Published Papers - SUGIMOTO Naoki

Stabilization of DNA Loop Structures by Large Cations

S. Nakano, T. Ayusawa, Y. Tanino, N. Sugimoto

J Phys Chem B.   123   7687 - 7694   2019.09  [Refereed]

Joint Work

Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency

T. Endoh and N. Sugimoto

Molecules   24   1613   2019.04  [Refereed]

Joint Work

RNA-Capturing Microsphere Particles (R-CAMPs) for Optimization of Functional Aptamers

T. Endoh, T. Ohyama, and N. Sugimoto

Small     1805062   2019.04  [Refereed]

Joint Work

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   2019.02  [Refereed]

Joint Work

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]

Joint Work

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)   55   11679 - 11682   2019  [Refereed]

Joint Work

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]

Joint Work

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]

Joint Work

[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]

Joint Work

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]

Single Work

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   2018.12  [Refereed]

Joint Work

Recovery of the formation and function of oxidized G-quadruplexes by a pyrene-modified guanine-tract

S. Takahashi, K. T. Kim, P. Podbevšek, J. Plavec, B. H. Kim, and N. Sugimoto

J. Am. Chem. Soc.   140 ( 17 ) 5774 - 5783   2018.04

Joint Work

DOI

Alkylating Probes for G-Quadruplex Structure and Evaluation of the Properties of the Alkylated G-Quadruplex DNA

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   2018.01

Joint Work

DOI

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

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   2018.01  [Refereed]

Joint Work

DOI

Destabilization of DNA G-quadruplexes by chemical environment changes during tumor progression facilitates transcription

H. Tateishi-Karimata, K. Kawauchi, and N. Sugimoto

J. Am. Chem. Soc.   140   642 - 651   2018  [Refereed]

Joint Work

[Highligted as a Supplementary Cover]

DOI

Crowding Shifts the FMN Recognition Mechanism of Riboswitch AptameConformational Selection to Induced Fi

A. B. Rode, T. Endoh, and N. Sugimoto

Angew. Chem. Int. Ed.     2018

Joint Work

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]

Joint Work

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

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  [Refereed]

Joint Work

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]

Joint Work

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]

Joint Work

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

Joint Work

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]

Joint Work

Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition

Y. Teng, S. Pramanik, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto

Biochem. Biophys. Res. Commun.   496   601 - 607   2018  [Refereed]

Joint Work

DOI

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]

Joint Work

Modulation of Ribozyme and Deoxyribozyme Activities Using Tetraalkylammonium Ions

S. Nakano, T. Watabe, and N. Sugimoto

Chem. Phys. Chem.   18   3614 - 3619   2017.11

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

[Highlighted as a Front Cover]

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]

Joint Work

Model studies of the effects of intracellular crowding on nucleic acid interactions

S. Nakano, N. Sugimoto

Mol Biosyst.   13   32 - 41   2017  [Refereed]

Joint Work

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   2016.11  [Refereed]

Joint Work

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   2016.11  [Refereed]

Joint Work

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   2016.10  [Refereed]

Joint Work

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   2016.08  [Refereed]

Joint Work

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   2016.06  [Refereed]

Joint Work

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   2016.02  [Refereed]

Joint Work

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   2016.02  [Refereed]

Joint Work

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   2016.01  [Refereed]

Joint Work

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

Joint Work

Expansion of the DNA 'alphabet' beyond natural DNA recognition

H. Tateishi-Karimata and N. Sugimoto

ChemBioChem   17   1301 - 1303   2016  [Refereed]

Joint Work

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

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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]

Joint Work

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   2015.12  [Refereed]

Joint Work

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   2015.09

Joint Work

Effects of cosolvents on the folding and catalytic activities of the hammerhead ribozyme

S. Nakano, Y. Kitagawa, H. Yamashita, D. Miyoshi, and N. Sugimoto

ChemBioChem.   16   1803 - 1810   2015.08

Joint Work

DOI

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   2015.07  [Refereed]

Joint Work

Rational design and tuning of functional RNA switch to control an allosteric intermolecular interaction

T. Endoh and N. Sugimoto

Anal. Chem.   87   7628 - 7635   2015.07  [Refereed]

Joint Work

Loop nucleotides impact the stability of intrastrand i-motif structures at neutral pH

T. Fujii and N. Sugimoto

Phys. Chem. Chem. Phys.   17   16719 - 16722   2015.05  [Refereed]

Joint Work

DOI

A mRNA-responsive G-quadruplex-based drug release system.

