SUGIMOTO Naoki

J-GLOBAL         Last updated: Jan 21, 2020 at 02:40
 
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Name
SUGIMOTO Naoki
E-mail
sugimotokonan-u.ac.jp
URL
http://www.konan-fiber.jp
Affiliation
Konan University
Section
Faculty of Frontiers of Innovative Research in Science and Technology Faculty of Frontiers of Innovative Research in Science and Technology Department of Nanobiochemistry
Job title
Professor
Other affiliation
Konan UniversityKonan University

Research Areas

 
 

Academic & Professional Experience

 
Aug 2012
 - 
Today
Faculty of Frontiers of Innovative Research in Science and Technology Faculty of Frontiers of Innovative Research in Science and Technology Department of Nanobiochemistry, KONAN UNIVERSITY
 
Apr 2009
 - 
Today
Professor, Faculty of Frontiers of Innovative Research in Science and Technology Faculty of Frontiers of Innovative Research in Science and Technology Department of Nanobiochemistry, KONAN UNIVERSITY
 
Apr 2004
 - 
Today
Director in General, Frontier of Institute for Biomolecular Engineering Research in Science and Technology Department of Nanobiochemistry, KONAN UNIVERSITY
 
Apr 2001
 - 
Mar 2004
Director in General, KONAN UNIVERSITY
 
Apr 1994
 - 
Mar 2009
Professor, Faculty of Science, KONAN UNIVERSITY
 
Apr 1991
 - 
Mar 1994
Associate Professor (as old post name), Faculty of Science, KONAN UNIVERSITY
 
Apr 1988
 - 
Mar 1991
Lecturer, Faculty of Science, KONAN UNIVERSITY
 

Education

 
 
