Papers - SUGIMOTO Naoki

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

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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 (Mg²⁺) 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 Mg²⁺ 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.

DOI： 10.1002/chem.202501208

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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

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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

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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.

DOI： 10.1002/smtd.202401630

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

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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.

DOI： 10.1038/s42004-025-01532-z

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

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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

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

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Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical Environments Reviewed

Saptarshi Ghosh, Shuntaro Takahashi, Tatsuya Ohyama, Lutan Liu, Naoki Sugimoto

Journal of the American Chemical Society   146 ( 47 )   32479 - 32497   2024.11

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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

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

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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.

DOI： https://doi.org/10.21203/rs.3.rs-4185448/v1

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

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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

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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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Choline dihydrogen phosphate destabilizes G-quadruplexes and enhances transcription efficiency in vitro and in cells Reviewed

Hisae Tateishi-Karimata, Naoki Sugimoto

ACS Omega   9 ( 5 )   5675 - 5682   2024.1

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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.

DOI： https://doi.org/10.1021/acsomega.3c08087

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

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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

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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.

DOI： 10.1038/s41598-023-39407-9

Quantification of the concentration in a droplet formed by liquid–liquid phase separation of G-quadruplex-forming RNA Reviewed

Kohei Yokosawa, Mitsuki Tsuruta, Shinji Kajimoto, Naoki Sugimoto, Daisuke Miyoshi, Takakazu Nakabayashi

Chemical Physics Letters   826   140634   2023.9

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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.

DOI： 10.1016/j.cplett.2023.140634

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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

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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.

DOI： https://doi.org/10.1093/nar/gkad020

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

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

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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

Pressure-temperature control of activity of RNA polymerase ribozyme Reviewed International journal

S. Takahashi and N. Sugimoto

Biophys. Chem.   292   106914   2023.1

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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.

DOI： https://doi.org/10.1016/j.bpc.2022.106914

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

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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.

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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DOI： 10.1126/sciadv.adc9785

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

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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

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DOI： 10.1039/d2cc04383a

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

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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.

DOI： 10.1021/acs.analchem.2c01075

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

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DOI： 10.1039/d1cc07094k

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

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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

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

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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.

Thermodynamic Analysis to Elucidate the Behaviors Reviewed International journal

S. Takahashi, N.Sugimoto

49   14 - 19   2022.1

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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

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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.

DOI： 10.1038/s41598-022-05136-8

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

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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

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DOI： 10.1039/d1cc05523b

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

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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

PubMed

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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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Selected as a Supplementary Cover］

DOI： 10.1021/jacs.1c05468

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

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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［Selected as a Supplementary Cover］

DOI： 10.1021/acschembio.1c00133

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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DOI： 10.1246/bcsj.20210131

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

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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.

DOI： 10.1002/cbic.202100280

PubMed

researchmap

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

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

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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

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DOI： 10.3390/ijms22020947

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

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DOI： 10.1073/pnas.2020241118

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

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Publisher：MDPI  

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

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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

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[Selected as a HOT Article]

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

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[Selected as a Supplemental Cover]

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

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[Selected as a Cover]

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

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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

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[Selected as a Front Cover]

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

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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

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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

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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

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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

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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

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Joint Work

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

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DOI： 10.1039/c9ra06797c

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

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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

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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

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[Selected as an Inside Back Cover]

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

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[Selected as a Supplementary Cover]

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

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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

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[Selected as a Cover]

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

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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

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Joint Work

[Selected as a Supplementary Cover]

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

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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

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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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[Selected as a Supplementary Cover]

DOI： 10.1021/jacs.8b01577

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

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DOI： 10.1039/C7OB03179C

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

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DOI： 10.1038/s41594-018-0029-5

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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[Selected as a Supplementary Cover]

DOI： 10.1021/jacs.7b09449

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

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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

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Joint Work

DOI： 10.1016/j.bbrc.2018.01.083

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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[Highlighted as a Front Cover]