H. Yaku, T. Murashima, D. Miyoshi, and N. Sugimoto

Sensors   15 ( 4 ) 9388 - 9403   2015.04  [Refereed]

Joint Work

DOI

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   2015.04

Joint Work

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   2015.04  [Refereed]

Joint Work

[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   2015.02  [Refereed]

Joint Work

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   2015.01  [Refereed]

Joint Work

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   2015.01

Joint Work

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   2015.01

Joint Work

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

Joint Work

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]

Joint Work

Pressure-dependent formation of i-motif and G-quadruplex DNA structures

S. Takahashi and N. Sugimoto

Phys. Chem. Chem. Phys.   17   31004 - 31010   2015

Joint Work

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]

Joint Work

Methyl substitution regulates the enantioselectivity of supramolecular complex binding to human telomeric G-Quadruplex DNA

B. Xu, C. Zhao, Y. Chen, H. Tateishi-Karimata, J. Ren, N. Sugimoto, and X. Qu

Chem. Eur. J.   20 ( 50 ) 16467 - 16472   2014.12

Joint Work

DOI

Organelle-Mimicking Liposome Dissociates G-quadruplexes and Facilitates Transcription

Smritimoy Pramanik, Hisae Tateishi-Karimata, Naoki Sugimoto

Nucleic Acids Research   42 ( 20 ) 12949 - 12959   2014.11

Joint Work

DOI

Drastic stabilization of parallel DNA hybridizations by a polylysine com-type copolymer with hydrophilic graft chain

Daisuke Miyoshi, Yumi Ueda, Naohiko Shimada, Shu-ichi Nakano, Naoki Sugimoto, Atsushi Maruyama

ChemMedChem   Sep;9 ( 9 ) 2156 - 2163   2014.09

Joint Work

DOI

Aptamer-Based Universal Fluorometric Sensors Based on Allosteric Modulation of RNA-Peptide Interactions

T. Endoh, N. Sugimoto

ChemMedChem   Sep;9 ( 9 ) 2045 - 2048   2014.09

Joint Work

DOI

Dangling ends perturb the stability of RNA duplex responsive to surrounding condition

H. Tateishi-Karimata, S. Pramanik, S. Nakano, D. Miyoshi and N. Sugimoto

ChemMedChem   Sep;9 ( 9 ) 2150 - 2155   2014.09

Joint Work

DOI

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   2014.08  [Refereed]

Joint Work

The affinity of molecular ions for DNA structures is determined by solvent accessible surface area

M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto

J. Phys. Chem. B   118 ( 32 ) 9583 - 9594   2014.08

Joint Work

DOI

In vitro assays predicting of telomerase inhibitory effect of G-quadruplex ligands in cell nuclei

H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto

J. Phys. Chem. B.   118 ( 10 ) 2605 - 2614   2014.03

Joint Work

DOI

Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids

S. Nakano, D. Miyoshi, N. Sugimoto

Chem.Rev.   114 ( 5 ) 2733 - 2758   2014.03

Joint Work

DOI

New insights into transcription fidelity : thermal stability of non-cononical structures in template DNA regulates transcriptional arrest, pause, and slippage

H. Tateishi-Karimata, N. Isono and N. Sugimoto

PLoS ONE, DOI:10.1371   9 ( 3 ) e90580   2014.03

Joint Work

DOI

Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate

H. Tateishi-karimata, M. Nakano and N. Suigimoto

Sci. Rep.   4   3593   2014.01

Joint Work

DOI

Reduced Graphene Oxide Upconversion Nanoparticle Hybrid for Electrochemiluminescent Sensing of a Prognostic Indicator in Early-Stage Cancer

L. Wu, J. Wang, M. Yin, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu

Small   10   330 - 336   2014.01

Joint Work

DOI

Choline ion interactions with DNA atoms explain unique stabilization of A-T base pairs in DNA duplexes: A microscopic view