 - 
Mar 1985
Graduate School, Division of Natural Science, Kyoto University
 
 
 - 
Mar 1982
Graduate School, Division of Natural Science, Kyoto University
 
 
 - 
Mar 1979
Faculty of Science, Kyoto University
 

Published Papers

 
Stabilization of DNA Loop Structures by Large Cations
S. Nakano, T. Ayusawa, Y. Tanino, N. Sugimoto
J Phys Chem B.   123 7687-7694   Sep 2019   [Refereed]
Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency
T. Endoh and N. Sugimoto
Molecules   24 1613   Apr 2019   [Refereed]
RNA-Capturing Microsphere Particles (R-CAMPs) for Optimization of Functional Aptamers
T. Endoh, T. Ohyama, and N. Sugimoto
Small   1805062   Apr 2019   [Refereed]
Characterization of intracellular crowding environments with topology-based DNA quadruplex sensors
S. Takahashi, J. Yamamoto, A. Kitamura, M. Kinjo, and N. Sugimoto
Anal. Chem.   91(4) 2586-2590   Feb 2019   [Refereed]
C-rich sequence in a non-template DNA strand regulates structure change of G-quadruplex in a template strand during transcription
Y. Teng, H. Tateishi-Karimata, and N. Sugimoto
Bull. Chem. Soc. Jpn.   92(3) 527-577   2019   [Refereed]
Validation of the Nearest-neighbor Model for Watson–Crick Self-complementary DNA Duplexes in Molecular Crowding Condition
S. Ghosh, S. Takahashi, T. Endoh, H. Tateishi-Karimata, S. Hazra, N. Sugimoto
Nucleic Acids Res.   47 3284-3294   2019   [Refereed]
[Selected as a Supplementary Cover]
Bisubstrate function of RNA polymerases triggered by molecular crowding conditions
S. Takahashi, H. Okura, and N. Sugimoto
Biochemistry   58 1081-1093   2019   [Refereed]
Lighting up of thiazole orange on G-quadruplex DNA by high pressure
S. Bhowmik, S. Takahashi, and N. Sugimoto
ACS Omega   4 4325-4329   2019   [Refereed]
Preferential targeting cancer-related i-motif DNAs by the plant flavonol fisetin for theranostics applications
S. Takahashi, S. Bhattachargee, S. Ghosh, N. Sugimoto, and S. Bhowmik
Sci. Rep.   in press    2019   [Refereed]
In situ condensation of an anti-cancer drug into fibrin gel enabling effective inhibition of tumor cell growth
M. Kuwahara, H. Fujita, Y. Kataoka, Y. Nakajima, M. Yamada, N. Sugimoto
Chem Commun (Camb)   in press    2019   [Refereed]
Design and Properties of Ligand-Conjugated Guanine Oligonucleotides for Recovery of Mutated G-Quadruplexes
S. Takahashi, B. Chelobanov, K. T. Kim, B. H. Kim, D. Stetsenko, and N. Sugimoto
Molecules   23 3228   Dec 2018   [Refereed]
S. Takahashi, K. T. Kim, P. Podbevšek, J. Plavec, B. H. Kim, and N. Sugimoto
J. Am. Chem. Soc.   140(17) 5774-5783   Apr 2018
N. Satoa, S. Takahashi, H. Tateishi-Karimata, M. E. Hazemi, T. Chikuni, K. Onizuka, N. Sugimoto and F. Nagatsugi
Org. Biomol. Chem.   140 642-651   Jan 2018
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, S. A. Teichmann
Nat Struct Mol Biol.   25 279-299   Jan 2018   [Refereed]
H. Tateishi-Karimata, K. Kawauchi, and N. Sugimoto
J. Am. Chem. Soc.   140 642-651   2018   [Refereed]
[Highligted as a Supplementary Cover]
Y. Teng, S. Pramanik, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto
Biochem. Biophys. Res. Commun.   496 601-607   2018   [Refereed]
Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations
M. Trajkovski, T, Endoh, H. Tateishi-Karimata, T. Ohyama, S. Tanaka, J. Plavec and N. Sugimoto
Nucleic Acids Res.   46 4301-4315   2018   [Refereed]
Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit
A. B. Rode, T. Endoh, and N. Sugimoto
Angew. Chem. Int. Ed.   57 6868-6872   2018   [Refereed]
Co-Transcriptional Molecular Assembly Results in a Kinetically Controlled Irreversible RNA Conformational Switch
T. Endoh and N. Sugimoto
Anal. Chem.   90 11193-11197   2018   [Refereed]
Mirror-image Dependence: Targeting Enantiomeric G-quadruplex DNA by 10 Pairs of Triplex Metallohelices
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   [Refereed]
A Turn-On Detection of DNA Sequences by Means of Fluorescence of DNA-Templated Silver Nanoclusters via Unique Interactions of a Hydrated Ionic Liquid
Y. Teng, H. Tateishi-Karimata, T. Tsuruoka, and N. Sugimoto
Molecules   23 2889   2018
An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex
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   [Refereed]
Modulation of Ribozyme and Deoxyribozyme Activities Using Tetraalkylammonium Ions
S. Nakano, T. Watabe, and N. Sugimoto
Chem. Phys. Chem.   18 3614-3619   Nov 2017
Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure
S. Takahashi, S. Bhowmik and N. Sugimoto
Journal of Inorganic Biochemistry   166 199-207   2017   [Refereed]
Effects of metal ions and cosolutes on G-quadruplex topology
T. Fujii, P. Podbevšek, J. Plavec, N. Sugimoto
Journal of Inorganic Biochemistry   166 190-198   2017   [Refereed]
Through-bond effects in the ternary complexes of throumbin sandwiched by two DNA aptamers
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   [Refereed]
Model studies of the effects of intracellular crowding on nucleic acid interactions
S. Nakano, N. Sugimoto
Mol Biosyst.   13 32-41   2017   [Refereed]
Unexpected Position-Dependent Effects of Ribose G‑Quartets in G‑Quadruplexes
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   [Refereed]
Newly characterized interaction stabilizes DNA structure: oligoethylene glycols
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   [Refereed]
[Highlighted as a Front Cover]
Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure
S. Takahashi, N. Sugimoto
Biophys. Chem.   231 146-154   2017   [Refereed]
Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase
S. Takahashi, J. A. Brazier, N. Sugimoto
Proc. Natl. Acad. Sci. U. S. A.   114 9605-9610   2017   [Refereed]
Specific Light-Up System for Protein and Metabolite Targets Triggered by Initiation Complex Formation
H. Fujita, Y. Kataoka, R. Nagano, Y. Nakajima, M. Yamada, N. Sugimo, M. Kuwahara
Sci. Rep.   7(15191)    2017   [Refereed]
Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex
Y. Ueda, Y. Zouzumi, A. Maruyama, S. Nakano, N. Sugimoto and D. Miyoshi
Science and Technology of Advanced Materials   17 753-759   Nov 2016   [Refereed]
tRNA Shifts the G-quadruplex-hairpin conformational equilibrium in RNA towards the hairpin conformer [Selected as an Inside Back Cover]
A.B. Rode, T. Endoh, N. Sugimoto
Angew. Chem. Int. Ed.   46 14315-14319   Nov 2016   [Refereed]
Thermal stability of RNA structures with bulky cations in mixed aqueous solutions
S. Nakano, Y. Tanino, H. Hirayama, N. Sugimoto
Biophysical Journal   111 1350-1360   Oct 2016   [Refereed]
G-quadruplexes with tetraethylene glycol-modified deoxythymidines are resistant to nucleases and inhibit HIV-1 reverse transcriptase
