Biochemistry 166 199 - 207 2017
Joint Work
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Through-bond effects in the ternary complexes of throumbin sandwiched by two DNA aptamers Reviewed International coauthorship International journal
A. Pica, I. R. Krauss, V. Parente, H. Tateishi-Karimata, S. Nagatoishi, K. Tsumoto, N. Sugimoto and F. Sica
Nucleic Acids Res. 44 461 - 469 2017
Joint Work
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Effects of metal ions and cosolutes on G-quadruplex topology Reviewed International coauthorship International journal
T. Fujii, P. Podbevšek, J. Plavec, N. Sugimoto
Journal of Inorganic Biochemistry 166 190 - 198 2017
Joint Work
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Unexpected Position-Dependent Effects of Ribose G‑Quartets in G‑Quadruplexes Reviewed International coauthorship International journal
J. Zhou, S. Amrane, F. Rosu, G.F. Salgado, Y. Bian, H. Tateishi-Karimata, E. Largy, D. N. Korkut, A. Bourdoncle, D. Miyoshi, J. Zhang, H. Ju, W. Wang, N. Sugimoto, V. Gabelica, and J. Mergny
J. Am. Chem. Soc. 139 7768 - 7779 2017
Joint Work
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Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase Reviewed International coauthorship International journal
S. Takahashi, J. A. Brazier, N. Sugimoto
Proc. Natl. Acad. Sci. U. S. A. 114 9605 - 9610 2017
Joint Work
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Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure Reviewed International coauthorship International journal
S. Takahashi, N. Sugimoto
Biophys. Chem. 231 146 - 154 2017
Joint Work
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Newly characterized interaction stabilizes DNA structure: oligoethylene glycols Reviewed International coauthorship International journal
H.Tateishi-Karimata, T.Ohyama, T.Muraoka, P.Podbevsek, AM.Wawro, S.Tanaka, SI.Nakano, K.Kinbara, J.Plavec, N.Sugimoto
Nucleic Acids Res. 45 7021 - 7030 2017
Joint Work
[Highlighted as a Front Cover]
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Specific Light-Up System for Protein and Metabolite Targets Triggered by Initiation Complex Formation Reviewed International journal
H. Fujita, Y. Kataoka, R. Nagano, Y. Nakajima, M. Yamada, N. Sugimo, M. Kuwahara
Sci. Rep. 7 ( 15191 ) 2017
Joint Work
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Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex Reviewed International journal
Y. Ueda, Y. Zouzumi, A. Maruyama, S. Nakano, N. Sugimoto and D. Miyoshi
Science and Technology of Advanced Materials 17 753 - 759 2016.11
Joint Work
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tRNA Shifts the G-quadruplex-hairpin conformational equilibrium in RNA towards the hairpin conformer [Selected as an Inside Back Cover] Reviewed International journal
A.B. Rode, T. Endoh, N. Sugimoto
Angew. Chem. Int. Ed. 46 14315 - 14319 2016.11
Joint Work
Authorship：Lead author
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Thermal stability of RNA structures with bulky cations in mixed aqueous solutions Reviewed International journal
S. Nakano, Y. Tanino, H. Hirayama, N. Sugimoto
Biophysical Journal 111 1350 - 1360 2016.10
Joint Work
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G-quadruplexes with tetraethylene glycol-modified deoxythymidines are resistant to nucleases and inhibit HIV-1 reverse transcriptase Reviewed International journal
H. Tateishi-Karimata, T. Muraoka, K. Kinbara, N. Sugimoto
ChemBioChem. 17 1399 - 1402 2016.8
Joint Work
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Novel one-tube-one-step real-time methodology for rapid transcriptomic biomarker detection: signal amplification by ternary initiation complexes Reviewed International journal
H. Fujita, Y. Kataoka, S. Tobita, M. Kuwahara, N. Sugimoto
Anal. Chem. 88 7137 - 7144 2016.6
Joint Work
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Real-time monitoring of G-quadruplex formation during transcription Reviewed International journal
T. Endoh, AB Rode, S. Takahashi, Y. Kataoka, M. Kuwahara, N. Sugimoto
Anal. Chem. 88 1984 - 1989 2016.2
Joint Work
Authorship：Lead author
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Reevaluation of the stability of G-quadruplex structures under crowding conditions Reviewed International coauthorship International journal
J. Zhou, H. Tateishi-Karimata, JL Mergny, M. Cheng, Z. Feng, D. Miyoshi, N. Sugimoto, C. Li
Biochimie. 121 204 - 208 2016.2
Joint Work
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Incorporation of O6-methylguanine restricts the conformational conversion of the human telomere G-quadruplex under molecular crowding conditions Reviewed International coauthorship International journal
A. Zhao, C. Zhao, H. Tateishi-Karimata, J. Ren, N. Sugimoto, X. Qu
Chem. Commum. 52 1903 - 1906 2016.1
Joint Work
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Nucleobase-modified PNA suppresses translation by forming a triple helix with a hairpin structure in mRNA in vitro and in cells [Selected as a cover art] Reviewed International coauthorship International journal
T. Endoh, D. Hnedzko, E. Rozners, and N. Sugimoto
Angew. Chem. Int. Ed. 55 899 - 903 2016
Joint Work
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A reversible B-A transition of DNA duplexes induced by synthetic cationic copolymers Reviewed International journal
N. Yamaguchi, Y. Zouzumi, N. Shimada, S. Nakano, N. Sugimoto, A. Maruyama, D. Miyoshi
Chem Commun (Camb). 52 7446 - 7449 2016
Joint Work
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Triplex-forming peptide nucleic acid modified with 2-aminopyridine as a new tool for ditection of A-to-I editing [Selected as a Back Cover] Reviewed International coauthorship International journal
C. Annoni, T. Endoh, D. Hnedzko, E. Rozners, N. Sugimoto
Chem Commun (Camb) 52 7935 - 7938 2016
Joint Work
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Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells Reviewed International journal
T. Endoh, N. Sugimoto
Sci. Rep. 6 22719 2016
Joint Work
Authorship：Lead author
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Use of a ureido-substituted deoxycytidine module for DNA assemblies Reviewed International journal
S. Nakano, H. Oka, M. Fujii and Sugimoto
Nucleosides Nucleotides Nucleic Acids 35 370 - 378 2016
Joint Work
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Expansion of the DNA 'alphabet' beyond natural DNA recognition Reviewed International journal
H. Tateishi-Karimata and N. Sugimoto
ChemBioChem 17 1301 - 1303 2016
Joint Work
Authorship：Lead author
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Pressure effect on the folding of G-quadruplex DNA modified with hexaethylene glycol Reviewed International journal
S. Takahashi and N. Sugimoto
Mol. Enz. Drug Targ. 2 3 2016
Joint Work
Authorship：Lead author
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Local thermodynamics of the water molecules around single-and double-stranded DNA studied by grid inhomogeneous solvation theory Reviewed International journal
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto
Chemical Physics Letters 660 250 - 255 2016
Joint Work
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Triplex-forming PNA modified with unnatural nucleobases: the role of protonation entropy in RNA binding Reviewed International coauthorship International journal
T. Endoh, C. Annoni, D. Hnedzko, E. Rozners, N. Sugimoto
Phys. Chem. Chem. Phys. 18 32002 - 32006 2016
Joint Work
Authorship：Lead author
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Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory Reviewed International journal
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto
Nucleic Acids Res. 43 10114 - 10125 2015.12
Joint Work
Authorship：Lead author
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Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg(2+)-unsaturated solutions Reviewed International journal
S. Nakano, Y. Kitagawa, D. Miyoshi, and N. Sugimoto
J. Biol. Inorg. Chem. 20 1049 - 1058 2015.9
Joint Work
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Effects of cosolvents on the folding and catalytic activities of the hammerhead ribozyme Reviewed International journal
S. Nakano, Y. Kitagawa, H. Yamashita, D. Miyoshi, and N. Sugimoto
ChemBioChem. 16 1803 - 1810 2015.8
Joint Work
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DNA structures under molecular crowding conditions with a phosphorylcholine derivative (MPC) Reviewed International journal
Y. Ueda, T. Konno, K. Ishihara, N. Sugimoto, D. Miyoshi
Transact. Mater. Res. Soc. Japan 40 99 - 102 2015.7
Joint Work
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Rational design and tuning of functional RNA switch to control an allosteric intermolecular interaction Reviewed International journal
T. Endoh and N. Sugimoto
Anal. Chem. 87 7628 - 7635 2015.7
Joint Work
Authorship：Lead author
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Loop nucleotides impact the stability of intrastrand i-motif structures at neutral pH Reviewed International journal
T. Fujii and N. Sugimoto
Phys. Chem. Chem. Phys. 17 16719 - 16722 2015.5
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i-motifs are more stable than G-quadruplexes in a hydrated ionic liquid Reviewed International journal
H. Tateishi-Karimata, M. Nakano, S. Pramanik, S. Tanaka, and N. Sugimoto
Chem. Commun. 51 6909 - 6912 2015.4
Joint Work
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DNA sensor's selectivity enhancement and protection from contaminating nucleases due to a hydrated ionic liquid Reviewed International journal
H. Tateishi-Karimata, S. Pramanik, and N. Sugimoto
Analyst 140 4393 - 4398 2015.4
Joint Work
Authorship：Lead author
[Highlighted as a Front Cover]
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A mRNA-responsive G-quadruplex-based drug release system. Reviewed International journal
H. Yaku, T. Murashima, D. Miyoshi, and N. Sugimoto
Sensors 15 ( 4 ) 9388 - 9403 2015.4
-
Control of guanine-rich DNA secondary structures depending on the protease activity using a designed PNA peptide Reviewed International journal
K. Usui, A. Okada, K. Kobayashi, N. Sugimoto
Org. Biomol.Chem. 13 2022 - 2025 2015.2
Joint Work
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A fluorescent probe for detection of an intracellular prognostic indicator in early-stage cancer Reviewed International coauthorship International journal