M. Nakano, H. Tateishi-Karimata, S. Tanaka and N. Sugimoto

J. Phys. Chem. B.   118   379 - 389   2014.01

Joint Work

DOI

Unusual-1 ribosomal frameshift cused by statble RNA G-quadruplex in open reading frame

T. Endoh and N. Sugimoto

Anal. Chem.   85   11435 - 11439   2013.12

Joint Work

DOI

Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer

A. Pica, I. Russo Krauss, A. Merlino, S. Nagatoishi, N. Sugimoto and F. Sica

FEBS J.   280   6581 - 6588   2013.12

Joint Work

DOI

Effect of pressure on the stability of G-quadruplex DNA: Thermodynamics under crowding conditions

S. Takahashi and N. Sugimoto

Angew. Chem. Int. Ed.   52   13774 - 13778   2013.12

Joint Work

DOI

Translational halt during elongation caused by G-quadruplex formed by mRNA

T. Endoh, Y. Kawasaki and N. Sugimoto

Methods   64   73 - 78   2013.11

Joint Work

DOI

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   64   19 - 27   2013.11

Joint Work

DOI

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules

S. Nakano, Y. Uotani, Y. Sato, H. Oka, M. Fujii and N. Sugimoto

Nucleic Acids Res   41   8581 - 8590   2013.10

Joint Work

DOI

Real-time monitoring of DNA hybridization kinetics at living cell surfaces

A. B. Rode, T. Endoh, H. Tateishi-Karimata, S. Takahashi and N. Sugimoto

Chem. Commun.   49   8444 - 8446   2013.10

Joint Work

DOI

Sequence and Solvent Effects on Telomeric DNA Bimolecular G-Quadruplex Folding Kinetics

A. Marchand, R. Ferreira, H. Tateishi-Karimata, D. Miyoshi, N. Sugimoto and V. Gabelica

J. Phys. Chem. B   117   12391 - 12401   2013.10

Joint Work

DOI

A highly sensitive telomerase activity assay that eliminates false-negative results caused by PCR inhibitors

H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto

Molecules   18   11751 - 11767   2013.09

Joint Work

DOI

Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives

H. Fujita, Y. Imaizumi, Y. Kasahara, S. Kitadume, H. Ozaki, M. Kuwahara, and N. Sugimoto

Pharmaceuticals   6   1082 - 1093   2013.08

Joint Work

DOI

Stability of RNA quadruplex in open reading frame determines proteolysis of human estrogen receptor α

T. Endoh, Y. Kawasaki and N. Sugimoto

Nucleic. Acids Research   41   6222 - 6231   2013.07

Joint Work

DOI

Multiple and cooperative binding of fluorescence light-up probe Thioflavin T with human telomere DNA G-quadruplex

V. Gabelica, R. Maeda, T.Fujimoto, H. Yaku, T. Murashima, N. Sugimoto and D. Miyoshi

Biochemistry, 52, 5620-5628   52   5620 - 5628   2013.06

Joint Work

DOI

Efficacy of Base-modification on Target Binding of Small Molecule DNA Aptamers

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   2013.06

Joint Work

DOI

Control of stability and structure of nucleic acids using cosolutes

H. Tateishi-Karimata and N. Sugimoto

Methods   67 ( 2 ) 151 - 158   2013.05

Joint Work

DOI

Suppression of Gene Expression by G-quadruplexes in Open Reading Frames Depends on G-quadruplex Stability

T. Endoh, Y. Kawasaki and N. Sugimoto

Angew. Chem. Int. Ed.   52   5522 - 5526   2013.05

Joint Work

DOI

Selection of RNAs for Constructing Lighting-UP Biomolecular Switches in Response to Specific Small Molecules

T. Endoh and N. Sugimoto

PLoS ONE, 8(3), e60222   8   2013.03

Single Work

DOI

Thermodynamics - Hydration Relationships within Loops that Affect G-Quadruplexes under Molecular Crowding Conditions