H. Tateishi-Karimata, T. Muraoka, K. Kinbara, N. Sugimoto
ChemBioChem.   17 1399-1402   Aug 2016   [Refereed]
Novel one-tube-one-step real-time methodology for rapid transcriptomic biomarker detection: signal amplification by ternary initiation complexes
H. Fujita, Y. Kataoka, S. Tobita, M. Kuwahara, N. Sugimoto
Anal. Chem.   88 7137-7144   Jun 2016   [Refereed]
Real-time monitoring of G-quadruplex formation during transcription
T. Endoh, AB Rode, S. Takahashi, Y. Kataoka, M. Kuwahara, N. Sugimoto
Anal. Chem.   88 1984-1989   Feb 2016   [Refereed]
Reevaluation of the stability of G-quadruplex structures under crowding conditions
J. Zhou, H. Tateishi-Karimata, JL Mergny, M. Cheng, Z. Feng, D. Miyoshi, N. Sugimoto, C. Li
Biochimie.   121 204-208   Feb 2016   [Refereed]
Incorporation of O6-methylguanine restricts the conformational conversion of the human telomere G-quadruplex under molecular crowding conditions
A. Zhao, C. Zhao, H. Tateishi-Karimata, J. Ren, N. Sugimoto, X. Qu
Chem. Commum.   52 1903-1906   Jan 2016   [Refereed]
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]
T. Endoh, D. Hnedzko, E. Rozners, and N. Sugimoto
Angew. Chem. Int. Ed.   55 899-903   2016
Expansion of the DNA 'alphabet' beyond natural DNA recognition
H. Tateishi-Karimata and N. Sugimoto
ChemBioChem   17 1301-1303   2016   [Refereed]
Use of a ureido-substituted deoxycytidine module for DNA assemblies
S. Nakano, H. Oka, M. Fujii and Sugimoto
Nucleosides Nucleotides Nucleic Acids   35 370-378   2016   [Refereed]
Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells
T. Endoh, N. Sugimoto
Sci. Rep.   6 22719   2016   [Refereed]
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]
C. Annoni, T. Endoh, D. Hnedzko, E. Rozners, N. Sugimoto
Chem Commun (Camb)   52 7935-7938   2016   [Refereed]
A reversible B-A transition of DNA duplexes induced by synthetic cationic copolymers
N. Yamaguchi, Y. Zouzumi, N. Shimada, S. Nakano, N. Sugimoto, A. Maruyama, D. Miyoshi
Chem Commun (Camb).   52 7446-7449   2016   [Refereed]
Local thermodynamics of the water molecules around single-and double-stranded DNA studied by grid inhomogeneous solvation theory
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto
Chemical Physics Letters   660 250-255   2016   [Refereed]
Pressure effect on the folding of G-quadruplex DNA modified with hexaethylene glycol
S. Takahashi and N. Sugimoto
Mol. Enz. Drug Targ.   2 3   2016   [Refereed]
Triplex-forming PNA modified with unnatural nucleobases: the role of protonation entropy in RNA binding
T. Endoh, C. Annoni, D. Hnedzko, E. Rozners, N. Sugimoto
Phys. Chem. Chem. Phys.   18 32002-32006   2016
Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto
Nucleic Acids Res.   43 10114-10125   Dec 2015   [Refereed]
Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg(2+)-unsaturated solutions
S. Nakano, Y. Kitagawa, D. Miyoshi, and N. Sugimoto
J. Biol. Inorg. Chem.   20 1049-1058   Sep 2015
S. Nakano, Y. Kitagawa, H. Yamashita, D. Miyoshi, and N. Sugimoto
ChemBioChem.   16 1803-1810   Aug 2015
DNA structures under molecular crowding conditions with a phosphorylcholine derivative (MPC)
Y. Ueda, T. Konno, K. Ishihara, N. Sugimoto, D. Miyoshi
Transact. Mater. Res. Soc. Japan   40 99-102   Jul 2015   [Refereed]
Rational design and tuning of functional RNA switch to control an allosteric intermolecular interaction
T. Endoh and N. Sugimoto
Anal. Chem.   87 7628-7635   Jul 2015   [Refereed]
T. Fujii and N. Sugimoto
Phys. Chem. Chem. Phys.   17 16719-16722   May 2015   [Refereed]
i-motifs are more stable than G-quadruplexes in a hydrated ionic liquid
H. Tateishi-Karimata, M. Nakano, S. Pramanik, S. Tanaka, and N. Sugimoto
Chem. Commun.   51 6909-6912   Apr 2015
H. Yaku, T. Murashima, D. Miyoshi, and N. Sugimoto
Sensors   15(4) 9388-9403   Apr 2015   [Refereed]
DNA sensor's selectivity enhancement and protection from contaminating nucleases due to a hydrated ionic liquid
H. Tateishi-Karimata, S. Pramanik, and N. Sugimoto
Analyst   140 4393-4398   Apr 2015   [Refereed]
[Highlighted as a Front Cover]
Control of guanine-rich DNA secondary structures depending on the protease activity using a designed PNA peptide
K. Usui, A. Okada, K. Kobayashi, N. Sugimoto
Org. Biomol.Chem.   13 2022-2025   Feb 2015   [Refereed]
A fluorescent probe for detection of an intracellular prognostic indicator in early-stage cancer
H. Ji, Y. Guan, L. Wu, J. Ren, D. Miyoshi, N. Sugimoto, and X. Qu
Chem. Commun.   51 1479-1482   Jan 2015   [Refereed]
Tuning Riboswitch-mediated Gene Regulation via Rational Control of Aptamer Ligand Binding Properties
A.B.Rode, T. Endoh, N. Sugimoto
Angew. Chem. Int. Ed.   54(3) 905-909   Jan 2015
Structural foundation for DNA behavior in hydrated ionic liquid: An NMR study
M. Marušič, H. Tateishi-Karimata, N. Sugimoto, and J. Plavec
Biochimie   108 169-177   Jan 2015
Choline ions stabilize A-T base pairs by fitting into minor groove
M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
JPS Conf. Proc.   5 011008   2015
Key tertiary interactions in FMN riboswitch aptamers required for ligand binding [Highlighted as a Selected Paper]
A.B. Rode, T. Endoh, and N. Sugimoto
Bull. Chem. Soc. Jpn.   88 946-948   2015   [Refereed]
Pressure-dependent formation of i-motif and G-quadruplex DNA structures
S. Takahashi and N. Sugimoto
Phys. Chem. Chem. Phys.   17 31004-31010   2015
DNA G-quadruplex detection system employing a protein fibril ligand
R. Maeda, H. Yaku, T. Nakabayashi, T. Murashima, N. Sugimoto, N. Ohta, D. Miyoshi
Telomere and Telomerase.   2(e691)    2015   [Refereed]
B. Xu, C. Zhao, Y. Chen, H. Tateishi-Karimata, J. Ren, N. Sugimoto, and X. Qu
Chem. Eur. J.   20(50) 16467-16472   Dec 2014
Smritimoy Pramanik, Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic Acids Research   42(20) 12949-12959   Nov 2014
Daisuke Miyoshi, Yumi Ueda, Naohiko Shimada, Shu-ichi Nakano, Naoki Sugimoto, Atsushi Maruyama
ChemMedChem   Sep;9(9) 2156-2163   Sep 2014
H. Tateishi-Karimata, S. Pramanik, S. Nakano, D. Miyoshi and N. Sugimoto
ChemMedChem   Sep;9(9) 2150-2155   Sep 2014
T. Endoh, N. Sugimoto
ChemMedChem   Sep;9(9) 2045-2048   Sep 2014
Roles of the amino group of purine bases in the thermodynamic stability of DNA base paring
S. Nakano, and N. Sugimoto
Molecules   19 11613-11627   Aug 2014   [Refereed]
M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
J. Phys. Chem. B   118(32) 9583-9594   Aug 2014
H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto
J. Phys. Chem. B.   118(10) 2605-2614   Mar 2014