H. Ji, Y. Guan, L. Wu, J. Ren, D. Miyoshi, N. Sugimoto, and X. Qu
Chem. Commun. 51 1479 - 1482 2015.1
Joint Work
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Tuning Riboswitch-mediated Gene Regulation via Rational Control of Aptamer Ligand Binding Properties Reviewed International journal
A.B.Rode, T. Endoh, N. Sugimoto
Angew. Chem. Int. Ed. 54 ( 3 ) 905 - 909 2015.1
Joint Work
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Structural foundation for DNA behavior in hydrated ionic liquid: An NMR study Reviewed International coauthorship International journal
M. Marušič, H. Tateishi-Karimata, N. Sugimoto, and J. Plavec
Biochimie 108 169 - 177 2015.1
Joint Work
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Choline ions stabilize A-T base pairs by fitting into minor groove Reviewed International journal
M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
JPS Conf. Proc. 5 011008 2015
Joint Work
Authorship：Lead author
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Key tertiary interactions in FMN riboswitch aptamers required for ligand binding [Highlighted as a Selected Paper] Reviewed International journal
A.B. Rode, T. Endoh, and N. Sugimoto
Bull. Chem. Soc. Jpn. 88 946 - 948 2015
Joint Work
Authorship：Lead author
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DNA G-quadruplex detection system employing a protein fibril ligand Reviewed International journal
R. Maeda, H. Yaku, T. Nakabayashi, T. Murashima, N. Sugimoto, N. Ohta, D. Miyoshi
Telomere and Telomerase. 2 ( e691 ) 2015
Joint Work
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Pressure-dependent formation of i-motif and G-quadruplex DNA structures International journal
S. Takahashi and N. Sugimoto
Phys. Chem. Chem. Phys. 17 31004 - 31010 2015
Joint Work
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Methyl substitution regulates the enantioselectivity of supramolecular complex binding to human telomeric G-Quadruplex DNA Reviewed International coauthorship International journal
B. Xu, C. Zhao, Y. Chen, H. Tateishi-Karimata, J. Ren, N. Sugimoto, and X. Qu
Chem. Eur. J. 20 ( 50 ) 16467 - 16472 2014.12
Joint Work
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Organelle-Mimicking Liposome Dissociates G-quadruplexes and Facilitates Transcription Reviewed International journal
Smritimoy Pramanik, Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic Acids Research 42 ( 20 ) 12949 - 12959 2014.11
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Drastic stabilization of parallel DNA hybridizations by a polylysine com-type copolymer with hydrophilic graft chain Reviewed International journal
Daisuke Miyoshi, Yumi Ueda, Naohiko Shimada, Shu-ichi Nakano, Naoki Sugimoto, Atsushi Maruyama
ChemMedChem Sep;9 ( 9 ) 2156 - 2163 2014.9
Joint Work
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Aptamer-Based Universal Fluorometric Sensors Based on Allosteric Modulation of RNA-Peptide Interactions Reviewed International journal
T. Endoh, N. Sugimoto
ChemMedChem Sep;9 ( 9 ) 2045 - 2048 2014.9
Joint Work
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Dangling ends perturb the stability of RNA duplex responsive to surrounding condition Reviewed International journal
H. Tateishi-Karimata, S. Pramanik, S. Nakano, D. Miyoshi and N. Sugimoto
ChemMedChem Sep;9 ( 9 ) 2150 - 2155 2014.9
Joint Work
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Roles of the amino group of purine bases in the thermodynamic stability of DNA base paring Reviewed International journal
S. Nakano, and N. Sugimoto
Molecules 19 11613 - 11627 2014.8
Joint Work
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The affinity of molecular ions for DNA structures is determined by solvent accessible surface area Reviewed International journal
M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
J. Phys. Chem. B 118 ( 32 ) 9583 - 9594 2014.8
Joint Work
DOI： 10.1021/jp505107g.
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In vitro assays predicting of telomerase inhibitory effect of G-quadruplex ligands in cell nuclei Reviewed International journal
H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto
J. Phys. Chem. B. 118 ( 10 ) 2605 - 2614 2014.3
Joint Work
DOI： 10.1021/jp410669t.
-
New insights into transcription fidelity : thermal stability of non-cononical structures in template DNA regulates transcriptional arrest, pause, and slippage Reviewed International journal
H. Tateishi-Karimata, N. Isono and N. Sugimoto
PLoS ONE, DOI:10.1371 9 ( 3 ) e90580 2014.3
Joint Work
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Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids Reviewed International journal
S. Nakano, D. Miyoshi, N. Sugimoto
Chem.Rev. 114 ( 5 ) 2733 - 2758 2014.3
Joint Work
DOI： 10.1021/cr400113m.
-
Choline ion interactions with DNA atoms explain unique stabilization of A-T base pairs in DNA duplexes: A microscopic view Reviewed International journal
M. Nakano, H. Tateishi-Karimata, S. Tanaka and N. Sugimoto
J. Phys. Chem. B. 118 379 - 389 2014.1
Joint Work
DOI： 10.1021/jp406647b.
-
Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate Reviewed International journal
H. Tateishi-karimata, M. Nakano and N. Suigimoto
Sci. Rep. 4 3593 2014.1
Joint Work
DOI： 10.1038/srep03593.
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Reduced Graphene Oxide Upconversion Nanoparticle Hybrid for Electrochemiluminescent Sensing of a Prognostic Indicator in Early-Stage Cancer Reviewed International coauthorship International journal
L. Wu, J. Wang, M. Yin, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu
Small 10 330 - 336 2014.1
Joint Work
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Effect of pressure on the stability of G-quadruplex DNA: Thermodynamics under crowding conditions Reviewed International journal
S. Takahashi and N. Sugimoto
Angew. Chem. Int. Ed. 52 13774 - 13778 2013.12
Joint Work
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Unusual-1 ribosomal frameshift cused by statble RNA G-quadruplex in open reading frame Reviewed International journal
T. Endoh and N. Sugimoto
Anal. Chem. 85 11435 - 11439 2013.12
Joint Work
DOI： 10.1021/ac402497x.
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Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer Reviewed International coauthorship International journal
A. Pica, I. Russo Krauss, A. Merlino, S. Nagatoishi, N. Sugimoto and F. Sica
FEBS J. 280 6581 - 6588 2013.12
Joint Work
DOI： 10.1111/febs.12561
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Translational halt during elongation caused by G-quadruplex formed by mRNA Reviewed International journal
T. Endoh, Y. Kawasaki and N. Sugimoto
Methods 64 73 - 78 2013.11
Joint Work
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Study on Effects of Molecular Crowding on G-quadruplex-ligand Binding and Ligand-mediated Telomerase Inhibition Reviewed International journal
H. Yaku, T. Murashima, H. Tateishi-Karimata S. Nakano, D. Miyoshi and N. Sugimoto
METHODS 64 19 - 27 2013.11
Joint Work
-
Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules Reviewed International journal
S. Nakano, Y. Uotani, Y. Sato, H. Oka, M. Fujii and N. Sugimoto
Nucleic Acids Res 41 8581 - 8590 2013.10
Joint Work
DOI： 10.1093/nar/gkt608
-
Real-time monitoring of DNA hybridization kinetics at living cell surfaces Reviewed International journal
A. B. Rode, T. Endoh, H. Tateishi-Karimata, S. Takahashi and N. Sugimoto
Chem. Commun. 49 8444 - 8446 2013.10
Joint Work
DOI： 10.1039/c3cc42990c
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Sequence and Solvent Effects on Telomeric DNA Bimolecular G-Quadruplex Folding Kinetics Reviewed International coauthorship International journal
A. Marchand, R. Ferreira, H. Tateishi-Karimata, D. Miyoshi, N. Sugimoto and V. Gabelica
J. Phys. Chem. B 117 12391 - 12401 2013.10
Joint Work
DOI： 10.1021/jp406857s.
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A highly sensitive telomerase activity assay that eliminates false-negative results caused by PCR inhibitors Reviewed International journal
H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto
Molecules 18 11751 - 11767 2013.9
Joint Work
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Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives Reviewed International journal
H. Fujita, Y. Imaizumi, Y. Kasahara, S. Kitadume, H. Ozaki, M. Kuwahara, and N. Sugimoto
Pharmaceuticals 6 1082 - 1093 2013.8
Joint Work
DOI： 10.3390/ph6091082.
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Stability of RNA quadruplex in open reading frame determines proteolysis of human estrogen receptor α Reviewed International journal
T. Endoh, Y. Kawasaki and N. Sugimoto
Nucleic. Acids Research 41 6222 - 6231 2013.7
Joint Work
DOI： 10.1093/nar/gkt286.
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Efficacy of Base-modification on Target Binding of Small Molecule DNA Aptamers Reviewed International journal
Y. Imaizumi, Y. Kasahara, S. Kitadume, H. Ozaki, T. Endoh, M. Kuwahara and N. Sugimoto
J. Am. Chem. Soc., 135, 9412-9419 (2013) 135 9412 - 9419 2013.6
Joint Work
DOI： 10.1021/la4012222
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Multiple and cooperative binding of fluorescence light-up probe Thioflavin T with human telomere DNA G-quadruplex Reviewed International coauthorship International journal
V. Gabelica, R. Maeda, T.Fujimoto, H. Yaku, T. Murashima, N. Sugimoto and D. Miyoshi
Biochemistry, 52, 5620-5628 52 5620 - 5628 2013.6
Joint Work
DOI： 10.1021/bi4006072.
-
Control of stability and structure of nucleic acids using cosolutes Reviewed International journal
H. Tateishi-Karimata and N. Sugimoto
Methods 67 ( 2 ) 151 - 158 2013.5
Joint Work
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Suppression of Gene Expression by G-quadruplexes in Open Reading Frames Depends on G-quadruplex Stability Reviewed International journal
T. Endoh, Y. Kawasaki and N. Sugimoto
Angew. Chem. Int. Ed. 52 5522 - 5526 2013.5
Joint Work
-
Selection of RNAs for Constructing Lighting-UP Biomolecular Switches in Response to Specific Small Molecules Reviewed International journal
T. Endoh and N. Sugimoto
PLoS ONE, 8(3), e60222 8 2013.3
Single Work
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Thermodynamics - Hydration Relationships within Loops that Affect G-Quadruplexes under Molecular Crowding Conditions Reviewed International journal
T. Fujimoto, S. Nakano, N. Sugimoto and D. Miyoshi
J. Phys. Chem. B (Highlighted as the cover) 117 963 - 972 2013.1
Joint Work
DOI： 10.1021/jp308402v.
