Papers - NAKANO Shuuichi
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Comprehensive analysis of stability and variability of DNA minimal i-motif structures Invited Reviewed
K. Ashida, A. Kitabayashi, K. Nishiyama, and S. Nakano
Molecules 30 1831 2025.4
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Inhibition of RNA phosphodiester backbone cleavage in the presence of organic cations of different sizes Invited Reviewed International journal
S. Yoshioka, A. Doi, and S. Nakano
ChemBioChem 25 ( 13 ) e202400276 2024.5
Joint Work
Authorship：Last author, Corresponding author Publisher：Wiley
Living cells contain various types of organic cations that may interact with nucleic acids. In order to understand the nucleic acid–binding properties of organic cations of different sizes, we investigated the ability of simple organic cations to inhibit the RNA phosphodiester bond cleavage promoted by Mg2+, Pb2+, and RNA-cleaving serum proteins. Kinetic analysis using chimeric DNA–RNA oligonucleotides showed that the cleavage at ribonucleotide sites was inhibited in the presence of monovalent cations comprising alkyl chains or benzene rings. The comparison of the cleavage rates in the presence of quaternary ammonium and phosphonium ions indicated that the steric hindrance effect of organic cations on their binding to the RNA backbone is significant when the cation size is larger than the phosphate–phosphate distance of a single-stranded nucleic acid. The cleavage inhibition was also observed for ribonucleotides located in long loops but not in short loops of oligonucleotide structures, indicating less efficient binding of bulky cations to structurally constrained regions. These results reveal the unique nucleic acid–binding properties of bulky cations distinct from those of metal ions.
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Basic protein- and peptide-induced stabilization of long-loop DNA G-quadruplexes Reviewed International journal
K. Tanabe, K. Miyazaki, H. Umeno, M. Takemoto, and S. Nakano
Biochimie 219 110 - 117 2024.4
Joint Work
Authorship：Last author, Corresponding author Publisher：Elsevier
The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.
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Evaluation of thermal stability of DNA oligonucleotide structures embedded in hydrogels Invited Reviewed International journal
D. Yamaguchi, M. Yoshida, S. Nakano
DNA 2 ( 4 ) 302 - 313 2022.12
Joint Work
Authorship：Last author, Corresponding author Publisher：MDPI
Understanding the self-assembly and hybridization properties of DNA oligonucleotides in confined spaces can help to improve their applications in biotechnology and nanotechnology. This study investigates the effects of spatial confinement in the pores of hydrogels on the thermal stability of DNA oligonucleotide structures. The preparation of oligonucleotides embedded in agarose gels was simple, whereas the preparation of oligonucleotides embedded in polyacrylamide gels was required to remove unpolymerized monomers. In the latter case, a method for rehydrating a washed dry gel with a buffer solution containing oligonucleotides was developed. Fluorescence measurements of oligonucleotides bearing fluorescent probes revealed no significant influence of the internal environment of the gel pores on the stability of DNA duplex, hairpin, and G-quadruplex structures. Moreover, the effects of poly(ethylene glycol) on the stability of DNA structures in the gels were similar to those in solutions. It is likely that the oligonucleotides are not strongly constrained in the gels and may be preferentially located in a water-rich environment in the gel matrix. The gel preparation was also applied to the assessment of the stability of DNA structures under the conditions of a reduced number of water molecules. The studies using hydrogels provide insights into the ability of self-assembly and hybridization of oligonucleotides in confined environments and under low-water-content conditions.