Misc

 
Biological and nanotechnological applications using interactions between ionic liquids and nucleic acids
H. Tateishi-Karimata, N. Sugimoto
Biophysical Reviews   1-10   Apr 2018
Quantitative analysis of nucleic acid stability with ligands under high pressure to design novel drugs targeting G-quadruplexes
S. Takahashi, N. Sugimoto
Curr. Protoc. Nucleic. Acid Chem.   70(17) 9.1-9.17   Sep 2017
Conformational Dynamics of mRNA in Gene Expression as New Pharmaceutical Target
T. Endoh and N. Sugimoto
Chem. Rec.   17 817-832   2017
[Highlighted as a Front Cover]
The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents
S. Nakano, N. Sugimoto
Biophysical Reviews   8 11-23   2016
The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents
S. Nakano, N. Sugimoto
Biophys. Rev.   8 11-23   2016
Regulation of transcription and translation by quadruplex structure of nucleic acids and its stabilizers
N. Sugimoto
Bull. Jpn. Soc. Coord. Chem.   65 23-29   2015
Effects of molecular crowding on the structures, interactions, and functions of nucleic acids
S. Nakano, D. Miyoshi and N. Sugimoto
Chem. Rev.   114(5) 2733-2758   2014
Structure, stability and behavior of nucleic acids in ionic liquids
H. Tateishi-Karimata and N. Sugimoto
Nucleic Acids Res.   42 8831-8844   2014
Quantitative Analyses of Nucleic Acid Stability under the Molecular Crowding Condition Induced by Cosolutes
H. Tateishi-Karimata, S. Nakano and N. Sugimoto
Current Protocols in Nucleic Acid Chemistry   7(Unit7.19)    2013
Effect of pressure on thermal stability of G-quadruplex DNA and double-stranded DNA structures
S. Takahashi and N. Sugimoto
Molecules   18 13297-13319   2013
Peptide-DNA hybrid G-quadruplex structures for regulation of protein expression depending on protease activity
A. Okada, M. Taniguchi, D. Miyoshi and N. Sugimoto
Peptides   2013 180   2013
Specific Binding of Anionic Porphyrin and Phthalocyanine to the G-quadruplex with a variety of in vitro and in vivo applications
H. Yaku, T. Murashima, D. Miyoshi, and N. Sugimoto
Molecules   17 10586-10613   2012
Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications
H. Yaku, T, Fujimoto, T. Murashima, D. Miyoshi and N. Sugimoto
Chem. Commun.   48 6203-6216   2012
Effects of protein binding on DNA G-quadruplex structures
S. Nagatoishi, D. Miyoshi and N. Sugimoto
IREBIC   2 129-134   2011
Molecular evolution of functional Nucleic Acids with chemical modifications
M. Kuwahara and N. Sugimoto
Molecules   15 5423-5444   2010
Effect of LNA modification on the thermal stability of non-canonical DNA structures
J. Bhattacharyya, S. Maiti, S. Muhuri, D. Miyoshi and N. Sugimoto
Nucleic Acids Symp. Ser. (Oxf)   54 172-173   2010
Roles of Anionic Functional Groups in G-quadruplex-ligands for Efficient Telomerase Inhibition
H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto
Nucleic Acids Symp. Ser. (Oxf)   54 148-149   2010
Comparative thermodynamic analysis of RNA-protein interaction on surface and in solution
Y. Tanaka, K. Ishidate, K. Kishimoto, N. Sugimoto and J. Kawakami
Proc. 37th Intl. Symp. Nucleic Acids Chemistry   276-277   2010
Unpaired region affecting hydration state of duplex
T. Fujimoto, D. Miyoshi, S. Nakano and N. Sugimoto
Nucleic Acids Symp. Ser. (Oxf).   54 210-211   2010
Thermal stability and hydration state of DNA G-quadruplex regulated by loop regions
T. Fujimoto, D. Miyoshi, H. Tateishi-Karimata and N. Sugimoto
Nucleic Acids Symp. Ser. (Oxf)   53 237-238   2009
Designable DNA functions toward new nanobiotechnology
N. Sugimoto
Bull. Chem. Soc. Jpn.   82 1-10   2009
DNA junction structure stabilized by molecular crowding conditions
D. Miyoshi, S. Muhuri, K. Mimura, and N. Sugimoto
Nucleic Acids Symp. Ser. (Oxf)   53 59-60   2009
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
Cu(Ⅱ) ion inhibits early stages of amyloid β fibril formation in vitro
S. Fujii, K. Yagi, D. Miyoshi, H. Sakai and N. Sugimoto
J. Biol. Inorg. Chem.   1 118   2009
Molecular crowding effects on structure and stability of DNA
D. Miyoshi and N. Sugimoto
Biochimie   90 1040-1051   Feb 2008
Cationic porphyrin induced a telomeric DNA to G-quadruplex form in water
T. Murashima, D. Sakiyama, D. Miyoshi, M. Kuriyama, T. Yamada, T. Miyazawa and N. Sugimoto
Bioinorg. Chem. Appl., 294756      2008
Molecular crowding effect on metal ion binding properties of the hammerhead ribozyme
S. Nakano, Y. Kitagawa, H. Tateishi-Karimata and N. Sugimoto
Nucleic Acids Symp. Ser.   52 519-520   2008
Thermodynamics of DNA structures under molecular crowding conditions with neutral and positive charged cosolutes
D. Miyoshi, K. Nakamura, S. Muhuri, H. Tateishi-Karimata and N. Sugimoto
Nucleic Acids Symp. Ser.   52 413-414   2008
Enhanced amplification of polymerase chain reaction by addition of cosolutes derived from a cellular compatible solute
K. Koumoto, H. Ochiai and N. Suigmoto
Nucleic Acids Symp. Ser.   52 257-258   2008
Kazuya Koumoto, Hirofumi Ochiai, Naoki Sugimoto
Chem. Lett.   37(8) 864-865   2008
Angew. Chem. Int. Ed.   (47) 9034-9038   2008
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
Effects of cosolutes on the thermodynamic stability of parallel DNA duplex and triplex.
K. Nakamura, H. Karimata, T. Ohmichi, D. Miyoshi and N. Sugimoto
Nucleic Acids Symp. Ser. (Oxf)   51 167-168   2007
Conformational switch of a functional nanowire based on the DNA G-quadruplex
H. Karimata, D. Miyoshi, T. Fujimoto, K. Koumoto, Z. M. Wang and N. Sugimoto
Nucleic Acids Symp. Ser. (Oxf)   51 251-252   2007
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
The roles of cosolutes on the hammerhead ribozyme activity
H. Karimata, S. Nakano and N. Sugimoto
Nucleic Acids Symp. Ser.   50 81-82   2006
Recognition of the base pair-mimic nucleosides by DNA polymerases
N. Sugimoto
Nucleic Acids Symp. Ser.   50 201-202   2006
Factors regulating thermodynamic stability of DNA structures under molecular crowding conditions
D. Miyoshi, H. Karimata and N. Sugimoto
Nucleic Acids Symp. Ser.   50 203-204   2006
The effect of the structure of cosolutes on the DNA duplex formation
N. Sugimoto
Nucleic Acids Symp. Ser.   50 205-206   2006
Properties of long telomeric DNAs under cell-mimicking conditions
H.Q. Yu, D. Miyoshi and N. Sugimoto
Nucleic Acids Symp. Ser.   50 207-208   2006
Development of molecular logic gates using the structural switch of telomere DNAs
M. Inoue, D. Miyoshi and N. Sugimoto
Nucleic Acids Symp. Ser.   50 315-316   2006
Functional role of the cofactor on activation process of L-histidine dependent ribozyme
J. Kawakami, C. Maiya and N. Sugimoto
Nucleic Acids Symp. Ser.   50 241-242   2006
Molecularly Imprinting within a Single Peptide Molecule for Synthesizing a Water-soluble ATP Receptor
J. Matsui, Y. Kamitaka, J. Nagano, Y. Ono, S. Komai, D. Miyoshi, K. Tamaki and N. Sugimoto
Proceedings of the International Conference of 43rd Japanese Peptide Symposium and 4th Peptide Engineering Meeting   396-397   2006
Hybrid material of biomimetic polymer geland gold nanoparticles for sensing catechol amines
56. J. Matsui, K. Akamatsu, D. Miyoshi, H. Nawafune, K. Tamaki, N. Sugimoto
Proc. Of the Second Int. Symp. Biomol. Chem.   53-53   2006
Controlling thermal stability of DNA duplex immobilized on gold substrate
M. Shimada, M. Kimura, Y. Shibata, S. Nakano, D. Miyoshi, K. Akamatsu, H. Nawafune, N. Sugimoto
Proc. Of the Second Int. Symp. Biomol. Chem.   54-54   2006
Influence of cosolute structure on the thermal stability od Hoogsteen base pairs in DNA triplex under molecular crowding conditions
K. Koumoto, Yong-Mei Hao, H. Ochiai, N. Sugimoto
Proc. Of the Second Int. Symp. Biomol. Chem.   57-57   2006
Nucleotide derivatives forming Watson-Crick base pair and base flipping conformations
S. Nakano, Y. Uotani, H. Oka, K. Uenishi, M. Fujii, N. Sugimoto
Proc. Of the Second Int. Symp. Biomol. Chem.   64-64   2006
The effect of cosolutes on the thermodynamic and kinetic properties of DNA duplex formation
X. -B. Gu, S.Nakano, N. Sugimoto
Proc. Of the Second Int. Symp. Biomol. Chem.   67-67   2006
Large enhancement of the hammerhead ribozyme activity by molecular crowding
H. karimata, S. Nakano, N. Sugimoto
Proc. Of the Second Int. Symp. Biomol. Chem.   68-68   2006