T. Fujimoto, S. Nakano, N. Sugimoto and D. Miyoshi

J. Phys. Chem. B (Highlighted as the cover)   117   963 - 972   2013.01

Joint Work

DOI

Construction of Artificial Peptides for Control of DNA G-quadruplex Structures Depending on Protease Activity toward Regulation of Protein Expression

A. Okada, K. Usui, M. Taniguchi, K. Kobayashi and N. Sugimoto

Peptide Science   2012   285 - 276   2013

Joint Work

A?T Base Pairs are More Stable Than G?C Base Pairs in a Hydrated Ionic Liquid

N. Sugimoto

Angew. Chem. Int. Ed.   51   1416 - 1419   2012

Single Work

DOI

A–T Base Pairs are More Stable Than G–C Base Pairs in a Hydrated Ionic Liquid

H. Tateishi-Karimata and N. Sugimoto

Angew. Chem. Int. Ed.   51   1416 - 1419   2012

Joint Work

Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative

S. Nakano, H. Oka, D. Yamaguchi, M. Fujii and N. Sugimoto

Org Biomol Chem.   10   9664 - 9670   2012

Joint Work

Aptamer carbon nanodot sandwich used for fluorescent detection of protein

B. Xu, C. Zhao, W. Wei, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu

Analyst   137   5483 - 5486   2012

Joint Work

Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein

S. Nagatoishi and N. Sugimoto

Mol Biosyst   8   2766 - 2770   2012

Joint Work

Dimerization of Nucleic Acid Hairpins in the Conditions Caused by Neutral Cosolutes

S. Nakano, H. Hirayama, D. Miyoshi and N. Sugimoto

J. Phys. Chem. B   116   7406 - 7415   2012

Joint Work

Dehydration from conserved stem regions is fundamental for ligand-dependent conformational transition of the adenine-specific riboswitch

V. Kumar, T. Endoh, K. Murakami and N. Sugimoto

Chem. Commun.   48   9693 - 9695   2012

Joint Work

Beads-on-a-string structure of long telomeric DNAs under molecular crowding conditions

H. Yu, X. Gu, S. Nakano, D. Miyoshi and N. Sugimoto

J. Am. Chem. Soc.   134   20060 - 20069   2012

Joint Work

Hydration Changes upon DNA Folding Studied by Osmotic Stress Experiments

S. Nakano, D. Yamaguchi, H. Tateishi-Karimata, D. Miyoshi and N. Sugimoto

Biophysical Journal   102   2808 - 2817   2012

Joint Work

Structural and Functional Characterization of RecG Helicase under Dilute and Molecular Crowding Conditions

S. Saxena, S. Nagatoishi, D. Miyoshi and N. Sugimoto

Journal of Nucleic Acids, ID 392039 8 pages   2012   2012

Joint Work

Development of PNA-Peptides Controlling DNA G-Quadruplex Structures Depending on Protease Activity

K. Usui, K. Kobayashi and N. Sugimoto

Peptide Science   2011   315 - 316   2012

Joint Work

DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles

S. Pramanik, S. Nagatoishi and N. Sugimoto

Chem. Commun.   48   4815 - 4817   2012

Joint Work

The yield of transcripts for RNA polymerase regulated by hairpin structures in nascent　RNA

S. Nagatoishi, R. Ono and N. Sugimoto

Chem. Commun.   48   5121 - 5123   2012

Joint Work

Detection of a Prognostic Indicator in Early-Stage Cancer Using Functionalized Graphene-Based Peptide Sensors

L. Feng, L. Wu, J. Wang, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu

Advanced Materials   24   125 - 131   2012

Joint Work

Rational design of a new IMP aptamer based on a TPP riboswitch and a hypoxanthine aptamer

M. Tokui, T. Yamauchi, D. Miyoshi, H. Kamiya, A. Nishimura and N. Sugimoto

Chem. Lett.   40   1313 - 1314   2012

Joint Work

Synchronized Translation for Detection of Temporal Stalling of Ribosome during Single-Turnover Translation

T. Endoh, Y. Kawasaki and N. Sugimoto

Anal. Chem.   84   857 - 861   2012

Joint Work

Hydration is required in DNA G-quadruplex-protein binding

S. Nagatoishi, N. Isono, K. Tsumoto and N. Sugimoto

ChemBioChem   12   1822 - 1826   2011.07

Joint Work

Effect of Locked Nucleic Acid modification on Thermal Stability of Non-canonical DNA Structure