DOI： 10.3390/dna2040021
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Evaluation of weak interactions of proteins and organic cations with DNA duplex structures Reviewed International journal
R. Morimoto, M. Horita, D. Yamaguchi, H. Nakai, and S. Nakano
Biophys. J. 121 ( 15 ) 2873 - 2881 2022.8
Joint Work
Authorship：Last author, Corresponding author Publisher：Cell Press
Molecular interactions and reactions in living cells occur with high background concentrations of organic compounds including proteins. Uncharged water-soluble polymers are commonly used cosolutes in studies on molecular crowding, and most studies argue about the effects of intracellular crowding based on results obtained using polymer cosolutes. Further investigations using protein crowders and organic cations are important in understanding the effects of cellular environments on nucleic acids with negatively charged surfaces. We assessed the effects of using model globular proteins, serum proteins, histone proteins, structurally flexible polypeptides, di- and polyamines, and uncharged polymers. Thermal stability analysis of DNA oligonucleotide structures revealed that unlike conventional polymer cosolutes, basic globular proteins (lysozyme and cytochrome c) at high concentrations stabilized long internal and bulge loop structures but not fully matched duplexes. The selective stabilization of long loop structures suggests preferential binding to unpaired nucleotides in loops through weak electrostatic interactions. Furthermore, the ability of the proteins to stabilize the loop structures was enhanced under macromolecular crowding conditions. Remarkably, the effects of basic proteins on the stability of fully matched duplexes were dissimilar to those of basic amino-acid-rich polypeptides and polyamines. This study provides new insights into the interaction of nucleic acid structures with organic cations.
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Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations. Reviewed International journal
Shu-Ichi Nakano, Hirofumi Yamashita, Naoki Sugimoto
ChemBioChem 22 ( 17 ) 2721 - 2728 2021.7
Joint Work
Authorship：Lead author, Corresponding author
Catalytic turnover is important for the application of ribozymes to biotechnology. However, the turnover is often impaired because of the intrinsic high stability of base pairs with cleaved RNA products. Here, organic cations were used as additives to improve the catalytic performance of hammerhead ribozyme constructs that exhibit different kinetic behaviors. Kinetic analysis of substrate cleavage demonstrated that bulky cations, specifically tetra-substituted ammonium ions containing pentyl groups or a benzyl group, have the ability to greatly increase the turnover rate of the ribozymes. Thermal stability analysis of RNA structures revealed that the bulky cations promote the dissociation of cleaved products and refolding of incorrectly folded structures with small disruption of the catalytic structure. The use of bulky cations is a convenient method for enhancing the catalytic activity of hammerhead ribozymes, and the approach may be useful for advancing ribozyme technologies.
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Controlling interfacial ion-transport kinetics using polyelectrolyte membranes for additive- and effluent-free, high-performance electrodeposition Reviewed International journal
K. Akamatsu, S. Nakano, K. Kimura, Y. Takashima, T. Tsuruoka, H. Nawafune, Y. Sato, J. Murai, and H. Yanagimoto
ACS Appl. Mater. Interfaces 13 ( 11 ) 13896 - 13906 2021.3
Joint Work
Publisher：ACS Publications
The development of high-performance, environmentally friendly electrodeposition processes is critical for emerging coating technologies because current technologies use highly complex baths containing metal salts, supporting electrolytes, and various kinds of organic additives, which are problematic from both environmental and cost perspectives. Here, we show that a 200 μm-thin polyelectrolyte membrane sandwiched between electrodes effectively concentrates metal ions through interfacial penetration, which increases the conductance between the electrodes to 0.30 S and realizes solid-state electrodeposition that produces no mist, sludge, or even waste effluent. Both, experimental results and theoretical calculations, reveal that electrodeposition is controlled by ion penetration at the solution/polyelectrolyte interface, providing an intrinsically different ion-transport mechanism to that of conventional diffusion-controlled electrodeposition. The setup, which includes 0.50 mol L–1 copper sulfate and no additives, delivers a maximum current density of 300 mA cm–2, which is nearly fivefold higher than that of a current commercial plating bath containing organic additives.