Books etc

 
Development and Application of a Highly Efficient Protein Synthesis Technique Using Riboswitches in Microorganisms
T. Yamauchi, N. Sugimoto (Part:Joint Work)
Applied RNA Bioscience (Springer)   Apr 2018   
Noncanonical Structures and Their Thermodynamics of DNA and RNA Under Molecular Crowing: Beyond the Watson-Crick Double Helix
N. Sugimoto
International Review of Cell and Molecular Biology (Elsevier), 307, 205-273   2014   
Effect of Ionic Liquid and Liposomes on the Structure, Stability, and Function of Nucleic Acids
N. Sugimoto
Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications (Springer), in press   2014   
Molecular Crowding and Hydration Regulating of G-Quadruplex Formation
D. Miyoshi, T. Fujimoto and N. Sugimoto (Part:Joint Work)
Quadruplex Nucleic Acids (Springer) , 330, 87-110   2013   
Chapter 8 Nucleic Acid Aptamers as Molecular Tags for Omics Analyses Involving Sequencing
M. Kuwahara and N. Sugimoto (Part:Joint Work)
DNA SEQUENCING, METHODS AND APPLICATIONS (InTech), 157-174   2012   
Improved parameters for prediction of RNA secondary structure and insights into why RNA forms double helixes
D. H. Turner, S. M. Freier, N. Sugimoto, D. R. Hickey, J. A. Jaeger, A. Sinclair, D. Alkema, T. Neilson, M. H. Caruthers and R. Kierzek (Part:Joint Work)
Structure and Dynamics of RNA (P. H. van Knippenberg and C. W. Hibers, Eds.), Plenum Press, NY, pp1-13   1986   