-
Construction of Artificial Peptides for Control of DNA G-quadruplex Structures Depending on Protease Activity toward Regulation of Protein Expression
A. Okada, K. Usui, M. Taniguchi, K. Kobayashi and N. Sugimoto
Peptide Science 2012 285 - 276 2013
Joint Work
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A–T Base Pairs are More Stable Than G–C Base Pairs in a Hydrated Ionic Liquid Reviewed International journal
H. Tateishi-Karimata and N. Sugimoto
Angew. Chem. Int. Ed. 51 1416 - 1419 2012
Joint Work
-
Synchronized Translation for Detection of Temporal Stalling of Ribosome during Single-Turnover Translation Reviewed International journal
T. Endoh, Y. Kawasaki and N. Sugimoto
Anal. Chem. 84 857 - 861 2012
Joint Work
-
Rational design of a new IMP aptamer based on a TPP riboswitch and a hypoxanthine aptamer Reviewed International journal
M. Tokui, T. Yamauchi, D. Miyoshi, H. Kamiya, A. Nishimura and N. Sugimoto
Chem. Lett. 40 1313 - 1314 2012
Joint Work
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Structural and Functional Characterization of RecG Helicase under Dilute and Molecular Crowding Conditions Reviewed International journal
S. Saxena, S. Nagatoishi, D. Miyoshi and N. Sugimoto
Journal of Nucleic Acids, ID 392039 8 pages 2012 2012
Joint Work
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Hydration Changes upon DNA Folding Studied by Osmotic Stress Experiments Reviewed International journal
S. Nakano, D. Yamaguchi, H. Tateishi-Karimata, D. Miyoshi and N. Sugimoto
Biophysical Journal 102 2808 - 2817 2012
Joint Work
-
Development of PNA-Peptides Controlling DNA G-Quadruplex Structures Depending on Protease Activity
K. Usui, K. Kobayashi and N. Sugimoto
Peptide Science 2011 315 - 316 2012
Joint Work
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The yield of transcripts for RNA polymerase regulated by hairpin structures in nascent RNA Reviewed International journal
S. Nagatoishi, R. Ono and N. Sugimoto
Chem. Commun. 48 5121 - 5123 2012
Joint Work
-
DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles Reviewed International journal
S. Pramanik, S. Nagatoishi and N. Sugimoto
Chem. Commun. 48 4815 - 4817 2012
Joint Work
-
Detection of a Prognostic Indicator in Early-Stage Cancer Using Functionalized Graphene-Based Peptide Sensors Reviewed International coauthorship International journal
L. Feng, L. Wu, J. Wang, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu
Advanced Materials 24 125 - 131 2012
Joint Work
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Beads-on-a-string structure of long telomeric DNAs under molecular crowding conditions Reviewed International journal
H. Yu, X. Gu, S. Nakano, D. Miyoshi and N. Sugimoto
J. Am. Chem. Soc. 134 20060 - 20069 2012
Joint Work
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Dehydration from conserved stem regions is fundamental for ligand-dependent conformational transition of the adenine-specific riboswitch Reviewed International journal
V. Kumar, T. Endoh, K. Murakami and N. Sugimoto
Chem. Commun. 48 9693 - 9695 2012
Joint Work
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Dimerization of Nucleic Acid Hairpins in the Conditions Caused by Neutral Cosolutes Reviewed International journal
S. Nakano, H. Hirayama, D. Miyoshi and N. Sugimoto
J. Phys. Chem. B 116 7406 - 7415 2012
Joint Work
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Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein Reviewed International journal
S. Nagatoishi and N. Sugimoto
Mol Biosyst 8 2766 - 2770 2012
Joint Work
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Aptamer carbon nanodot sandwich used for fluorescent detection of protein Reviewed International coauthorship International journal
B. Xu, C. Zhao, W. Wei, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu
Analyst 137 5483 - 5486 2012
Joint Work
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Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative Reviewed International journal
S. Nakano, H. Oka, D. Yamaguchi, M. Fujii and N. Sugimoto
Org Biomol Chem. 10 9664 - 9670 2012
Joint Work
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Hydration is required in DNA G-quadruplex-protein binding Reviewed International journal
S. Nagatoishi, N. Isono, K. Tsumoto and N. Sugimoto
ChemBioChem 12 1822 - 1826 2011.7
Joint Work
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DNA Morphologic Changes Induced by Spermine on a Gold Surface under DNA Crowding Conditions Reviewed International journal
K. Kobayashi, H. Tateishi-Karimata, K. Tsutsui, Y. Wada and N. Sugimoto
Chemistry Letters 40 855 - 857 2011.7
Joint Work
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Effect of Locked Nucleic Acid modification on Thermal Stability of Non-canonical DNA Structure Reviewed International journal
J. Bhattacharyya, S. Maiti, S. Muhuri, S. Nakano, D. Miyoshi and N. Sugimoto
Biochemistry 50 ( 34 ) 7414 - 7425 2011.7
Joint Work
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Measurements of the binding of a large protein using a substrate density-controlled DNA chip Reviewed International journal
S. Nakano, T. Kanzaki, M. Nakano, D. Miyoshi and N. Sugimoto
Anal. Chem. 83 6368 - 6372 2011.7
Joint Work
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Label-free colorimetric and quantitative detection of cancer marker protein using noncrosslinking aggregation of Au/Ag nanoparticles induced by target-specific peptide probe Reviewed International coauthorship International journal
X. Wang, L. Wu, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu
Biosens. Bioelectron. 26 4804 - 4809 2011.6
Joint Work
-
Gene Regulation System with an Artificial RNA Switch Operating in Human Cell. Reviewed International journal
T. Endoh and N. Sugimoto
ChemBioChem. 12 1174 - 1178 2011.5
Joint Work
-
Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding. Reviewed International journal
S. Nagatoishi, N. Isono, K. Tsumoto and N. Sugimoto
Biochimie 93 1231 - 1238 2011.5
Joint Work
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Thermodynamic stability of Hoogsteen and Watson–Crick base pairs in the presence of histone H3-mimicking peptide Reviewed International journal
S. Pramanik, K. Nakamura, K. Usui, S. Nakano, S. Saxena, J. Matsui, D. Miyoshi and N. Sugimoto
Chem. Commun. 47 2790 - 2792 2011.2
Joint Work
-
A PNA peptide inducing DNAs to form G-quadruplex structures depending on a protease activity
K. Usui, K. Kobayashi and N. Sugimoto
Peptides 2011 152 - 153 2011
Joint Work
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Conformational Flexibility Influences Degree of Hydration of Nucleic Acid Hybrids Reviewed International journal
S. Pramanik, S. Nagatoishi, S. Saxena, J. Bhattacharyya and N. Sugimoto
The Journal of Physical Chemistry 115 13862 - 13872 2011
Joint Work
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Triplet analysis that identifies unpaired regions of functional RNAs Reviewed International journal
J. Kawakami, Y. Yamaguchi and N. Sugimoto
J. Nucleic Acids, ID 471843 6pages 2011
Joint Work
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Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions Reviewed International journal
S. Nakano, M. Fujii and N. Sugimoto
Journal of Nucleic Acids, ID 967098 11pages 2011
Joint Work
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The effects of molecular crowding on the structure and stability of G-quadruplexes with an abasic site Reviewed International journal
T. Fujimoto, S. Nakano, D. Miyoshi and N. Sugimoto
Journal of Nucleic Acids, ID 857149 9pages 2011
Joint Work
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Construction of detection system for amyloid beta peptide localization and aggregation using fluorescent and luminescent fusion proteins
K. Usui, M. Mie, T. Andou, N. Sugimoto, H. Mihara and E. Kobatake
Peptide Science 2009 111 - 112 2010.11
Joint Work
-
Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides Reviewed International journal
S. Nakano, H. Oka, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto
Mol. Biosys. 6 2023 - 2029 2010.10
Joint Work
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A rapid and sensitive “add-mix-measure” assay for multiple proteinases based on Goldnanoparticle-peptide-fluorophore conjugate. Reviewed International coauthorship International journal
X. Wang, J. Geng, D. Miyoshi, J. Ren, N. Sugimoto and X. Qu
Biosens. Bioelectron. 26 743 - 747 2010.10
Joint Work
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Ultrasensitive and Selective Detection of a Prognostic Indicator in Early-Stage Cancer using Grapheme Oxide and Carbon Nanotubes Reviewed International journal
X. Wang, C. Wang, K. Qu, Y. Song, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu
Advanced Functional Materials 20 3967 - 3971 2010.8
Joint Work
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Development of new functional nanostructures consisting of both DNA duplex Reviewed International journal
K. Dutta, T. Fujimoto, M. Inoue, D. Miyoshi and N. Sugimoto
Chem Commun. 46 7772 - 7774 2010.8
Joint Work
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Sole and stable RNA duplexes of G-rich sequences located in the 5'-untranslated region of protooncogenes Reviewed International journal
S. Saxena, D. Miyoshi and N. Sugimoto
Biochemistry 49 7190 - 7201 2010.8
Joint Work
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Anionic phthalocyanines Targeting G-quadruplexes and Inhibiting Telomerase Activity in the Presence of Excessive DNA Duplexes Reviewed International journal
H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto
Chem. Commun. 46 5740 - 5742 2010.7
Joint Work
-
Utilization of salmon milt DNA against UV damage International journal
Y. Sasaki, D. Miyoshi and N. Sugimoto