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Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA Reviewed
H. Tateishi-Karimata, D. Banerjee, T. Ohyama, S. Matsumoto, D. Miyoshi, S. Nakano, and N. Sugimoto
525 177 - 183 2020.2
Joint Work
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Bulky cations greatly increase the turnover of a native hammerhead ribozyme Reviewed
S. Nakano, H. Yamashita, K. Tanabe, N. Sugimoto
9 35820 - 35824 2019.11
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Stabilization of DNA loop structures by large cations Reviewed
S. Nakano, T. Ayusawa, Y. Tanino, N. Sugimoto
J. Phys. Chem. B 123 7687 - 7694 2019.8
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Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels
S. Nakano, D. Yamaguchi, and N. Sugimoto
Mol. Biol. Rep. ４5 403 - 411 2018.4
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Modulation of the ribozyme and deoxyribozyme activities using tetraalkylammonium ions Reviewed
S. Nakano, T. Watabe, and N. Sugimoto
ChemPhysChem 18 ( 24 ) 3614 - 3619 2017.12
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Catalytic activities of ribozymes and DNAzymes in water and mixed aqueous media Invited Reviewed
S. Nakano, M. Horita, M. Kobayashi, and N. Sugimoto
Catalysis 7 ( 12 ) 355 - 348 2017.11
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DNA G-wire formation using an artificial peptide is controlled by protease activity Reviewed
K. Usui, A. Okada, S. Sakashita, M. Shimooka, T. Tsuruoka, S. Nakano, D. Miyoshi, T. Mashima, M. Katahira, and Y. Hamada
Molecules 22 ( 11 ) 1991 - 2002 2017.11
Joint Work
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Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH–π interactions Reviewed
H. Tateishi-Karimata, T. Ohyama, T. Muraoka, P. Podbevsek, A. M. Wawro, S. Tanaka, S. Nakano, K. Kinbara, J. Plavec, N. Sugimoto
Nucleic Acids Res. 45 7021 - 7030 2017.7
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Model studies of the effects of intracellular crowding on nucleic acid interactions Invited Reviewed
13 32 - 41 2016.12
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Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex Reviewed
Y. Ueda, Y. Zouzumi, A. Maruyama, S. Nakano, N. Sugimoto, and D. Miyoshi
Sci. Tech. Adv. Mat. 17 753 - 759 2016.11
Joint Work
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Thermal stability of RNA structures with bulky cations in mixed aqueous solutions Reviewed
S. Nakano, Y. Tanino, H. Hirayama, and N. Sugimoto
Biophys. J. 111 1350 - 1360 2016.10
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Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory Reviewed
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tamab, O. Miyashita, S. Nakano, and N. Sugimoto
Chem. Phys. Lett. 660 ( 1 ) 250 - 255 2016.9
Joint Work
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Use of a ureido-substituted deoxycytidine module for DNA assemblies Invited Reviewed
S. Nakano, H. Oka, M. Fujii, and N. Sugimoto
Nucleosides, Nucleotides and Nucleic Acids 35 ( 7 ) 370 - 378 2016.5
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A reversible B-A transition of DNA duplexes induced by synthetic cationic copolymers Invited Reviewed
M. Yamaguchi, Y. Zouzumi, N. Shimada, S. Nakano, N. Sugimoto, A. Maruyama, and D. Miyoshi
Chem. Commun. 52 7446 - 7449 2016.4
Joint Work
DOI： 10.1039/C6CC02237E
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The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents Invited Reviewed
S. Nakano and N. Sugimoto
Biophys. Rev. 8 ( 1 ) 11 - 23 2016.1
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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
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, and N. Sugimoto
Nucleic Acids Res. 43 10114 - 10125 2015.11
Joint Work
DOI： 10.1093/nar/gkv1133
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Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg2+-unsaturated solutions Reviewed
S. Nakano, Y. Kitagawa, D. Miyoshi, and N. Sugimoto
J. Biol. Inorg. Chem 20 ( 6 ) 1049 - 1058 2015.7
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Effects of cosolvents on the folding and catalytic activities of the hammerhead ribozyme Reviewed
S. Nakano, Y. Kitagawa, H. Yamashita, D. Miyoshi, and N. Sugimoto
ChemBioChem 16 ( 12 ) 1803 - 1810 2015.7
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Preparation of hydrogels for the study of the effects of spatial confinement on DNA Reviewed
S. Nakano, M. Yoshida, D. Yamaguchi, and N. Sugimoto
Trans. Mat. Res. Soc. Jpn. 39 435 - 438 2014.12
Joint Work
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Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing Reviewed
S. Nakano and N. Sugimoto
Molecules 19 ( 8 ) 11613 - 11627 2014.8
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Dangling ends perturb the stability of RNA duplexes responsive to surrounding conditions Reviewed
H. Tateishi-Karimata, S. Pramanik, S. Nakano, D. Miyoshi, and N. Sugimoto
ChemMedChem 9 ( 9 ) 2150 - 2155 2014.7
Joint Work
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Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds Reviewed
S. Nakano, Y. Kitagawa, D. Miyoshi, N. Sugimoto
FEBS Open Bio 4 643 - 650 2014.7
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Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain Reviewed
D. Miyoshi, Y. Ueda, N. Shimada, S. Nakano, N. Sugimoto, and A. Maruyama
ChemMedChem 9 ( 9 ) 2156 - 2163 2014.7
Joint Work
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Effects of molecular crowding on the structures, interactions, and functions of nucleic acids Reviewed
S. Nakano, D. Miyoshi, and N. Sugimoto
Chem. Rev. 114 2733 - 2758 2014.3
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Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules Reviewed
S. Nakano, Y. Uotani, Y. Sato, H. Oka, M. Fujii, and N. Sugimoto
Nucleic Acids Res. 41 8581 - 8590 2013.7
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Quantitative analyses of nucleic Acid stability under the molecular crowding condition induced by cosolutes Invited Reviewed
Tateishi-Karimata H, Nakano S, Sugimoto N.