Conference Activities & Talks

 
Adventure on the World of Noncanonical Nucleic Acids
N. Sugimoto
The Department seminar of Padova University   17 Nov 2019   
Adventure on the World of Noncanonical Nucleic Acids
N
The Symposium on Nucleic Acid Chemistry   7 Nov 2019   
Adventure on the World of Noncanonical Nucleic Acids
N. Sugimoto
The Department seminar of Sogang University   7 Nov 2019   
Adventure on the World of Noncanonical Nucleic Acids
N. Sugimoto
The Department seminar of Sungkyunkwan University School of Medicine   6 Nov 2019   
Adventure on the World of Noncanonical Nucleic Acids
N. Sugimoto
The Department seminar of Konkuk University   6 Nov 2019   
Prediction method for DNA duplex stability in molecular crowding conditions
S. Ghosh, S. Takahashi, T. Ohyama, T. Endoh, H. Kateishi-Karimata, and N. Sugimoto
第46回国際核酸化学シンポジウム   29 Oct 2019   
Topology-based DNA quadruplex sensors for characterization of intracellular crowding environments
S. Takahashi, J. Yamamoto, A. Kitamura, M. Kinjo, and N. Sugimoto
第46回国際核酸化学シンポジウム   29 Oct 2019   
Effect of RNA topology on phase separation of peptides and proteins in neurodegenerative diseases
H. Tateishi-Karimata, Y. Teng, T. Ohyama, S. Tanaka, E. Chatani, and N. Sugimoto
第46回国際核酸化学シンポジウム   29 Oct 2019   
Screening of transcriptomic RNAs that interact with thioflavin T derivative
T. Endoh, M. Kuwahara, Y. Kataoka, and N. Sugimoto
第46回国際核酸化学シンポジウム   29 Oct 2019   
Development of new prediction parameters for RNA/DNA hybrid duplex stability under a physiological
D. Banerjee, H. Tateishi-Karimata, T. Ohyama, T. Endoh, S. Takahashi, and N. Sugimoto
第46回国際核酸化学シンポジウム   29 Oct 2019   
Phase separation of RNA G-quadruplexes induced bycationic peptides
K. Kohata, W. Sugimoto, K. Kawauchi, N. Sugimoto, and D. Miyoshi
第46回国際核酸化学シンポジウム   29 Oct 2019   
Analysis of the behavior of crowding molecules and their effects on DNAs at atomic level
T. Ohyama, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
第46回国際核酸化学シンポジウム   29 Oct 2019   
Development of new prediction parameters for RNA/DNA hybrid duplex stability under a physiological buffer condition
D. Banerjee, H. Tateishi-Karimata, T. Ohyama, T. Endoh, S. Takahashi, and N. Sugimoto
第46回国際核酸化学シンポジウム   29 Oct 2019   
“To B or not to B” in Nucleic Acids Chemistry (3)
N. Sugimoto
Advances in Noncanonical Nucleic Acids "ANNA2019",   17 Oct 2019   
Adventures of Nucleic Acids in the Molecular Crowding World
N. Sugimoto
The seminar at Faculty of Chemistry and Chemical Biology at TU Dortmund University   4 Oct 2019   
Effects of malignant alteration in cancer cells on the DNA G-quadruplex formation and transcript mutations
H. Tateishi-Karimata, K. Kawauchi, and N. Sugimoto
International Conference on Genomes and AI: From Packing to Regulation   2 Oct 2019   
Adventures of Nucleic Acids in the Molecular Crowding World
N. Sugimoto
Solvation Science Meets High Pressure Bioscience RESOLV – 10th IMBP – DFG FOR 1979   29 Sep 2019   
Adventures of Nucleic Acids in the Molecular Crowding World
N. Sugimoto
The conference"Chemistry meets Biomedicine"   19 Sep 2019   Skoltech
Adventures of Nucleic Acids in the Molecular Crowding World
N. Sugimoto
The Seminar of Department of Chemistry   18 Sep 2019   M. V. Lomonosov Moscow State University
RNA-capturing microsphere particles (R-CAMPs) for optimization of functional RNAs
T. Endoh, N. Sugimoto
10th RSC-CSJ Joint Symposium– Chemistry for Complex Biological Systems–   7 Sep 2019   
Role for G-quadruplexes of Nucleic Acids During Tumor Progression
H. Tateishi-Karimata and N. Sugimoto
10th RSC-CSJ Joint Symposium   7 Sep 2019   
Adventures of Guanine-quadruplex in Molecular Crowding World
N. Sugimoto
7th International Meeting on Quadruplex Nucleic Acids   6 Sep 2019   
Nucleic Acids Chemistry under the Molecular Crowding World
N. Sugimoto
第29回バイオ・高分子シンポジウム   25 Jul 2019   
To B or Not to B : The Watson-Crick world is not enough
N. Sugimoto
The Commemorative International Symposium of Nucleic Acid Chemistry (CISNAC2019)   22 Jul 2019   Japan Society of Nucleic Acids Chemistry (JSNAC)
Adventure of Nucleic Acids in Molecular Crowding World
N. Sugimoto
The Seminar of Chemistry Department   28 Jun 2019   
The Watson-Crick World Is Not Enough
N. Sugimoto
Gordon Research Conference(Nucleosides, Nucleotides and Oligonucleotides)   23 Jun 2019   
Functions of Non-canonical Nucleic Acids (2)