Applied Biochem. Biotech. 160 2458 - 2466 2010.7
Joint Work
-
Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors Reviewed International journal
D.H. Zhang, T. Fujimoto, S. Saxena, H.Q. Yu, D. Miyoshi and N. Sugimoto
Biochemisry 49 4554 - 4563 2010.4
Joint Work
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Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH Reviewed International journal
A. Rajendran, S. Nakano and N. Sugimoto
Chem. Commun. 46 1299 - 1301 2010.1
Joint Work
-
Fluorescent and luminescent fusion proteins for detection of amyloid beta peptide localization and aggregation
K. Usui, M. Mie, T. Andou, N. Sugimoto, H. Mihara and E. Kobatake
Peptides 2010 488 - 489 2010
Joint Work
-
PNA-peptide conjugates for regulation of DNA and RNA G-quadruplex structures depending on a particular protease concentration
K. Usui, K. Kobayashi and N. Sugimoto
Peptides 2010 608 - 609 2010
Joint Work
-
An approach to peptide-based ATP receptors by a combination of random selection, rational design, and molecular imprinting Reviewed International journal
J. Matsui, J. Nagano, D. Miyoshi, K. Tamaki and N. Sugimoto
Biosens. Bioelectron. 25 563 - 567 2009.11
Joint Work
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Neuronal differentiation of neural progenitor cells by intracellular delivery of synthetic oligopeptide derived from von Hippel-Lindau protein Reviewed
H. Kanno, S. Nakano, A. Kubo, T. Mimura, N. Tajima and N. Sugimoto
Protein & Peptide Letters 16 1291 - 1296 2009.11
Joint Work
-
Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes Reviewed International journal
S. Nakano, H. Tateishi-Karimata, Y. Kitagawa and N. Sugimoto
J. Am. Chem. Soc. 131 16881 - 16888 2009.10
Joint Work
-
Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides Reviewed International journal
S. Nakano, H. Oka, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto
Biochemistry 48 11304 - 11311 2009.10
Joint Work
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Stabilization of three-way junctions of DNA under molecular crowding conditions Reviewed International journal
S. Muhuri, K. Mimura, D. Miyoshi and N. Sugimoto
J. Am. Chem. Soc. 131 9268 - 9280 2009.6
Joint Work
-
Reversible stability switching of a hairpin DNA via a photo-responsive linker unit Reviewed International journal
L. Wu, K. Koumoto and N. Sugimoto
Chem. Commun. 14 1915 - 1917 2009.4
Joint Work
-
Hydration of Watson-Crick base pairs and dehydration of hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions Reviewed International journal
D. Miyoshi, K. Nakamura, Hisae Tateishi-Karimata, T. Ohmichi and N. Sugimoto
J. Am. Chem. Soc. 131 3522 - 3531 2009.2
Joint Work
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Molecularly imprinted nanocomposites for highly sensitive SPR detection of a non-aqueous atrazine sample Reviewed International journal
J. Matsui, M. Takayose, K. Akamatsu, H. Nawafune, K. Tamaki and N. Sugimoto
Analyst 134 80 - 86 2009.1
Joint Work
-
Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem Reviewed International journal
H. Yaku, T. Yukimasa, S. Nakano, N. Sugimoto and H. Oka
Electrophoresis 29 4130 - 4140 2008.11
Joint Work
-
Regulation of Telomerase Activity by the Thermodynamic Stability of a DNA·RNA Hybrid Reviewed International journal
H.Q. Yu, D.H. Zhang, X.B. Gu, D. Miyoshi and N. Sugimoto
Angew. Chem. Int. Ed. Engl. 47 9034 - 9038 2008.10
Joint Work
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Recognition of a flipped base in a hairpinloop DNA by a small peptide Reviewed International journal
J. Kawakami, S. Okabe, Y. Tanabe and N. Sugimoto
Nucleosides Nucleotides Nucleic Acids 27 292 - 308 2008.8
Joint Work
-
Hydration is an important factor to regulate thermodynamic stability of a DNA duplex under molecular crowding conditions Reviewed International journal
K. Koumoto, H. Ochiai and N. Sugimoto
Chem. Lett. 37 864 - 865 2008.5
Joint Work
-
Riboswitches for enhancing target gene expression in eukaryotes Reviewed International journal
T. Yamauchi, D. Miyoshi, T. Kubodera, M. Ban, A. Nishimura and N. Sugimoto
Chemical Communications, 9 1040 - 1043 2008.3
Joint Work
-
Capture of cationic ligands bound diffusely to base pairs during the DNA refolding Reviewed International journal
S. Nakano, T. Kirihata and N. Sugimoto
Chem. Commun. 14 700 - 702 2008.2
Joint Work
-
Structural effect of synthetic zwitterionic cosolutes on the stability of DNA duplexes Reviewed International journal
K. Koumoto, H. Ochiai and N. Sugimoto
Tetrahedron 64 168 - 174 2008.1
Joint Work
-
Small-molecule-directed assembly of DNA: a gold-nanoparticle-based strategy for screening of a DNA duplex binders Reviewed International coauthorship International journal
G. Song, C. Chen, X. Qu, D. Miyoshi, J. Ren and N. Sugimoto
Adv. Mater. 20 706 - 710 2008.1
Joint Work
-
Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media Reviewed International journal
S. Nakano, L. Wu, H. Oka, H. Tateishi-Karimata, T. Kirihata, Y. Sato, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai and N. Sugimoto
Mol. Biosys. 4 579 - 588 2008
Joint Work
-
Regulation of Telomerase Activity by the Thermodynamic Stability of a DNA?RNA Hybrid Reviewed International journal
N. Sugimoto
Angew. Chem. Int. Ed. Engl. 47 9034 - 9038 2008
Single Work
-
Synthesis, structure and thermal stability of fully hydrophobic porphyrin-DNA conjugates Reviewed International journal
T. Murashima, K. Hayata, Y. Saiki, J. Matsui, D. Miyoshi, T. Yamada, T. Miyazawa and N. Sugimoto
Tetrahedron Lett. 48 8514 - 8517 2007.11
Joint Work
-
Consecutive GC base pairs determine the energy barrier of DNA duplex formation under molecularly crowded conditions Reviewed International journal
X.B. Gu, S. Nakano and N. Sugimoto
Chem. Commun. 2750 - 2752 2007.7
Joint Work
-
Regulation of DNA nucleases by molecular crowding Reviewed International journal
Y. Sasaki, D. Miyoshi and N. Sugimoto
Nucleic Acids Res. 35 4086 - 4093 2007.6
Joint Work
-
Hydration regulates thermodynamic stability of DNA structures under molecular crowding conditions Reviewed International journal
D. Miyoshi, H. Karimata and N. Sugimoto
Nucleosides Nucleotides Nucleic Acids 26 589 - 595 2007.6
Joint Work
-
Artificial G-wire Switch with 2,2’-Bipyridine Units Responsive to Divalent Metal Ions Reviewed International journal
D. Miyoshi, H. Karimata, Z.M. Wang, K. Koumoto and N. Sugimoto
J. Am. Chem. Soc. 129 5919 - 5925 2007.4
Joint Work
-
Effects of polyethylene glycol on a DNA duplex stability differed by the NaCl concentration Reviewed International journal
H. Karimata, S. Nakano and N. Sugimoto
Bull. Chem. Soc. Jpn. 80 1987 - 1994 2007.4
Joint Work
-
Molecular Imprinting Under Molecular Crowding Conditions: an Aid to the synthesis of a High-capacity Polymeric Sorbent for Triazine Herbicides Reviewed International journal
J. Matsui, S. Goji, T. Murashima, D. Miyoshi, S. Komai, A. Shigeyasu, T. Kushida, T. Miyazawa, T. Yamada, K. Tamaki and N. Sugimoto
Anal. Chem. 79 1749 - 1757 2007.2
Joint Work
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Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides Reviewed International journal
S. Nakano, T. Kirihata, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai and N. Sugimoto
Nucleic Acids Res. 35 486 - 494 2007.1
Joint Work
-
Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions Reviewed International journal
杉本 直己
J. Am. Chem. Soc., 128 7957 - 7963 2006.11
Single Work
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Characterization of Structure and Stability of Long Telomeric DNA G-Quadruplexes Reviewed International journal
H.Q. Yu, D. Miyoshi and N. Sugimoto
J. Am. Chem. Soc. 128 15461 - 15468 2006.11
Joint Work
-
DNA logic gates based on structural polymorphism of telomere DNAs responding to chemical input signals Reviewed International journal
D. Miyoshi, M. Inoue and N. Sugimoto
Angew. Chem. Int. Ed. 45 7716 - 7719 2006.11
Joint Work
-
A novel stable RNA pentaloop that interacts specifically with a motif peptide of lambda-N protein Reviewed International journal
J. Kawakami, H. Tokitoh, Y. Tanabe and N. Sugimoto
Nucleosides Nucleotides Nucleic Acids 25 397 - 416 2006.11
Joint Work
-
A DNA duplex with Extremely Enhanced Thermal Stability Based on Controlled Immobilization on Gold Nanoparticles Reviewed International journal
K. Akamatsu, M. Kimura, Y. Shibata, S. Nakano, D. Miyoshi, H. Nawafune and N. Sugimoto
Nano Lett. 6 491 - 495 2006
Joint Work
-
Molecularly-Imprinted Polymeric Logic Gates Selective for Predetermined Chemical Input Species Reviewed International journal
J. Matsui, T. Sodeyama, K. Tamaki and N. Sugimoto
Chem. Comm. 14 3217 - 3219 2006
Joint Work
-
Effect of molecular crowding on DNA polymerase activity Reviewed International journal
Y. Sasaki, D. Miyoshi and N. Sugimoto
Biotech. J. 1 440 - 446 2006
Joint Work
-
Site-Selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside Reviewed International journal
S. Nakano, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto
J. Am. Chem. Soc. 127 518 - 519 2005.11
Joint Work
-
DNA base flipping by a base pair-mimic nucleoside Reviewed International journal
S. Nakano, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto
Nucleic Acids Res. 33 7111 - 7119 2005.11
Joint Work
-
Simple and fast screening for structure-selective G-quadruplex ligands Reviewed International journal
Y. Hashimoto, Y. Imagawa, K. Nagano, R. Maeda, N. N.agahama, T. Torii, N. Kinoshita, N. Takamiya, K. Kawauchi, H. Tateishi-Karimata, N. Sugimoto and D. Miyoshi
Chem. Commun. 59 4891 - 4894 2005.4
-
Thermodynamic Analysis of Duplex Formation of the Heterochiral DNA with L-Deoxyadenosine Reviewed International journal
J. Kawakami, K. Tsujita and N. Sugimoto
Anal.Sci. 21 77 - 82 2005
Joint Work
-
A nano-circular single-stranded DNA as a novel tool for SNPs detection Reviewed International journal