Curr Protoc Nucleic Acid Chem. Chapter 7 Unit7.19 2013.6
Joint Work
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Study on effects of molecular crowding on G-quadruplex-ligand binding and ligand-mediated telomerase inhibition
H. Yaku, T. Murashima, H. Tateishi-Karimata, S. Nakano, D. Miyoshi, and N. Sugimoto
Methods S1046-2023 ( 13 ) 00097-2 2013.4
Joint Work
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Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions Reviewed
T. Fujimoto, S. Nakano, N. Sugimoto, and D. Miyoshi
J. Phys. Chem. B 117 ( 4 ) 963 - 972 2013.1
Joint Work
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Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative Reviewed
Nakano S, Oka H, Yamaguchi D, Fujii M, Sugimoto N.
Org Biomol Chem 10 ( 48 ) 9664 - 9670 2012.12
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The beads-on-a-string structure of long telomeric DNAs under molecular crowding conditions Reviewed
Yu H, Gu X, Nakano S, Miyoshi D, Sugimoto N.
J Am Chem Soc. 134 ( 49 ) 20060 - 20069 2012.12
Joint Work
DOI： 10.1021/ja305384c
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Mechanistic study on microstructural tuning of metal nanoparticle/polymer composite thin layers: Hydrogenation and decomposition of polyimide matrices catalyzed by embedded nickel nanoparticles. Reviewed
K. Akamatsu, M. Fujii, T. Tsuruoka, S. Nakano, T. Murashima, and H. Nawafune
J. Phys. Chem. C 116 17947 - 17954 2012.8
Joint Work
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Dimerization of nucleic acid hairpins in the conditions caused by neutral cosolutes Reviewed
S. Nakano, H. Hirayama, D. Miyoshi, and N. Sugimoto
J. Phys. Chem. B 116 ( 25 ) 7406 - 7415 2012.6
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Hydration changes upon DNA folding studied by osmotic stress experiments Reviewed
S. Nakano, D. Yamaguchi, H. Tateishi-Karimata, D. Miyoshi, and N. Sugimoto
Biophys. J. 102 ( 12 ) 2808 - 2817 2012.5
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The effects of molecular crowding on the structure and stability of G-quadruplexes with an abasic site Invited Reviewed
T. Fujimoto, S. Nakano, D. Miyoshi, and N. Sugimoto
Journal of Nucleic Acids (Hindawl Publishing Corporation) 2011 ( 857149 ) 857149 2011.9
Joint Work
DOI： 10.4061/2011/857149
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Measurements of the binding of a large protein using a substrate density-controlled DNA chip Reviewed
S. Nakano, T. Kanzaki, M. Nakano, D. Miyoshi, and N. Sugimoto
Anal. Chem. 83 ( 16 ) 6768 - 6372 2011.8
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Effect of locked nucleic acid modifications on the thermal stability of noncanonical DNA structure Reviewed
J. Bhattacharyya, S. Maiti, S. Muhuri, S. Nakano, D. Miyoshi, and N. Sugimoto
Biochemistry 50 ( 34 ) 7414 - 7425 2011.8
Joint Work
DOI： 10.1021/bi200477g
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Use of nucleic acid analogs for the study of nucleic acid interactions Invited Reviewed
S. Nakano, M. Fujii, and N. Sugimoto
Journal of Nucleic Acids 2011 ( 967098 ) 967098 2011.7
Joint Work
DOI： 10.4061/2011/967098
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Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide Reviewed
S. Pramanik, K. Nakamura, K. Usui, S. Nakano, S. Saxena, J. Matsui, D. Miyoshi and N. Sugimoto
Chem. Commun. 47 ( 10 ) 2790 - 2792 2011.2
Joint Work
DOI： 10.1039/C0CC05776B
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Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides Reviewed
S. Nakano, H. Oka, Y. Uotani, K. Uenishi, M. Fujii, and N. Sugimoto
Mol. BioSyst. 6 2023 - 2029 2010.10
Joint Work
DOI： 10.1039/C0MB00002G
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Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH Reviewed
