Papers - NAKANO Shuuichi
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Basic protein- and peptide-induced stabilization of long-loop DNA G-quadruplexes Reviewed
K. Tanabe, K. Miyazaki, H. Umeno, M. Takemoto, and S. Nakano
Biochimie 219 110 - 117 2024.4
Authorship：Last author, Corresponding author
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Evaluation of thermal stability of DNA oligonucleotide structures embedded in hydrogels Invited Reviewed International coauthorship International journal
D. Yamaguchi, M. Yoshida, S. Nakano
DNA 2 ( 4 ) 302 - 313 2022.12
Authorship：Last author, Corresponding author Publisher：MDPI
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
Authorship：Last author, Corresponding author Publisher：Cell Press
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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
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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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
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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