T. Ohmichi, A. Takashima and N. Sugimoto
Nucleosides Nucleotides Nucleic Acids 24 359 - 366 2005
Joint Work
-
Thermodynamic and Kinetic Analyses of Nucleic Acid Structures for Pharmacogenomics Reviewed International journal
D. Miyoshi and N. Sugimoto
Current Pharmacogenomics 3 217 - 236 2005
Joint Work
-
Central Dogma for a Molecular Design Based on DNA: DNB (Databasing/Designable Nanobio) → ENB (Engineering Nanobio) → FNB (Functional Nanobio) Reviewed International journal
S. Nakano and N. Sugimoto
Chemistry Letters 34 1206 - 1211 2005
Joint Work
-
Synthesis of Water-soluble Porphyrine and the Corresponding Hughly Planar Benzoporphyrin without meso-Substituents Reviewed International journal
T. Murashima, S. Tsujimoto, T. Yamada, T. Miyazawa, H. Uno, N. Ono and N.Sugimoto
Tetrahedron Lett. 46 113 - 116 2005
Joint Work
-
Nucleic Acid with guanidium modification exhibits efficient cellular uptake Reviewed International journal
T. Ohmichi, M. Kuwahara, N. Sasaki, M. Hasegawa, T. Nishikata, H. Sawai and N. Sugimoto
Angew. Chem. Int. Ed. Engl. 44 6682 - 6685 2005
Joint Work
-
Drastic effect of a single base difference between human and tetrahymena telomere sequences on their structures under molecular crowding conditions Reviewed International journal
D. Miyoshi, H. Karimata and N. Sugimoto
Angew. Chem. Int. Ed. Engl. 44 3740 - 3744 2005
Joint Work
-
DNA-based biosensor for monitoring pHin vitro and in living cells Reviewed International journal
T. Ohmichi, Y. Kawamoto, P. Wu, D. Miyoshi, H. Karimata and N. Sugimoto
Biochemistry 44 7125 - 7130 2005
Joint Work
-
An SPR Sensor Chip for Selective Detection of Small Molecules Using Molecularly Imprinted Polymer with Embedded Au Nanoparticles Reviewed International journal
J. Matsui, K. Akamatsu, N. Hara, D. Miyoshi, H. Nawafune, K. Tamaki and N.Sugimoto
Anal. Chem. 77 4282 - 4285 2005
Joint Work
-
Roles of Mg2+ in TPP-dependent riboswitch Reviewed International journal
T. Yamauchi, D. Miyoshi, T. kubodera, A. Nishimura, S. Nakai and N. Sugimoto
FEBS Lett. 579 2583 - 2588 2005
Joint Work
-
Duplex dissociation of telomere DNAs induced by molecular crowding Reviewed International journal
D. Miyoshi, S. Matsumura, S. Nakano and N. Sugimoto
J. Am. Chem. Soc. 126 165 - 169 2004
Joint Work
-
Introduction of peptide functions into DNA by nucleic asid peptides,NAPs Reviewed International journal
J. Kawakami, Z.M. Wang, H. Fujiki, S. Izumi and N. Sugimoto
Chem. Lett 33 1554 - 1555 2004
Joint Work
-
Synthetic cinchonidine receptors obtained by cross-linking linear poly(methacrylic acid) derivertives as an alternative molecular imprinting technique Reviewed International journal
J. Matsui, N. Minamimura, K. Nishimoto, K. Tamaki and N. Sugimoto
J. Chromatogr. 804 223 - 229 2004
Joint Work
-
Mechanical force analysis of peptide interactions using atomic force microscopy Reviewed International journal
C. Nakamura, S. Takeda, M. Kageshima, M. Ito, N. Sugimoto, K. Sekizawa and J. Miyake
Biopolymers (Peptide Science) 76 48 - 54 2004
Joint Work
-
Composite of Au Nanoparticles and molecularly imprinted polymer as a sensing material Reviewed International journal
J. Matsui, K. Akamatsu, S. Nishiguchi, D. Miyoshi, H. Nawafune, K. Tamaki and N. Sugimoto
Anal. Chem. 76 1310 - 1315 2004
Joint Work
-
Influences of ribonucleotide on a duplex conformation and its thermal stability:Study with the chimeric RNA-DNA strands Reviewed International journal
S. Nakano, T. Kanzaki and N. Sugimoto
J. Am. Chem. Soc. 126 1088 - 1095 2004
Joint Work
-
The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability Reviewed International journal
S. Nakano, H. Karimata, T. Ohmichi, J. Kawakami and N. Sugimoto
J. Am. Chem. Soc. 126 14330 - 14331 2004
Joint Work
-
An oligopeptide containing the C-terminal sequence of RNase A has a potent RNase A binding property Reviewed International journal
S. Nakano and N. Sugimoto
J. Am. Chem. Soc. 125 8728 - 8729 2003.11
Joint Work
-
Factors that contribute to efficient catalytic activity of a small Ca2+-dependent deoxyribozyme in relation to its RNA cleavage function Reviewed International journal
Y. Okumoto, Y. Tanabe and N. Sugimoto
Biochemistry 42 2158 - 2165 2003
Joint Work
-
Structural competition involving G-quadruplex DNA and its complement Reviewed International journal
W. Li, D. Miyoshi, S. Nakano and N. Sugimoto
Biochemistry 42 11736 - 11744 2003
Joint Work
-
Large stabilization of a DNA duplex by the deoxyadenosine derivatives tethering an aromatic hydrocarbon group Reviewed International journal
S. Nakano, Y. Uotani, S. Nakashima, Y. Anno, M. Fujii and N. Sugimto
J. Am. Chem. Soc. 125 8086 - 8087 2003
Joint Work
-
Structural polymorphism of telomeric DNA regulated by pH and divalent cation Reviewed International journal
D. Miyoshi, S. Matsumura, W. Li and N. Sugimoto
Nucleosides, Nucleotides Nucleic Acids 22 203 - 221 2003
Joint Work
-
Effect of putrescine and PEG on a structural transition of DNA G-quadruplex Reviewed International journal
D. Miyoshi, A. Nakao and N. Sugimoto
Nucleosides, Nucleotides Nucleic Acids 22 1591 - 1594 2003
Joint Work
-
Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+ Reviewed International journal
D. Miyoshi, A. Nakao and N. Sugimoto
Nucleic Acids Res. 31 1156 - 1163 2003
Joint Work
-
Immobilized small deoxyribozyme to distinguish RNA secondary structures Reviewed International journal
Y. Okumoto, T. Ohmichi and N. Sugimoto
Biochemistry 41 2769 - 2773 2002
Joint Work
-
Molecular crowding regulates the structural switch of the DNA G-quadruplex Reviewed International journal
D. Miyoshi, A. Nakao and N. Sugimoto
Biochemistry 41 15017 - 15024 2002
Joint Work
-
Quartz crystal microbalance sensor targeting low molecular weight compounds using oligopeptide binder and peptide-immobilized latex beads Reviewed International journal
C. Nakamura, S. H. Song, S. M. Change, N. Sugimoto and J. Miyake
Anal. Chim. Acta. 469 183 - 188 2002
Joint Work
-
Long RNA dangling end has large energetic contribution to duplex stability Reviewed International journal
T. Ohmichi, S. Nakano, D. Miyoshi and N. Sugimoto
J. Am. Chem. Soc. 124 10367 - 10372 2002
Joint Work
-
Characterization and thermodynamic properties of quadruplex/duplex competition. Reviewed International journal
W. Li, P. Wu, T. Ohmichi and N. Sugimoto
FEBS Lett. 526 77 - 81 2002
Joint Work
-
Molecular imprinting in alcohols: utility of a pre-polymer based strategy for synthesizing stereoselective artificial receptor polymers in hydrophilic media Reviewed International journal
J. Matsui, K. Tamaki and N. Sugimoto
Anal. Chem. Acta. 466 11 - 15 2002
Joint Work
-
Effect of divalent cations and cytosine protonation on thermodynamic properties of intermolecular DNA double and triple helices Reviewed International journal
P. Wu, Y. Kawamoto, H. Hara and N. Sugimoto
J. Inorg. Biochem. 91 277 - 285 2002
Joint Work
-
Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation Reviewed International journal
P. Wu, S. Nakano and N. Sugimoto
Eur. J. Biochem. 269 2821 - 2830 2002
Joint Work
-
A stable DNA tetraloop and its structural tolerance for modification Reviewed International journal
J. Kawakami, M. Yoneyama, D. Miyoshi and N. Sugimoto
Chem. Lett. 258 - 259 2001
Joint Work
-
Detection of porphyrin using a short peptide immobilized on a surface plasmon resonance sensor chip Reviewed International journal
C. Nakamura, Y. Inuyama, K. Shirai, N. Sugimoto and J. Miyake
Biosensors & Bioelectronics 16 1095 - 1100 2001
Joint Work
-
Thermodynamic stability of base pairs between 2-hydroxyadenine and incoming nucleotides as a determinant of nucleotide incorporation specificity during replication Reviewed International journal
J. Kawakami, H. Kamiya, K. Yasuda, H. Fujiki, H. Kasai and N. Sugimoto
Nucleic Acids Res. 29 3289 - 3296 2001
Joint Work
-
pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes Reviewed International journal
N. Sugimoto, P. Wu, H. Hara and Y. Kawamoto
Biochemistry 40 9396 - 9405 2001
Joint Work
-
Stabilization factors affecting duplex formation of peptide nucleic acid with DNA Reviewed International journal
N. Sugimoto, N. Satoh, K. Yasuda and S. Nakano
Biochemistry 40 8444 - 8451 2001
Joint Work
-
Utilization of ribozymes for loss-of-function analyses of the early development of the ascidian Ciona intestinalis
M. Katano, A. Yamada, K. Tanaka, J. Murakami, K. Taira, J. Kawakami, N. Sugimoto and T. Nishikata
Mem. Konan Univ., Sci. Eng. Ser. 48 11 - 20 2001
Joint Work
-
Cu2+ inhibits the aggregation of amyloid b-peptide(1-42) in vitro Reviewed International journal
J. Zou, K. Kajita and N. Sugimoto
Angew. Chem. Int. Ed. Engl. 40 2274 - 2277 2001
Joint Work
-
Effect of divalent cations on antiparallel G-quartet structure of d(G4T4G4) Reviewed International journal
D. Miyoshi, A. Nakao, T. Toda and N. Sugimoto
FEBS Lett. 496 128 - 133 2001
Joint Work
-
DNA recognition of a 24-mer peptide derived from RecA protein Reviewed International journal
N. Sugimoto
Biopolymers (Peptide Science) 55 416 - 424 2001
Single Work
-
Effect of extending the CD reference spectra to 168 nm on the prediction of protein secondary structures Reviewed International journal
J. Zou and N. Sugimoto
J. Biochem. Mol. Biol. Biophy 5 15 - 24 2001
Joint Work
-
Transition characteristics and thermodynamic analysis of DNA duplex formation: a quantitative consideration for the extent of duplex association Reviewed International journal
杉本 直己
Nucleic Acids Res., 28 4762 - 4768 2000.11
Single Work
-
Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes Reviewed International journal
N. Sugimoto, M. Nakano and S. Nakano
Biochemistry 39 11270 - 11281 2000
Joint Work
-
Kinetic property of bulged helix formation: analysis of kinetic behavior using nearest-neighbor parameters Reviewed International journal
T. Ohmichi, H. Nakamuta, K. Yasuda and N. Sugimoto