A. Rajendran, S. Nakano, and N. Sugimoto
Chem. Commun. 46 1299 - 1301 2010.1
Joint Work
DOI： 10.1039/B922050J
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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 2009.12
Joint Work
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Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides Reviewed
S. Nakano, H. Oka, Y. Uotani, K. Uenishi, M. Fujii, and N. Sugimoto
Biochemistry 48 11304 - 11311 2009.12
Joint Work
DOI： 10.1021/bi901496q
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Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes Reviewed
S. Nakano, H. T. Karimata, Y. Kitagawa, and N. Sugimoto
J. Am. Chem. Soc. 131 16881 - 16888 2009.10
Joint Work
DOI： 10.1021/ja9066628
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Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence
S. Nakano, H. Hirayama, and N. Sugimoto
Nucleic Acids Symp. Ser. 53 229 - 230 2009.9
Joint Work
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Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem Reviewed
H. Yaku, T. Yukimasa, S. Nakano, N. Sugimoto, and H. Oka
Electrophoresis, 29 4130 - 4140 2008.12
Joint Work
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Molecular crowding effect on metal ion binding properties of the hammerhead ribozyme
S. Nakano, Y. Kitagawa, H. T. Karimata, and N. Sugimoto
Nucleic Acids Symp. Ser. 52 519 - 520 2008.9
Joint Work
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Capture of cationic ligands bound diffusely to base pairs during the DNA refolding
S. Nakano, T. Kirihata, and N. Sugimoto
Chem. Commun. ( 6 ) 700 - 702 2008.2
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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 Invited Reviewed
S. Nakano, L. Wu, H. Oka, H. T. Karimata, T. Kirihata, Y. Sato, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai, and N. Sugimoto
Mol. BioSyst. 4 579 - 588 2008.2
Joint Work
DOI： 10.1039/B718806D
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Molecular crowding effect on metal ion binding properties of the hammerhead ribozyme
S. Nakano, Y. Kitagawa, H. T. Karimata, and N. Sugimoto
Nucleic Acids Symp. Ser. 52 519 - 520 2008
Joint Work
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Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides Reviewed
S. Nakano, T. Kirihata, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai, and N. Sugimoto
Nucleic Acids Research 35 486 - 494 2007.12
Joint Work
DOI： 10.1093/nar/gkl1073
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Effects of polyethylene glycol on a DNA duplex stability differed by the NaCl concentration Reviewed
H. Karimata, S. Nakano, and N. Sugimoto
Bull. Chem. Soc. Jpn. 80 1987 - 1994 2007.11
Joint Work
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The base-pairing ability of the base pair-mimic nucleosides
S. Nakano, K. Uenishi, M. Fujii, and N. Sugimoto
Nucleic Acids Symp. Ser. 51 71 - 72 2007.11
Single Work
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Functionalization of DNA by the base pair-mimic nucleosides
H. Oka, S. Nakano, Y. Uotani, K. Uenishi, M. Fujii, and N. Sugimoto
Nucleic Acids Symp. Ser. 51 151 - 152 2007.11
Joint Work
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Consecutive GC base pairs determine the energy barrier of DNA duplex formation under molecularly crowded conditions Reviewed
X. Gu, S. Nakano, and N. Sugimoto
Chem. Commun. 2750 - 2752 2007.4
Joint Work
DOI： 10.1039/B702865B
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Mechanistic characterization of the HDV genomic ribozyme: A mutant of the C41 motif provides insight into positioning and thermodynamic linkage of metal ions and protons Reviewed
S. Nakano and P. C. Bevilacqua
Biochemistry 46 3001 - 3012 2007.2
Joint Work
DOI： 10.1021/bi061732s