J. Bhattacharyya, S. Maiti, S. Muhuri, S. Nakano, D. Miyoshi and N. Sugimoto

Biochemistry   50 ( 34 ) 7414 - 7425   2011.07

Joint Work

DNA Morphologic Changes Induced by Spermine on a Gold Surface under DNA Crowding Conditions

K. Kobayashi, H. Tateishi-Karimata, K. Tsutsui, Y. Wada and N. Sugimoto

Chemistry Letters   40   855 - 857   2011.07

Joint Work

Measurements of the binding of a large protein using a substrate density-controlled DNA chip

S. Nakano, T. Kanzaki, M. Nakano, D. Miyoshi and N. Sugimoto

Anal. Chem.   83   6368 - 6372   2011.07

Joint Work

Label-free colorimetric and quantitative detection of cancer marker protein using noncrosslinking aggregation of Au/Ag nanoparticles induced by target-specific peptide probe

X. Wang, L. Wu, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu

Biosens. Bioelectron.   26   4804 - 4809   2011.06

Joint Work

Gene Regulation System with an Artificial RNA Switch Operating in Human Cell.

T. Endoh and N. Sugimoto

ChemBioChem.   12   1174 - 1178   2011.05

Joint Work

Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding.

S. Nagatoishi, N. Isono, K. Tsumoto and N. Sugimoto

Biochimie   93   1231 - 1238   2011.05

Joint Work

Thermodynamic stability of Hoogsteen and Watson–Crick base pairs in the presence of histone H3-mimicking peptide

S. Pramanik, K. Nakamura, K. Usui, S. Nakano, S. Saxena, J. Matsui, D. Miyoshi and N. Sugimoto

Chem. Commun.   47   2790 - 2792   2011.02

Joint Work

A PNA peptide inducing DNAs to form G-quadruplex structures depending on a protease activity

K. Usui, K. Kobayashi and N. Sugimoto

Peptides   2011   152 - 153   2011

Joint Work

The effects of molecular crowding on the structure and stability of G-quadruplexes with an abasic site

T. Fujimoto, S. Nakano, D. Miyoshi and N. Sugimoto

Journal of Nucleic Acids, ID 857149 9pages     2011

Joint Work

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

S. Nakano, M. Fujii and N. Sugimoto

Journal of Nucleic Acids, ID 967098 11pages     2011

Joint Work

Triplet analysis that identifies unpaired regions of functional RNAs

J. Kawakami, Y. Yamaguchi and N. Sugimoto

J. Nucleic Acids, ID 471843 6pages     2011

Joint Work

Conformational Flexibility Influences Degree of Hydration of Nucleic Acid Hybrids

S. Pramanik, S. Nagatoishi, S. Saxena, J. Bhattacharyya and N. Sugimoto

The Journal of Physical Chemistry   115   13862 - 13872   2011

Joint Work

Construction of detection system for amyloid beta peptide localization and aggregation using fluorescent and luminescent fusion proteins

K. Usui, M. Mie, T. Andou, N. Sugimoto, H. Mihara and E. Kobatake

Peptide Science   2009   111 - 112   2010.11

Joint Work

A rapid and sensitive “add-mix-measure” assay for multiple proteinases based on Goldnanoparticle-peptide-fluorophore conjugate.

X. Wang, J. Geng, D. Miyoshi, J. Ren, N. Sugimoto and X. Qu

Biosens. Bioelectron.   26   743 - 747   2010.10

Joint Work

Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides

S. Nakano, H. Oka, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto

Mol. Biosys.   6   2023 - 2029   2010.10

Joint Work

Ultrasensitive and Selective Detection of a Prognostic Indicator in Early-Stage Cancer using Grapheme Oxide and Carbon Nanotubes