J. Am. Chem. Soc. 122 11286 - 11294 2000
Joint Work
-
In vitro selection of aptamers that act with Zn2+ Reviewed International journal
J. Kawakami, H. Imanaka, Y. Yokota and N. Sugimoto
J. Inorg. Biochem. 82 197 - 206 2000
Joint Work
-
Effects of metal ions and catalytic loop sequences on the complex formation of a deoxyribozyme and its RNA substrate Reviewed International journal
Y. Okumoto and N. Sugimoto
J. Inorg. Biochem. 82 189 - 195 2000
Joint Work
-
A role of the Trp-His interaction in the conformational switch between a-helix and b-sheet in short alanine-based peptides Reviewed International journal
J. Zou and N. Sugimoto
J. Chem. Soc., Perkin Trans. 2 2135 - 2140 2000
Joint Work
-
Development of small peptides recognizing a monosaccharide by combinatorial chemistry Reviewed International journal
N. Sugimoto, D. Miyoshi and J. Zou
Chem. Commun. 2295 - 2296 2000
Joint Work
-
Ribozyme-metal ion interaction Reviewed
N. Sugimoto and T. Ohmichi
Rep. Prog. Poly. Phys. Jpn. 43 897 - 910 2000
Joint Work
-
Complexation of peptide with Cu2+ responsible to inducing and enhancing the formation of a-helix conformation Reviewed International journal
J. Zou and N. Sugimoto
BioMetals 13 349 - 359 2000
Joint Work
-
RNA cleavage by a short catalytic DNA Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 42 561 - 564 1999.11
Single Work
-
a-b structural transition of short oligopeptides by water/organic solvent titration Reviewed International journal
N. Sugimoto, J. Zou, H. Kazuta and D. Miyoshi
Chem. Lett. 637 - 638 1999
Joint Work
-
Effect of copper ion on conformations of short alanine-based peptides with single Trp/His stacking interactions Reviewed
J. Zou and N. Sugimoto
Protein and Peptide Lett. 6 373 - 378 1999
Joint Work
-
Effect of DNA sequences on its catalytic activity for porphyrin metallation Reviewed
N. Sugimoto and T. Toda
Rep. Prog. Poly. Phys. Jpn. 42 573 - 576 1999
Joint Work
-
Thermodynamic stabilities of the short PNA/DNA hybrid duplexes Reviewed
N. Sugimoto and N. Sato
Rep. Prog. Poly. Phys. Jpn. 42 569 - 572 1999
Joint Work
-
Fishing out tryptophan selective peptides from combinatorial library Reviewed
N. Sugimoto and H. Kazuta
Rep. Prog. Poly. Phys. Jpn. 42 565 - 568 1999
Joint Work
-
Stabilization of the a-helix conformation of short peptides Reviewed
J. Zou and N. Sugimoto
Rep. Prog. Poly. Phys. Jpn. 42 511 - 514 1999
Joint Work
-
Development of new biotechnology for the 21st century (II) structural and thermodynamic studies of PNA/DNA hybrids containing single bulge nucleotides Reviewed
K. Yasuda, J. Kawakami and N. Sugimoto
Mem. Konan Univ., Sci. Ser. 46 61 - 69 1999
Joint Work
-
Development of new biotechnology for the 21st century (I) role of side-chain interactions of peptides in some neurodegenerative diseases Reviewed
J. Zou and N. Sugimoto
Mem. Konan Univ., Sci. Ser. 46 49 - 60 1999
Joint Work
-
A selection of short peptides that interact with a porphyrin as a small target by immobilized phage display Reviewed International journal
J. Kawakami, T. Kitano, and N. Sugimoto
Chem. Commun. 1765 - 1766 1999
Joint Work
-
Nucleic acid duplex stability: influence of base composition on cation effects Reviewed International journal
S. Nakano, M. Fujimoto, H. Hara and N. Sugimoto
Nucleic Acids Res. 27 2957 - 2965 1999
Joint Work
-
Effect of metal ions and sequence of deoxyribozymes on their RNA cleavage activity Reviewed International journal
N. Sugimoto, Y. Okumoto and T. Ohmichi
J. Chem. Soc., Perkin Trans. 2 1381 - 1386 1999
Joint Work
-
A novel screening method for combinatorial chemistry for low affinity interactions Reviewed International journal
N. Sugimoto, H. Kazuta, J. Zou and D. Miyoshi
Chem. Commun. 677 - 678 1999
Joint Work
-
Selection of peptides that recognize tryptophan by combinatorial chemistry
N. Sugimoto, H. Kazuta, and D. Miyoshi
Peptide Science 281 - 284 1999
Joint Work
-
Effect of substrate RNA sequence on the cleavage reaction by a short ribozyme Reviewed International journal
T. Ohmichi, Y. Okumoto and N. Sugimoto
Nucleic Acids Res. 26 5655 - 5661 1998
Joint Work
-
Effect of Cu2+ on complex formation between a deoxyribozyme and its substrates Reviewed International journal
N. Sugimoto and N. Wakizaka
Nucleosides & Nucleotides 17 565 - 574 1998
Joint Work
-
In vitro selection of aptamers that recognize a monosaccharide Reviewed International journal
J. Kawakami, Y. Kawase and N. Sugimoto
Anal. Chem. Acta. 365 95 - 100 1998
Joint Work
-
Model reaction between TAR RNA and Tat protein in HIV Reviewed
N. Sugimoto, I. Hirai and T. Ohmichi
Rep. Prog. Poly. Phys. Jpn. 41 663 - 666 1998
Joint Work
-
Stability of internal single A・A mismatches in RNA/DNA hybrids Reviewed
N. Sugimoto and M. Fujimoto
Rep. Prog. Poly. Phys. Jpn. 41 659 - 662 1998
Joint Work
-
Thermodynamic stability of DNA triple helixes Reviewed
N. Sugimoto and K. Aoki
Rep. Prog. Poly. Phys. Jpn. 41 655 - 658 1998
Joint Work
-
Reaction field for efficient porphyrin metallation catalysis produced by self-assembly of a short DNA oligonucleotide Reviewed International journal
N. Sugimoto, T. Toda and T. Ohmichi
Chem. Commun. 1533 - 1534 1998
Joint Work
-
Single-stranded DNA recognition of a 24-mer peptide derived from RecA protein Reviewed International journal
S. Nakano and N. Sugimoto
Bull. Chem. Soc. Jpn. 71 2205 - 2210 1998
Joint Work
-
生命関連分子の微視的相互作用 (3) RNA鎖を切断するデオキシリボザイムと金属イオンの関係
奥本泰秀, 川上純司, 杉本直己
甲南大学紀要、理学編 45 125 - 133 1998
Joint Work
-
生命関連分子の微視的相互作用 (4) ミスマッチを含む RNA/DNA ハイブリッドの安定性に及ぼすミスマッチの隣接塩基対の影響 International journal
杉本直己
甲南大学紀要、理学編 45 135 - 143 1998
Single Work
-
生命関連分子の微視的相互作用 (II) ペプチドの分子内αヘリックスと分子間bシートの構造遷移
杉本 直己
甲南大学紀要、理学編, 44 17 - 26 1997.11
Single Work
-
Roles of 2’-hydroxyls of leadzyme on an RNA cleavage Reviewed International journal
T. Ohmichi and N. Sugimoto
Bull. Chem. Soc. Jpn. 70 2743 - 2747 1997
Joint Work
-
Role of Nd3+ and Pb2+ on the RNA cleavage reaction by a small ribozyme Reviewed International journal
T. Ohmichi and N. Sugimoto
Biochemistry 36 3514 - 3521 1997
Joint Work
-
Effect of cation concentration on stability of short DNA triplexes Reviewed
N. Sugimoto and K. Aoki
Rep. Prog. Poly. Phys. Jpn. 657 - 660 1997
Joint Work
-
Stability of the duplexes between a peptide nucleic acid and DNA Reviewed
N. Sugimoto and Y. Okumoto
Rep. Prog. Poly. Phys. Jpn. 40 661 - 664 1997
Joint Work
-
Stability of internal G・T mismatches in RNA/DNA hybrids Reviewed
N. Sugimoto and M. Fujimoto
Rep. Prog. Poly. Phys. Jpn. 40 665 - 668 1997
Joint Work
-
A 24 mer peptide derived from RecA protein can discriminate a single-stranded DNA from a double-stranded DNA Reviewed International journal
N. Sugimoto and S. Nakano
Chem. Commun. 2125 - 2126 1997
Joint Work
-
Sandwiching interaction of peptides with a porphyrin Reviewed International journal
N. Sugimoto and S. Nakano
Chem. Lett. 939 - 940 1997
Joint Work
-
Site-specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions Reviewed International journal
杉本 直己
FEBS Lett., 393 97 - 100 1996.11
Single Work
-
A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme Reviewed International journal
杉本 直己
Biochemistry, 35 648 - 658 1996.11
Single Work
-
The stability of DNA and RNA G-quartets Reviewed International journal
杉本 直己
Nucleosides & Nucleotides, 15 559 - 567 1996.11
Single Work
-
Interactions of 5-(1-pyrenyl)-10,15,20-tris(4-methylpyridinium)porphine with double-helix and triple-helix nucleic acids Reviewed International journal
杉本 直己
Nucleosides & Nucleotides, 15 743 - 747 1996.11
Single Work
-
Stability of long RNA/DNA hybrids Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 39 667 - 670 1996.11
Single Work
-
Stability of long dangling ends on RNA double helices Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 39 671 - 674 1996.11
Single Work
-
Stability of G・A mismatches in RNA/DNA hybrids and DNA double helices Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 39 675 - 678 1996.11
Single Work
-
生命関連分子の微視的相互作用 (I) バルジを含むDNA二重らせんの熱力学的安定性に及ぼすイノシン置換の影響
楢木泰俊彦, 川上純司, 杉本直己
甲南大学紀要、理学編 43 37 - 47 1996
Joint Work
-
Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes Reviewed International journal
N. Sugimoto, S. Nakano, M. Yoneyama and K. Honda
Nucleic Acids Res. 24 4501 - 4505 1996
Joint Work
-
核酸の機能と構造に関する微視的相互作用XI DNAの一本鎖部位の安定性とペプチド認識における役割
杉本 直己
甲南大学紀要、理学編, 42 37 - 43 1995.11
Single Work
-
Energetics of oligodeoxyribonucleotides with a bulge Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 38 691 - 694 1995.11
Single Work
-
Energetics of oligodeoxyribonucleotides with 5-methylcytosine Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 38 695 - 698 1995.11
Single Work
-
On the mechanism of preferential incorporation of dAMP at abasic sites in translational DNA synthesis. Role of proofreading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site Reviewed International journal
杉本 直己
Nucleic Acids Res., 23 123 - 129 1995.11
Single Work
-
Influence of a-deoxyadenosine on the stability and structure of DNA. Thermodynamic and molecular mechanics studies Reviewed International journal
杉本 直己
Biochemistry, 34 6947 - 6955 1995.11
Single Work
-
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes Reviewed International journal
杉本 直己
Biochemistry, 34 11211 - 11216 1995.11
Single Work
-
RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs have identical stability Reviewed International journal
杉本 直己
FEBS Lett., 354 74 - 78 1994.11
Single Work
-
Application of the thermodynamic parameters of DNA stability prediction to double-helix formation of deoxyribooligonucleotides Reviewed International journal
杉本 直己
Nucleosides & Nucleotides, 13 1311 - 1317 1994.11
Single Work
-
The study of biomodel solution containing various salts: fourier transform infrared attenuated total reflectance (FTIR ATR) spectrometry of phosphate-family solution Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 37 815 - 818 1994.11