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The roles of cosolutes on the hammerhead ribozyme activity
中野 修一
Nucleic Acids Symp. Ser. 50 81 - 82 2006.11
Joint Work
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The effect of the structure of cosolutes on the DNA duplex formation
中野 修一
Nucleic Acids Symp. Ser. 50 205 - 206 2006.11
Joint Work
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Recognition of the base pair-mimic nucleosides by DNA polymerases
中野 修一
Nucleic Acids Symp. Ser. 50 201 - 202 2006.11
Joint Work
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A DNA duplex with extremely enhanced thermal stability based on controlled immobilization on gold nanoparticles Reviewed
K. Akamatsu, M. Kimura, Y. Shibata, S. Nakano, D. Miyoshi, H. Nawafune, and N. Sugimoto
Nano Lett. 3 491 - 495 2006.1
Joint Work
DOI： 10.1021/nl0524748
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DNA base flipping by a base pair-mimic nucleoside Reviewed
S. Nakano, Y. Uotani, K. Uenishi, M. Fujii, and N. Sugimoto
Nucleic Acids Research, 33 7111 - 7119 2005.12
Single Work
DOI： 10.1093/nar/gki1018
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Conformational switch of oligonucleotides induced by spermine
中野 修一
Nucleic Acids Symp. Ser. 49 241 - 242 2005.11
Single Work
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Linkage between proton binding and folding in RNA: implications for RNA catalysis
中野 修一
Biochem. Soc. Trans. 33 466 - 470 2005.11
Single Work
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Central dogma for a molecular design based on DNA: DNB (databasing/designable nanobio) -> ENB (engineering nanobio) -> FNB (functional nanobio) Reviewed
S. Nakano and N. Sugimoto
Chemistry Letters 34 1206 - 1211 2005.7
Single Work
DOI： 10.1246/cl.2005.1206
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Site-selective RNA cleavage by DNA bearing a base pair-mimic nucleoside Reviewed
S. Nakano, Y. Uotani, K. Uenishi, M. Fujii, and N. Sugimoto
J. Am. Chem. Soc. 127 518 - 519 2005.1
Single Work
DOI： 10.1021/ja045445s
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Duplex dissociation of telomere DNAs induced by molecular crowding. Reviewed
D. Miyoshi, S. Matsumura, S. Nakano, and N. Sugimoto
J. Am. Chem. Soc. 128 165 - 169 2004.12
Single Work
DOI： 10.1021/ja036721q
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Conformational change of a nucleotide by a base-pair mimic nucleoside in the complementary DNA strand
中野 修一
Nucleic Acids Symp. Ser. 48 259 - 260 2004.11
Single Work
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Secondary structure change of oligonucleotides induced by salts
中野 修一
Nucleic Acids Symp. Ser. 48 109 - 110 2004.11
Single Work
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Stabilization of a DNA duplex under molecular crowding conditions of PEG
中野 修一
Nucleic Acids Symp. Ser. 48 107 - 108 2004.11
Single Work
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The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. Reviewed
S. Nakano, H. Karimata, T. Ohmichi, J. Kawakami, and N. Sugimoto
J. Am. Chem. Soc. 126 14330 - 14331 2004.10
Single Work
DOI： 10.1021/ja0463029
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Influences of ribonucleotide on a duplex conformation and its thermal stability: Study with the chimeric RNA-DNA strands. Reviewed
S. Nakano, T. Kanzaki, and N. Sugimoto
J. Am. Chem. Soc. 126 1088 - 1095 2004.1
Single Work
DOI： 10.1021/ja037314h
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Catalytic roles for proton transfer and protonation in ribozymes: Current understanding and future possibilities. Reviewed
P. C. Bevilacqua, T. S. Brown, S. Nakano, and R. Yajima
Biopolymers 73 90 - 109 2004.1
Single Work
DOI： 10.1002/bip.10519
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Novel biomaterials derived from deoxyribozyme and napzyme.