N. Sugimoto
International Workshop“Trends in Nucleic Acid (TINA) 2019”   12 Apr 2019   Nankai University
Adventures of Nucleic Acids in Molecular Crowding World
N. Sugimoto
The seminar of College of Chemistry   11 Apr 2019   
Adventures of Nucleic Acids in Molecular Crowding World
N. Sugimoto
The seminar of School of Pharmaceutical Sciences   11 Apr 2019   
Adventures of Nucleic Acids in Molecular Crowding World
N. Sugimoto
The Department Seminar of City University of Hong Kong   26 Mar 2019   City University of Hong Kong
RNAs in Molecular Crowding World
N. Sugimoto
The Seminar of Hong Kong RNA Club   25 Mar 2019   Hong Kong RNA Club
Adventures of Nucleic Acids in Molecular Crowding World
N. Sugimoto
The Department Seminar of Sun Yat-sen University   23 Mar 2019   Sun Yat-sen University
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (49): Validation of the nearest-neighbor model for self-complementary DNA duplex under molecular crowding
S. Ghosh, S.Takahashi, T. Endoh, H. Tateishi-Karimata, and N. Sugimoto
日本化学会第99回春季年会(2019)   16 Mar 2019   日本化学会
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (48) :Imaging of crowding in cells by using guanine-quadruplex DNA
S.Takahashi, J. Yamamoto, A. Kitamura, M. Kinjo, and N. Sugimoto
日本化学会第99回春季年会(2019)   16 Mar 2019   
ucleic Acids Chemistry beyond the Watson-Crick Double Helix (52) : Optimization of RNA conformational switch using RNA-capturing microsphere particle (R-CAMP)
T. Endoh and N. Sugimoto
日本化学会第99回春季年会(2019)   16 Mar 2019   日本化学会
脱ワトソン・クリックの核酸化学(56): DNAの構造安定性に及ぼすメチル化と分子クラウディングの複合効果
杉谷優衣, 造住有輝, 杉本直己, 三好大輔
日本化学会第99回春季年会(2019)   16 Mar 2019   日本化学会
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix(50):Phase separation of RNA/peptides in neurodegenerative diseases is promoted by chemical environment changes in cell
H. Tateishi-Karimata, Y. TENG, T.Ohyama, and N. Sugimoto
日本化学会第99回春季年会(2019)   16 Mar 2019   日本化学会
Elucidation for mechanism of diseases caused by non-canonical structures of DNA and regulation for DNA function
H. Tateishi-Karimata
日本化学会第99回春季年会(2019)   16 Mar 2019   日本化学会
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (52) : Optimization of RNA conformational switch using RNA-capturing microsphere particle (R-CAMP)
T. Endoh and N. Sugimoto,
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (52) : Optimization of RNA conformational switch using RNA-capturing microsphere particle (R-CAMP)   16 Mar 2019   
Functions of Nucleic Acids under Molecular Crowding Conditions
N. Sugimoto
The Lecture of Institute of Biophysics Czech Academy of Sciences   13 Mar 2019   Institute of Biophysics Czech Academy of Sciences
Molecular Crowding Regulates RNA Phase Separations in Repeat Expansion Disorders
Y. Teng, H. Tateishi-Karimata, and N. Sugimoto
Gordon Research Conference(RNA Nanotechnology)   13 Jan 2019   
Molecular Crowding Effect on Functions of Nucleic Acids:
N. Sugimoto
The Department seminar   20 Dec 2018   
Molecular Crowding Effect on Functions of Nucleic Acids:
N. Sugimoto
The Department seminar   19 Dec 2018   
Molecular Crowding Effect on Functions of Nucleic Acids:
N. Sugimoto
The Department seminar   19 Dec 2018   
THE WORLD OF NON-CANONICAL NUCLEIC ACIDS
N. Sugimoto
The 9th Asian Biological Inorganic Chemistry “AsBIC9”   9 Dec 2018   
Functions of Nucleic Acids with Non-canonical Structures:To B or not to B
N. Sugimoto
KONAN RESEARCH SUMMIT   4 Dec 2018   FIBER, Konan University
Roles of Noncanonical Nucleic Acids on Gene Expressions
N. Sugimoto
The 2nd International Symposium on “Functional Nucleic Acids: From Laboratory to Targeted Molecular Therapy"   22 Nov 2018   
Optimization of junction sequence between two aptamers for constructing signaling aptamer by using RNA library on microsphere
T. Endoh, N. Sugimoto
第45回国際核酸化学シンポジウム   7 Nov 2018   日本核酸化学会
Investigation for effects of polyethylene glycols on DNA structure and stability using molecular dynamics simulations
T. Ohyama, H.Tateishi-Karimata, S. Tanaka, and N. Sugimoto
第45回国際核酸化学シンポジウム   7 Nov 2018   日本核酸化学会
Phase separation of repeated RNA with amyloid-like protein in neurodegenerative diseases is promoted by RNA G-quadruplexes
Y. Teng, H. Tateishi-Karimata, N. Sugimoto
第45回国際核酸化学シンポジウム   7 Nov 2018   日本核酸化学会
Effect of G-quadruplex stability and structure in the template DNA on transcript mutations in normal and cancer cells
H. Tateishi-Karimata, N. Sugimoto