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

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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

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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

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Authorship：Lead author  

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

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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

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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

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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

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Authorship：Lead author  

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

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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

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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

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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

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Authorship：Lead author  

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

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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

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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

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Authorship：Lead author  

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

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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

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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

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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

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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

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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

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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

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DOI： 10.1002/cbic.201500139

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

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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

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Authorship：Lead author  

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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Authorship：Lead author  

DOI： 10.1039/C5CP02794B

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

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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

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[Highlighted as a Front Cover]

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

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Authorship：Lead author  

DOI： 10.3390/s150409388

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

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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

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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

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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

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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

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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

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Authorship：Lead author  

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

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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

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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

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DOI： 10.1002/chem.201404854

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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Authorship：Lead author  

DOI： 10.1093/nar/gku998

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

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DOI： 10.1002/cmdc.201402157.

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

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DOI： 10.1002/cmdc.201402167

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

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DOI： 10.1002/cmdc.201402151.

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

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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

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DOI： 10.1021/jp505107g.

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

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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

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DOI： 10.1371/jpurnal.pone.0090580

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

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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

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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

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DOI： 10.1038/srep03593.

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

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DOI： 10.1002/smll.201301273.

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

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DOI： 10.1002/anie.201307714.

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

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DOI： 10.1021/ac402497x.

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

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DOI： 10.1111/febs.12561

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

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DOI： 10.1016/j.ymeth.2013.05.026

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

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DOI： 10.1016/j.ymeth.2013.03.028

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

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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

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DOI： 10.1039/c3cc42990c

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

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DOI： 10.1021/jp406857s.

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

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DOI： 10.3390/molecules181011751

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

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DOI： 10.3390/ph6091082.

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

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DOI： 10.1093/nar/gkt286.

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

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DOI： 10.1021/la4012222

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

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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

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DOI： 10.1016/j.ymeth.2013.11.002.

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

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DOI： 10.1002/anie.201300058.

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

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DOI： 10.1371/journal.pone.0060222.

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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DOI： 10.1002/anie.200803577

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Effect of molecular crowding on DNA polymerase activity Reviewed International journal

Y. Sasaki, D. Miyoshi and N. Sugimoto

Biotech. J.   1   440 - 446   2006

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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

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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

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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   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

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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

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Thermodynamic and Kinetic Analyses of Nucleic Acid Structures for Pharmacogenomics Reviewed International journal

D. Miyoshi and N. Sugimoto

Current Pharmacogenomics   3   217 - 236   2005

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Immobilized small deoxyribozyme to distinguish RNA secondary structures Reviewed International journal

Y. Okumoto, T. Ohmichi and N. Sugimoto

Biochemistry   41   2769 - 2773   2002

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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DNA recognition of a 24-mer peptide derived from RecA protein Reviewed International journal

N. Sugimoto

Biopolymers (Peptide Science)   55   416 - 424   2001

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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

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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

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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

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Ribozyme-metal ion interaction Reviewed

N. Sugimoto and T. Ohmichi

Rep. Prog. Poly. Phys. Jpn.   43   897 - 910   2000

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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

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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

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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

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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

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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

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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

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RNA cleavage by a short catalytic DNA Reviewed

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 42   561 - 564   1999.11

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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

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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

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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

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Thermodynamic stabilities of the short PNA/DNA hybrid duplexes Reviewed

N. Sugimoto and N. Sato

Rep. Prog. Poly. Phys. Jpn.   42   569 - 572   1999

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Fishing out tryptophan selective peptides from combinatorial library Reviewed

N. Sugimoto and H. Kazuta

Rep. Prog. Poly. Phys. Jpn.   42   565 - 568   1999

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Stabilization of the a-helix conformation of short peptides Reviewed

J. Zou and N. Sugimoto

Rep. Prog. Poly. Phys. Jpn.   42   511 - 514   1999

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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

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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

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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