中野 修一
Macromol. Symp. 201 245 - 252 2003.11
Single Work
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Large stacking stability of a base pair-mimic nucleotide on the DNA duplex.
中野 修一
Nucleic Acids Res. Supple. 3 79 - 80 2003.11
Single Work
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An oligopeptide containing the C-terminal sequence of RNase A inhibits an RNA hydrolysis by RNase A.
S. Nakano, A. L. Cerrone, and P. C. Bevilacqua
First International Symposium on Biomolecular Chemistry 240 - 241 2003.11
Single Work
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Structural competition involving G-quadruplex DNA and its complement. Reviewed
W. Li, D. Miyoshi, S. Nakano, and N. Sugimoto
Biochemistry, 42 11736 - 11744 2003.9
Single Work
DOI： 10.1021/bi034168j
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An Oligopeptide containing the C-terminal sequence of RNase A has a potent RNase A binding property. Reviewed
S. Nakano and N. Sugimoto
J. Am. Chem. Soc. 125 8728 - 8729 2003.6
Single Work
DOI： 10.1021/ja034659r
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Large stabilization of a DNA duplex by the deoxyadenosine derivatives tethering an aromatic hydrocarbon group. Reviewed
S. Nakano, Y. Uotani, S. Nakashima, Y. Anno, M. Fujii, and N. Sugimoto
J. Am. Chem. Soc. 125 8086 - 8087 2003.6
Single Work
DOI： 10.1021/ja034465b
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Mechanistic chracterization of the HDV genomic ribozyme: Classifying the catalitic and structural metal ion sites within a multichannel mechanism. Reviewed
中野 修一
Biochemistry 42 2982 - 2994 2003.2
Single Work
DOI： 10.1021/bi026815x
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Important effects of non-Watson-Crick interactions and cation binding on nucleic acid structures.
中野 修一
Recent research development in nucleosides＆nucleotides （Transworld Research Networks）, Vol. 1, 59-80 2003
Single Work
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Temparature dependence of themodynamic properties for DNA/DNA and RNA/DNA duplex formation. Reviewed
P. Wu, S. Nakano, and N. Sugimoto
Eur. J. Biochem. 269 2821 - 2830 2002.11
Single Work
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Role of 2'-OH on Thermodynamic Stability and Structure of Chimeric Oligonucleotides
中野 修一
Nucleic Acids Res. Supple. 2 189 - 190 2002.11
Single Work
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Long RNA Dangling end Has Large Energetic Contribution to Duplex Stability. Reviewed
T. Ohmichi, S. Nakano, D. Miyoshi, and N. Sugimoto
J. Am. Chem. Soc. 124 10367 - 10372 2002.8
Single Work
DOI： 10.1021/ja0255406
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Proton Inventory of the Genomic HDV Ribozyme in Mg2+-Containing Solutions. Reviewed
S. Nakano and P. C. Bevilacqua
J. Am. Chem. Soc. 123 11333 - 11334 2001.10
Single Work
DOI： 10.1021/ja0166850
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Mechanistic Characterization of the HDV Genomic Ribozyme: Assessing the Catalytic and Structural Contributions of Divalent Metal Ions within a Multichannel Reaction Mechanism. Reviewed
S. Nakano, D. J. Proctor, and P. C. Bevilacqua
Biochemistry 40 12022 - 12038 2001.9
Single Work
DOI： 10.1021/bi011253n
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Stabilization Factors Affecting Duplex Formation fo Peptide Nucleic Acid with DNA. Reviewed
N. Sugimoto, N. Satoh, K. Yasuda, and S. Nakano
Biochemistry 40 8444 - 8451 2001.6
Single Work
DOI： 10.1021/bi010480m
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Thermodynamics-Structure Relationship of Single Mismatches in RNA/DNA Duplexes. Reviewed
N. Sugimoto, M. Nakano, and S. Nakano
Biochemistry 39 11270 - 11281 2000.8
Single Work
DOI： 10.1021/bi000819p
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A Role for Upstream RNA Structure in Facilitating the Catalytic Fold of the Genomic Hepatitis Delta Virus Ribozyme. Reviewed
D. M. Chadalavada, S. M. Knudsen, S. Nakano, and P. C. Bevilacqua
J. Mol. Biol. 301 349 - 367 2000.3
Single Work
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General Acid-Base Catalysis in the Mechanism of a Hepatitis Delta Virus Ribozyme. Reviewed
S. Nakano, D. M. Chadalavada, and P. C. Bevilacqua
Science 287 1493 - 1497 2000.2
Single Work
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Analysis for peptide binding to porphyrin using surface plasmon resonance
C. Nakamura, Y. Inuyama, K. Shirai, S. Nakano, N. Sugimoto, and J. Miyake
Synthetic Metals 117 127 - 129 2000
Joint Work
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Nucleic Acid Duplex Stability : Influence of Base Composition on Cation Effects. Reviewed
S. Nakano, M. Fujimoto, H. Hara, and N. Sugimoto
Nucleic Acids Res. 27 2957 - 2965 1999.7
Single Work
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Single-Stranded DNA Recognition of a 24 mer Peptide Derived from RecA Protein. Reviewed
S. Nakano and N. Sugimoto
Bull. Chem. Soc. Jpn. 71 2205 - 2210 1998.11
Single Work
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Effect of Cation Concentration on Duplex Stability of Nucleic Acids with Unnatural Base Pairs.