第45回国際核酸化学シンポジウム   7 Nov 2018   日本核酸化学会
Structural Perspectives of the DNA binding properties of Ruthenium Polypyridyl Complexes
K. McQuaid, J. Hall, H. Abell1, S. Takahashi, N. Sugimoto, D. Allan, D. Cardin, J. Brazier, and C. Cardin
第45回国際核酸化学シンポジウム   7 Nov 2018   日本核酸化学会
Transformation of selective i-motif DNAs into hairpin-like structures induced by a flavonoid compound
S. Takahashi, S. Bhowmik, S. Ghosh, N. Sugimoto
第45回国際核酸化学シンポジウム   7 Nov 2018   日本核酸化学会
Effects of molecular crowding on nearest-neighbor rules for Watson-Crick self-complementary DNA duplexes
S. Ghosh, S. Takahashi, T. Endoh, H. Tateishi-Karimata, S. Hazra and N, Sugimoto
第45回国際核酸化学シンポジウム   7 Nov 2018   日本核酸化学会
Optimization of junction sequence between two aptamers for constructing signaling aptamer by using RNA library on microspheres
T.Endoh, N.Sugimoto
第45回国際核酸化学シンポジウム   Nov 2018   
Effect of noncanonical DNA structures on transcription
N. Sugimoto
The Third A3 Roundtable Meeting on Chemical Probe Research Hub   31 Oct 2018   
“To B or not to B” in Nucleic Acids Chemistry (2)
N. Sugimoto
Advances in Noncanonical Nucleic Acids "ANNA2018"   25 Oct 2018   
Noncanonical world of nucleic acids under molecular crowding
N. Sugimoto
The seminar of the department f Pharmacy University of Naples "Federico II"   21 Oct 2018   
Analysis of structural dynamics of RNA aptamer using high pressure
S. Takahashi, T. Endoh, A. B. Rode, N. Sugimoto
The 10th International Conference on High Pressure Bioscience and Biotechnology (HPBB2018)   18 Sep 2018   
Noncanonical world of nucleic acids under molecular crowding and high pressure
N. Sugimoto
The 10th International Conference on High Pressure Bioscience and Biotechnology (HPBB2018)   18 Sep 2018   
Gelation of RNA repeats in ALS/FTD is promoted in crowding conditions
Teng Ye, 建石寿枝, 杉本直己
第12回バイオ関連化学シンポジウム   9 Sep 2018   
カリウムチャネルはがん遺伝子の転写活性をDNA四重鎖の形成によって制御しているのか?
建石寿枝, 川内敬子, 大山達也, 杉本直己
第12回バイオ関連化学シンポジウム   9 Sep 2018   
Noncanonical world of nucleic acids under molecular crowding:To B or not to B
N. Sugimoto
XXIII International Roundtable of Nucleosides,Nucleotides and Nucleic Acids (IRT2018)   26 Aug 2018   IS3NA(International Society for Nucleosides, Nucleotides, and Nucleic Acids)
Nucleic Acids World under Molecular Crowding
N. Sugimoto
The 5th Asian Chemical Biology Conference (ACBC-5)   19 Aug 2018   
Stability and Function of Noncanonical Nucleic Acids
N. Sugimoto
The seminar of Institute of Chemical Biology and Fundamental Medicine   19 Jul 2018   
Improved Efficiency of mRNA Sensing System by a Hydrated Ionic Liquid
Hisae Tateishi-Karimata, N. Sugimoto
Gordon Research Conference(Bioanalytical Sensors)   24 Jun 2018   
Nucleic Acids Chemistry Beyond the Watson-Crick Double Helix:“To B or not to B”
N. Sugimoto
The Department seminar   8 Jun 2018   Sungkyunkwan University school of medicine
Nucleic Acids Chemistry Beyond the Watson-Crick Double Helix:“To B or not to B”
N. Sugimoto
The Departmental seminar of College of Pharmacy   7 Jun 2018   College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University
The world of non-canonical nucleic acids: To B or not to B
N. Sugimoto
The seminer of “The role of non-canonical structure of nucleic acids”   8 May 2018   南京農業大学
Functions of Non-canonical Nucleic Acid
N. Sugimoto
International workshop“Trends in Nucleic Acid (TINA) 2018"   14 Apr 2018   
Functions of Non-canonical Nucleic Acids
N. Sugimoto
International workshop“Trends in Nucleic Acid (TINA) 2018”   13 Apr 2018   
Topological impact of non-canonical DNA structures on the replication
S. Takahashi, N. Sugimoto
Gordon Research Conference, DNA Damage, Mutation and Cancer   25 Mar 2018   
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (37): The formation of RNA foci in repeat expansion disorders is promoted in molecular crowding conditions
Y. Teng, H. Tateishi-Karimata, N. Sugimoto
日本化学会第98回春季年会   20 Mar 2018   
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (38): Effects of malignant alteration in cancer cells on the G-quadruplex formation and transcript mutations
H. Tateishi-Karimata, K. Kawaguchi, T, Ohyama, N. Sugimoto
日本化学会第98回春季年会   20 Mar 2018   
Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (39) : Control of replication of G-quadruplex containing oxidative lesion
S. Takahashi, P. Podbevsek, J. Plavec, B. H. Kim, N. Sugimoto
日本化学会第98回春季年会   20 Mar 2018