X. Wang, C. Wang, K. Qu, Y. Song, J. Ren, D. Miyoshi, N. Sugimoto and X. Qu

Advanced Functional Materials   20   3967 - 3971   2010.08

Joint Work

Development of new functional nanostructures consisting of both DNA duplex

K. Dutta, T. Fujimoto, M. Inoue, D. Miyoshi and N. Sugimoto

Chem Commun.   46   7772 - 7774   2010.08

Joint Work

Sole and stable RNA duplexes of G-rich sequences located in the 5'-untranslated region of protooncogenes

S. Saxena, D. Miyoshi and N. Sugimoto

Biochemistry   49   7190 - 7201   2010.08

Joint Work

Anionic phthalocyanines Targeting G-quadruplexes and Inhibiting Telomerase Activity in the Presence of Excessive DNA Duplexes

H. Yaku, T. Murashima, D. Miyoshi and N. Sugimoto

Chem. Commun.   46   5740 - 5742   2010.07

Joint Work

Utilization of salmon milt DNA against UV damage

Y. Sasaki, D. Miyoshi and N. Sugimoto

Applied Biochem. Biotech.   160   2458 - 2466   2010.07

Joint Work

Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors

D.H. Zhang, T. Fujimoto, S. Saxena, H.Q. Yu, D. Miyoshi and N. Sugimoto

Biochemisry   49   4554 - 4563   2010.04

Joint Work

Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH

A. Rajendran, S. Nakano and N. Sugimoto

Chem. Commun.   46   1299 - 1301   2010.01

Joint Work

PNA-peptide conjugates for regulation of DNA and RNA G-quadruplex structures depending on a particular protease concentration

K. Usui, K. Kobayashi and N. Sugimoto

Peptides   2010   608 - 609   2010

Joint Work

Fluorescent and luminescent fusion proteins for detection of amyloid beta peptide localization and aggregation

K. Usui, M. Mie, T. Andou, N. Sugimoto, H. Mihara and E. Kobatake

Peptides   2010   488 - 489   2010

Joint Work

Neuronal differentiation of neural progenitor cells by intracellular delivery of synthetic oligopeptide derived from von Hippel-Lindau protein

H. Kanno, S. Nakano, A. Kubo, T. Mimura, N. Tajima and N. Sugimoto

Protein & Peptide Letters   16   1291 - 1296   2009.11

Joint Work

An approach to peptide-based ATP receptors by a combination of random selection, rational design, and molecular imprinting

J. Matsui, J. Nagano, D. Miyoshi, K. Tamaki and N. Sugimoto

Biosens. Bioelectron.   25   563 - 567   2009.11

Joint Work

Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides

S. Nakano, H. Oka, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto

Biochemistry   48   11304 - 11311   2009.10

Joint Work

Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes

S. Nakano, H. Tateishi-Karimata, Y. Kitagawa and N. Sugimoto

J. Am. Chem. Soc.   131   16881 - 16888   2009.10

Joint Work

Stabilization of three-way junctions of DNA under molecular crowding conditions

S. Muhuri, K. Mimura, D. Miyoshi and N. Sugimoto

J. Am. Chem. Soc.   131   9268 - 9280   2009.06

Joint Work

Reversible stability switching of a hairpin DNA via a photo-responsive linker unit

L. Wu, K. Koumoto and N. Sugimoto

Chem. Commun.   14   1915 - 1917   2009.04

Joint Work

Hydration of Watson-Crick base pairs and dehydration of hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions

D. Miyoshi, K. Nakamura, Hisae Tateishi-Karimata, T. Ohmichi and N. Sugimoto

J. Am. Chem. Soc.   131   3522 - 3531   2009.02

Joint Work

Molecularly imprinted nanocomposites for highly sensitive SPR detection of a non-aqueous atrazine sample

J. Matsui, M. Takayose, K. Akamatsu, H. Nawafune, K. Tamaki and N. Sugimoto

Analyst   134   80 - 86   2009.01

Joint Work

Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem

H. Yaku, T. Yukimasa, S. Nakano, N. Sugimoto and H. Oka

Electrophoresis   29   4130 - 4140   2008.11

Joint Work

Regulation of Telomerase Activity by the Thermodynamic Stability of a DNA·RNA Hybrid