中野 修一
Nucleic Acids Symp. Ser. 39 121 - 122 1998.11
Single Work
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A 24 mer Peptide Derived from RecA Protein can Discriminate a Single-Stranded DNA from a Double-Stranded DNA. Reviewed
N. Sugimoto and S. Nakano
Chem. Commun. 2125 - 2126 1997.11
Single Work
DOI： 10.1039/A705575G
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A 24 mer Peptide with Activity of a Nucleic Acid Discrimination and Its Recombination.
中野 修一
First International Peptide Symp. ( P-108 ) 1997.11
Single Work
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Experimental Quantitation of Cation Effect on Nucleic Acid Stability.
中野 修一
Nucleic Acids Symp. Ser. 37 147 - 148 1997.11
Single Work
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Sandwiching Interaction of Peptides with a Porphyrin. Reviewed
N. Sugimoto and S. Nakano
Chem. Lett. 939 - 949 1997.11
Single Work
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Development of New SPR Chip with an Oligopeptide Recognizing a Single-Stranded DNA.
中野 修一
Nucleic Acids Symp. Ser. 35 303 - 304 1996.11
Single Work
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Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes. Reviewed
N. Sugimoto, S. Nakano, M. Yoneyama, and K. Honda
Nucleic Acids Res. 24 4501 - 4505 1996.11
Single Work
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Interactions of 5-(1-pyrenyl)-10,15,20,-tris(4-methyl-pyridinium)porphine with Double-Helix and Triple-Helix Nucleic Acids. Reviewed
N. Sugimoto, S. Nakano, M. Katoh, M. Sasaki, and S. Kugimiya
Nucleosides & Nucleotides 15 743 - 747 1996.8
Single Work
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Thermodynamic Parameters to Predict Stability of RNA/DNA Hybrid Duplexes.
中野 修一
J. Biomol. Struct. Dyn. 12 ( a233 ) 1995.11
Single Work
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Interaction of Oligonuleotides with a Single Stranded DNA Binding Site of RecA Protein.
中野 修一
Nucleic Acids Symp. Ser. 34 61 - 62 1995.11
Single Work
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Thermodynamic stability of RNA/DNA hybrids. Reviewed
N. Sugimoto, S. Nakano, M. Katoh, A. Matsumura, H. Nakamuta, T. Ohmichi, M. Yoneyama, and M. Sasaki
Biochemistry 34 11211 - 11216 1995.9
Single Work
DOI： 10.1021/bi00035a029
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Thermodynamic Parameters to Predict the Stability of RNA/DNA Hybrids in Antisense Interaction.
中野 修一
First International Antisence Conference of Japan ( P1-05 ) 1994.11
Single Work
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RNA/DNA Hybrid Duplexes with Identical Nearest-Neighbor Base-Pairs Have Identical Stability. Reviewed
N. Sugimoto, M. Katoh, S. Nakano, T. Ohmichi, and M. Sasaki
FEBS Lett. 354 74 - 78 1994.10
Single Work