Single Work
-
Thermodynamic study of RNA・DNA hybrids, (rA)8・(dT)8 and (dA)8・(rU)8 Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 37 819 - 822 1994.11
Single Work
-
Effect of Na+ and K+ ions on the stability of DNA G-quartet Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 37 823 - 824 1994.11
Single Work
-
核酸の構造と機能に関する微視的相互作用X 連続配列をもつ核酸の特異的構造とその安定性
杉本 直己
甲南大学紀要、理学編, 41 23 - 30 1994.11
Single Work
-
FTIR ATR法による無電解パラジウム リン合金めっき浴中の浴成分のモニタリング Reviewed
杉本 直己
表面技術, 45 85 - 87 1994.11
Single Work
-
Secondary structures of wild-type and mutant hairpin ribozymes Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 36 725 - 728 1993.11
Single Work
-
核酸の構造と機能に関与する微視的相互作用IX RNAの二次構造安定性へのダングリング・エンドとヘアピン・ループ部位の寄与
杉本 直己
甲南大学紀要、理学編, 40 83 - 92 1993.11
Single Work
-
Effect of GA and AA mismatches on interaction between substrate RNA and active site of ribozyme Reviewed International journal
杉本 直己
Chemistry Express, 8 613 - 616 1993.11
Single Work
-
Inclusion kinetics of p-(3-ethylsalicylazo)benzenesulfonate into a-cyclodextrin Reviewed International journal
杉本 直己
Chemistry Express, 8 137 - 140 1993.11
Single Work
-
Effect of GA and AA mismatches on RNA double helix Reviewed International journal
杉本 直己
Chemistry Express, 8 309 - 312 1993.11
Single Work
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Effect of berenil on stability of double-helix of octamers of deoxyriboadenylic and deoxyribothymidylic acids Reviewed International journal
杉本 直己
Chemistry Express, 8 313 - 316 1993.11
Single Work
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Relationship between catalytic activity and secondary structure of a hammerhead ribozyme: a study using thermodynamic parameters for RNA structure prediction Reviewed International journal
杉本 直己
Supramol. Chem., 2 99 - 102 1993.11
Single Work
-
Melting kinetics of self-complementary double-helix by a fluorescent oligonucleotide AUGCAUeA Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 35 745 - 746 1992.11
Single Work
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Stability of right-handed and left-handed double-helices of self-complementary hexanucleotide CGCGCG Reviewed International journal
杉本 直己
Chemistry Express, 7 493 - 496 1992.11
Single Work
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Effects of dimidium and ethidium on melting of double-helix by octamers of deoxyriboadenylic and deoxyribothymidylic acids Reviewed
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 35 741 - 744 1992.11
Single Work
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Stability of double-helix by deoxyribooligonucleotides containing 5-trifluoro-methyluracil and 5-cyanouracil Reviewed International journal
杉本 直己
Chemistry Express, 7 405 - 408 1992.11
Single Work
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Kinetics of double-helix melting of self-complementary deoxyribooctanucleotid d(TATGCATA) Reviewed International journal
杉本 直己
Chemistry Express, 7 325 - 328 1992.11
Single Work
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Melting behavior and stability of (dA)8・(dT)8 double helix Reviewed International journal
杉本 直己
Nucleosides & Nucleotides, 11 515 - 520 1992.11
Single Work
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核酸の構造と機能に関与する微視的相互作用VIII GC塩基対からなるRNA・DNAキメラ体の特性
杉本 直己
甲南大学紀要、理学編, 39 189 - 204 1992.11
Single Work
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Thermodynamics of triple-helix and double-helix formations by octamers of deoxyriboadenylic and deoxyribothymidylic acids Reviewed
杉本 直己
Bull. Chem. Soc. Jpn., 65 535 - 540 1992.11
Single Work
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Salt effects on binding of propidium with poly(A)・poly(U) and poly(I)・poly(C) Reviewed International journal
杉本 直己
Chemistry Express, 7 57 - 60 1992.11
Single Work
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Effect of base-triplet formation on binding of tetrakis(1-methyl-4-pyridyl)porphine with poly(A)・poly(U) Reviewed International journal
杉本 直己
Chemistry Express, 7 61 - 64 1992.11
Single Work
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Temperature and pressure effects on equilibrium of double-helix to single-strands by octamers of deoxyriboadenylic and deoxyribothymidylic acids Reviewed International journal
杉本 直己
Chemistry Express, 7 273 - 276 1992.11
Single Work
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核酸の構造と機能に関与する微視的相互作用VII RNA-DNAハイブリッド型オクタヌクレオチドr(CU)4・d(AG)4の二重らせんの性質
杉本 直己
甲南大学紀要、理学編, 39 29 - 35 1992.11
Single Work
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Ab initio MO calculations of model molecules for ribozyme reaction including an Mg2+ ion Reviewed International journal
杉本 直己
Chem. Lett., 2119 - 2122 1991.11
Single Work
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Double-helix melting of octamers of deoxyriboadenylic and deoxyribothymidylic acids in the presence of ethidium Reviewed International journal
杉本 直己
Chem. Lett 9 - 12 1991.11
Single Work
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Stabilization energy of the catalytic core of the Tetrahymena ribozyme Reviewed International journal
杉本 直己
Chem. Lett 345 - 348 1991.11
Single Work
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Influence of mononucleotides on the reaction of tetrakis(4-N-methylpyridyl)porphine with RNAs Reviewed International journal
杉本 直己
Chemistry Express, 6 205 - 208 1991.11
Single Work
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Influence of cis-diamminedichloroplatinum (II) on the reaction of propidium with RNAs Reviewed International journal
杉本 直己
Chemistry Express, 6 209 - 212 1991.11
Single Work
-
核酸の構造と機能に関与する微視的相互作用V 非塩基対部位をもつRNA二重らせんの異常な融解挙動
杉本 直己
甲南大学紀要、理学編, 38 43 - 52 1991.11
Single Work
-
Triple-helix and double-helix formations of octamers of deoxyriboadenylic and deoxyribothymidylic acids Reviewed
杉本 直己
Chem. Lett. 1287 - 1290 1991.11
Single Work
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Effect of dangling ends on the double-helix melting of ribooligonucleotides at different Na+ concentrations Reviewed International journal
杉本 直己
Chem. Lett. 1291 - 1294 1991.11
Single Work
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Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops Reviewed International journal
杉本 直己
Biochemistry, 30 6428 - 6436 1991.11
Single Work
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The effect of actinomycin D on the transition of poly(dG-dMeC) from right-handed to left-handed form Reviewed International journal
杉本 直己
Chemistry Express, 6, 507 - 510 1991.11
Single Work
-
Relationship between catalytic activity and stability of a hammerhead ribozyme with/without a hairpin Reviewed International journal
杉本 直己
Chemistry Express, 6, 691 - 694 1991.11
Single Work
-
核酸の構造と機能に関与する微視的相互作用VI DNAオリゴマーの三重らせん形成
杉本 直己
甲南大学紀要、理学編, 38, 99 - 114 1991.11
Single Work
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Effect of unpaired terminal nucleotides of substrate RNAs on the RNA ligation with T4 RNA ligase Reviewed International journal
杉本 直己
Bull. Chem. Soc. Jpn., 64, 2978 - 2982 1991.11
Single Work
-
Triple-helix formation of (dA)8 and (dT)8 Reviewed International journal
杉本 直己
Rep. Prog. Poly. Phys. Jpn. 34 643 - 646 1991.11
Single Work
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Self-complementary double-helix formation of d(TCATGA) and d(TGATCA) Reviewed International journal
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 34, 647 - 648 1991.11
Single Work
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Cationic micellar effect upon the protonation of 2,4-dimethyl-3-ethylpyrrole Reviewed International journal
杉本 直己
Chemistry Express, 5, 925 - 928 1990.11
Single Work
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Activation parameters for the proton-transfer reaction of 1,8-bis(dimethylamino) naphthalene in micellar solution Reviewed International journal
杉本 直己
Chemistry Express, 5, 41 - 44 1990.11
Single Work
-
Double-helix formation by oligodeoxyriboadenylic and oligodeoxyribothymidylic acids Reviewed International journal
杉本 直己
Chemistry Express, 5 765 - 768 1990.11
Single Work
-
Thermodynamics and kinetics of propidium binding to poly(A)・poly(U) in aqueous solution Reviewed International journal
杉本 直己
Bull. Chem. Soc. Jpn., 63, 697 - 701 1990.11
Single Work
-
Salt and pressure effects on reaction of drugs binding to nucleic acids Reviewed International journal
杉本 直己
Review of Physical Chemistry of Japan, Special issue, 39 - 48 1990.11
Single Work
-
核酸の構造と機能に関与する微視的相互作用III 塩基対逐次形成モデルのDNAオリゴマーへの適用 International journal
杉本 直己
甲南大学紀要、理学編, 37, 77 - 86 1990.11
Single Work
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Salt effects on equilibrium and kinetics of the reaction of tetrakis(1-methyl-4-pyridinio)porphine with DNA Reviewed International journal
杉本 直己
Bull. Chem. Soc. Jpn., 63, 1641 - 1646 1990.11
Single Work
-
Double-helix formation of CGCAGCG Reviewed International journal
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 33, 729 - 732 1990.11
Single Work
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Binding behavior of tetrakis(4-N-methylpyridyl)porphine with DNA in ethanol-buffer solution Reviewed International journal
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 33, 733 - 734 1990.11
Single Work
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Stability of oligonucleotide YAUGCAU helices Reviewed International journal
杉本 直己
Chemistry Express, 5, 581 - 584 1990.11
Single Work
-
Application of energy parameters of RNA stability to the reaction of hammerhead ribozymes Reviewed International journal
杉本 直己
Chemistry Express, 5, 585 - 588 1990.11
Single Work
-
核酸の構造と機能に関与する微視的相互作用IV 核酸ポリマーと薬物の反応
杉本 直己
甲南大学紀要、理学編, 37, 163 - 175 1990.11