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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

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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

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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

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Selection of peptides that recognize tryptophan by combinatorial chemistry

N. Sugimoto, H. Kazuta, and D. Miyoshi

Peptide Science   281 - 284   1999

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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

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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

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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

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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

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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

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Thermodynamic stability of DNA triple helixes Reviewed

N. Sugimoto and K. Aoki

Rep. Prog. Poly. Phys. Jpn.   41   655 - 658   1998

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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

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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

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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

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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

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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

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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

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Effect of cation concentration on stability of short DNA triplexes Reviewed

N. Sugimoto and K. Aoki

Rep. Prog. Poly. Phys. Jpn.   657 - 660   1997

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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

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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

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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

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Sandwiching interaction of peptides with a porphyrin Reviewed International journal

N. Sugimoto and S. Nakano

Chem. Lett.   939 - 940   1997

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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

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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

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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

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The stability of DNA and RNA G-quartets Reviewed International journal

杉本　直己

Nucleosides & Nucleotides, 15   559 - 567   1996.11

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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

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Single Work

Stability of long RNA/DNA hybrids Reviewed

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 39   667 - 670   1996.11

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Stability of long dangling ends on RNA double helices Reviewed

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 39   671 - 674   1996.11

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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

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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

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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

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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

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Single Work

Energetics of oligodeoxyribonucleotides with a bulge Reviewed

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 38   691 - 694   1995.11

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Single Work

Energetics of oligodeoxyribonucleotides with 5-methylcytosine Reviewed

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 38   695 - 698   1995.11

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Secondary structures of wild-type and mutant hairpin ribozymes Reviewed

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 36   725 - 728   1993.11

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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

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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

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Inclusion kinetics of p-(3-ethylsalicylazo)benzenesulfonate into a-cyclodextrin Reviewed International journal

杉本　直己

Chemistry Express, 8   137 - 140   1993.11

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Effect of GA and AA mismatches on RNA double helix Reviewed International journal

杉本　直己

Chemistry Express, 8   309 - 312   1993.11

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Triple-helix and double-helix formations of octamers of deoxyriboadenylic and deoxyribothymidylic acids Reviewed

杉本　直己

Chem. Lett.   1287 - 1290   1991.11

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Double-helix formation of CGCAGCG Reviewed International journal

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 33,   729 - 732   1990.11

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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

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Stability of oligonucleotide YAUGCAU helices Reviewed International journal

杉本　直己

Chemistry Express, 5,   581 - 584   1990.11

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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

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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

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Stability of oligonucleotide GGCGUC and CGGCUG helices Reviewed International journal

杉本　直己

Chemistry Express, 5,   673 - 676   1990.11

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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

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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

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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

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Double-helix formation by oligodeoxyriboadenylic and oligodeoxyribothymidylic acids Reviewed International journal

杉本　直己

Chemistry Express,   5   765 - 768   1990.11

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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

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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

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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

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Double-helix melting of octamers of deoxyriboguanylic and deoxyribocytidylic acids Reviewed

杉本　直己

Chemistry Express, 5,   765 - 768   1990.11

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Salt effect on double-helix formation of AUGCAU Reviewed

杉本　直己

Chemistry Express, 5,   249 - 252   1990.11

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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

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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

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Binding of a fluorescent oligonucleotide to a circularized intervening sequence from Tetrahymena thermophila Reviewed

杉本　直己

Chem. Lett.,   2223 - 2226   1989.11

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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

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Inclusion kinetics of crystal violet into g-cyclodextrin Reviewed International journal

杉本　直己

Chemistry Express, 4,   65 - 68   1989.11

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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

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Propidium binding to DNA and tRNA in solution Reviewed International journal

杉本　直己

Chemistry Express, 4,   385 - 388   1989.11

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Single Work

Pressure effect on ethidium binding to DNA Reviewed International journal

杉本　直己

Chemistry Express, 3,   487 - 490   1988.11

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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