Single Work
-
Stability of oligonucleotide GGCGUC and CGGCUG helices Reviewed International journal
杉本 直己
Chemistry Express, 5, 673 - 676 1990.11
Single Work
-
Melting of double-helix of the decamers of deoxyriboadenylic and deoxyribothymidylic acids in the presence of ethidium Reviewed International journal
杉本 直己
Chemistry Express, 5, 677 - 680 1990.11
Single Work
-
Double-helix melting of octamers of deoxyriboguanylic and deoxyribocytidylic acids Reviewed
杉本 直己
Chemistry Express, 5, 765 - 768 1990.11
Single Work
-
Salt effect on double-helix formation of AUGCAU Reviewed
杉本 直己
Chemistry Express, 5, 249 - 252 1990.11
Single Work
-
Reactions of tetrakis(4-N-methylpyridyl)porphine and propidium with poly(A)・poly(U) and poly(I)・poly(C) Reviewed International journal
杉本 直己
Chemistry Express, 5, 399 - 402 1990.11
Single Work
-
Inhibition of deoxyribooligonucleotides on the circle opening reaction of the intervening sequence from Tetrahymena thermophila Reviewed International journal
杉本 直己
Chem. Lett., 747 - 748 1990.11
Single Work
-
Binding of a fluorescent oligonucleotide to a circularized intervening sequence from Tetrahymena thermophila Reviewed
杉本 直己
Chem. Lett., 2223 - 2226 1989.11
Single Work
-
Binding of pyridine-2-azo-p-dimethylaniline to DNA in ethanol-water solution Reviewed International journal
杉本 直己
Chemistry Express, 4, 29 - 32 1989.11
Single Work
-
Inclusion kinetics of crystal violet into g-cyclodextrin Reviewed International journal
杉本 直己
Chemistry Express, 4, 65 - 68 1989.11
Single Work
-
Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: evidence for substrate and Mg2+ binding interactions Reviewed International journal
杉本 直己
Nucleic Acids Res., 17, 355 - 371 1989.11
Single Work
-
Propidium binding to DNA and tRNA in solution Reviewed International journal
杉本 直己
Chemistry Express, 4, 385 - 388 1989.11
Single Work
-
Behaviors of AA, CA, GA, terminal mismatches and UA terminal base-pair in ribooligonucleotide Reviewed International journal
杉本 直己
Chemistry Express, 4, 401 - 404 1989.11
Single Work
-
Mg2+ contribution to a formation of active form of ribozyme Reviewed International journal
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 32, 711 - 714 1989.11
Single Work
-
Ethanol and salts effects on the reaction of azure B with poly(A)poly(U) and poly(dA)poly(dT) Reviewed International journal
杉本 直己
Rep. Prog. Poly. Phys. Jpn., 32, 715 - 718 1989.11
Single Work
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Effect of a-cyclodextrin inclusion on kinetics of complex formation between Co(II) Ion and pyridine-2-azo-p-dimetylaniline Reviewed International journal
杉本 直己
Chemistry Express, 4, 475 - 478 1989.11
Single Work
-
Salt effect on the reactions of DNA with actinomycin D and tetrakis(4-N-methylpyridyl)porphine Reviewed International journal
杉本 直己
Chemistry Express, 4, 609 - 612 1989.11
Single Work
-
Thermodynamic parameters for melting of the stem regions in the self-splicing intervening sequence from Tetrahymena Reviewed International journal
杉本 直己
Chemistry Express, 4, 613 - 616 1989.11
Single Work
-
Application of improved free-energy parameters of RNA stability to codon-anticodon interactions Reviewed International journal
杉本 直己
Bull. Chem. Soc. Jpn., 62, 3745 - 3747 1989.11
Single Work
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核酸の構造と機能に関与する微視的相互作用II テトラヒメナ・リボザイムの活性位の構造 International journal
杉本 直己
甲南大学紀要、理学編, 36, 89 - 97 1989.11
Single Work
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Ethanol effect on the reactions of DNA with actinomycin D and tetrakis(4-N-methylpyridyl)porphine Reviewed International journal
杉本 直己
Chemistry Express, 4, 661 - 664 1989.11
Single Work
-
核酸の構造と機能に関与する微視的相互作用I RNAの二重らせん形成 International journal
杉本 直己
甲南大学紀要、理学編, 36, 41 - 50 1989.11
Single Work
-
Reaction of a circularized intervening sequence with the dinucleotide CU at high temperatures Reviewed International journal
杉本 直己
Chemistry Express, 4, 405 - 408 1989.11
Single Work
-
核酸の構造と機能に及ぼす非塩基対部位の影響 International journal
杉本 直己
甲南大学紀要、理学編, 35, 103 - 114 1988.11
Single Work
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Hydrogen bonding and stacking contributions to nucleic acid stability International journal
杉本 直己
Structure and Expression (R. H. Sarma and M. H. Sarma, Eds.), Adenine Press, NY, 1, 249 - 259 1988.11
Single Work
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Micellar effect on rate of proton-transfer reaction of 1,8-bis(dimethylamino) naphthalene in aqueous solution Reviewed International journal
杉本 直己
Chemistry Express, 3, 407 - 410 1988.11
Single Work
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Kinetics for reaction of a circularized intervening sequence with CU, UCU, CUCU, and CUCUCU: mechanistic implications from the dependence on temperature and on oligomer and Mg2+ concentrations Reviewed International journal
杉本 直己
Biochemistry, 27, 6384 - 6392 1988.11
Single Work
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T4 RNAリガーゼ反応に対するオリゴヌクレオチドの塩基対形成の影響 International journal
杉本 直己
Chemistry Express, 3, 483 - 486 1988.11
Single Work
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Pressure effect on ethidium binding to DNA Reviewed International journal
杉本 直己
Chemistry Express, 3, 487 - 490 1988.11
Single Work
-
Improved parameters for prediction of RNA structure International journal
杉本 直己
Cold Spring Harbor Symposia on Quantitative Biology, 52, 123 - 133 1987.11
Single Work
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Free energy increments for hydrogen bonds in nucleic acid base pairs Reviewed International journal
杉本 直己
J. Am. Chem. Soc., 109, 3783 - 3785 1987.11
Single Work
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Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic Acid Reviewed International journal
杉本 直己
Biochemistry, 26, 4554 - 4558 1987.11
Single Work
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Sequence dependence for the energetics of terminal mismatches in ribooligonucleotides Reviewed International journal
杉本 直己
Biochemistry, 26, 4559 - 4562 1987.11
Single Work
-
Improved free-energy parameters for predictions of RNA duplex stability Reviewed International journal
杉本 直己
Proc. Natl. Acad. Sci. USA, 83, 9373 - 9377 1986.11
Single Work
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Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: An empirical estimate of the energetics of hydrogen bonds in nucleic acids Reviewed International journal
杉本 直己
Biochemistry, 25, 3214 - 3219 1986.11
Single Work
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Energetics of internal GU mismatches in ribooligonucleotide helixes Reviewed International journal
杉本 直己
Biochemistry, 25, 5755 - 5759 1986.11
Single Work
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Substituent effects on proton tunnelling. Reaction between 2,4,6-trinitrotoluene and 1-substituted piperidines in acetonitrile Reviewed International journal
杉本 直己
J. Chem. Soc., Faraday Trans. 1, 81, 1441 - 1445 1985.11
Single Work
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Kinetic hydrogen isotope effects in the reaction between 2,4,6-trinitrotoluene and 1-ethylpiperidine in acetonitrile. The effect of pressure Reviewed International journal
杉本 直己
J. Chem. Soc., Faraday Trans. 1,81, 2959 - 2966 1985.11
Single Work
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溶液中でのプロトン移動反応に対する速度論的研究
杉本 直己
1985.3
Single Work
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Kinetic study of proton tunneling in the reaction between 2,4,6-trinitrotoluene and 1,8- diazabicyclo[5.4.0]-undec-7-ene in benzonitrile Reviewed International journal
杉本 直己
Bull. Chem. Soc. Jpn.,57, 366 - 369 1984.11
Single Work
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Solvent, pressure, and deuterium isotope effects on proton tunneling. The reaction between 2,4,6-trinitrotoluene and 1,8-diazabicyclo[5.4.0]undec-7-ene in aprotic solvents Reviewed International journal
杉本 直己
J. Chem. Soc., Perkin Trans. 2, 655 - 659 1984.11
Single Work
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Pressure effect on tunneling of the proton- and deuteron-transfer reaction of 2,4,6-trinitrotoluene with 1,8-diazabicyclo[5.4.0]undec-7-ene in acetonitrile Reviewed International journal
杉本 直己
J. Am. Chem. Soc., 105, 7676 - 7680 1983.11
Single Work
-
Pressure effect on proton/deuteron transfer reactions of 4-nitrophenylnitromethane + N,N,N’,N’-tetramethylguanidine (TMG), 2,4,6-trinitorotoluene (TNT) + TMG, and TNT + 1,8-diazabicyclo[5.4.0]undec-7-ene in some aprotic solvents Reviewed International journal
杉本 直己
High Pressure in Research and Industry,2, 676 - 679 1982.11
Single Work
-
Kinetics and tunneling in the proton- and deuteron-transfer reaction between 2,4,6,-trinitrotoluene and 1,8-diazabicyclo[5.4.0]undec-7-ene in some aprotic solvents Reviewed International journal
杉本 直己
J. Phys. Chem. 86 3418 - 3423 1982.11
Single Work
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Influence of pressure on primary kinetic isotope effects of the proton-transfer reaction between 4-nitrophenylnitromethane and 1,1’,3,3’-tetramethylguanidine in toluene and dichloromethane
杉本 直己
Bull. Chem. Res., Kyoto Univ., 59, 63 - 71 1981.11
Single Work
-
Pressure effect on rate constants of proton-transfer reactions from 2,4,6-trinitrotoluene to N,N,N’,N’-tetramethylguanidine and 1,8-diazabicyclo[5.4.0]undec-7-ene in acetonitrile and dichloromethane Reviewed International journal
杉本 直己
Bull. Chem. Soc. Jpn., 54, 2598 - 2602 1981.11
Single Work
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High-pressure stopped-flow kinetics of proton-transfer reaction between 4-nitrophenylnitromethane and 1,1’,3,3’-tetramethylguanidine in aprotic solvents Reviewed International journal
杉本 直己
Chem. Lett 887 - 890 1980.11
Single Work