H.Q. Yu, D.H. Zhang, X.B. Gu, D. Miyoshi and N. Sugimoto

Angew. Chem. Int. Ed. Engl.   47   9034 - 9038   2008.10

Joint Work

Recognition of a flipped base in a hairpinloop DNA by a small peptide

J. Kawakami, S. Okabe, Y. Tanabe and N. Sugimoto

Nucleosides Nucleotides Nucleic Acids   27   292 - 308   2008.08

Joint Work

Hydration is an important factor to regulate thermodynamic stability of a DNA duplex under molecular crowding conditions

K. Koumoto, H. Ochiai and N. Sugimoto

Chem. Lett.   37   864 - 865   2008.05

Joint Work

Riboswitches for enhancing target gene expression in eukaryotes

T. Yamauchi, D. Miyoshi, T. Kubodera, M. Ban, A. Nishimura and N. Sugimoto

Chemical Communications,   9   1040 - 1043   2008.03

Joint Work

Capture of cationic ligands bound diffusely to base pairs during the DNA refolding

S. Nakano, T. Kirihata and N. Sugimoto

Chem. Commun.   14   700 - 702   2008.02

Joint Work

Small-molecule-directed assembly of DNA: a gold-nanoparticle-based strategy for screening of a DNA duplex binders

G. Song, C. Chen, X. Qu, D. Miyoshi, J. Ren and N. Sugimoto

Adv. Mater.   20   706 - 710   2008.01

Joint Work

Structural effect of synthetic zwitterionic cosolutes on the stability of DNA duplexes

K. Koumoto, H. Ochiai and N. Sugimoto

Tetrahedron   64   168 - 174   2008.01

Joint Work

Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media

S. Nakano, L. Wu, H. Oka, H. Tateishi-Karimata, T. Kirihata, Y. Sato, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai and N. Sugimoto

Mol. Biosys.   4   579 - 588   2008

Joint Work

Regulation of Telomerase Activity by the Thermodynamic Stability of a DNA?RNA Hybrid

N. Sugimoto

Angew. Chem. Int. Ed. Engl.   47   9034 - 9038   2008

Single Work

DOI

Synthesis, structure and thermal stability of fully hydrophobic porphyrin-DNA conjugates

T. Murashima, K. Hayata, Y. Saiki, J. Matsui, D. Miyoshi, T. Yamada, T. Miyazawa and N. Sugimoto

Tetrahedron Lett.   48   8514 - 8517   2007.11

Joint Work

Consecutive GC base pairs determine the energy barrier of DNA duplex formation under molecularly crowded conditions

X.B. Gu, S. Nakano and N. Sugimoto

Chem. Commun.     2750 - 2752   2007.07

Joint Work

Hydration regulates thermodynamic stability of DNA structures under molecular crowding conditions

D. Miyoshi, H. Karimata and N. Sugimoto

Nucleosides Nucleotides Nucleic Acids   26   589 - 595   2007.06

Joint Work

Regulation of DNA nucleases by molecular crowding

Y. Sasaki, D. Miyoshi and N. Sugimoto

Nucleic Acids Res.   35   4086 - 4093   2007.06

Joint Work

Effects of polyethylene glycol on a DNA duplex stability differed by the NaCl concentration

H. Karimata, S. Nakano and N. Sugimoto

Bull. Chem. Soc. Jpn.   80   1987 - 1994   2007.04

Joint Work

Artificial G-wire Switch with 2,2’-Bipyridine Units Responsive to Divalent Metal Ions

D. Miyoshi, H. Karimata, Z.M. Wang, K. Koumoto and N. Sugimoto

J. Am. Chem. Soc.   129   5919 - 5925   2007.04

Joint Work

Molecular Imprinting Under Molecular Crowding Conditions: an Aid to the synthesis of a High-capacity Polymeric Sorbent for Triazine Herbicides

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   2007.02

Joint Work

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides

S. Nakano, T. Kirihata, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai and N. Sugimoto

Nucleic Acids Res.   35   486 - 494   2007.01

Joint Work

Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions

杉本　直己

J. Am. Chem. Soc., 128     7957 - 7963   2006.11

Single Work

A novel stable RNA pentaloop that interacts specifically with a motif peptide of lambda-N protein

J. Kawakami, H. Tokitoh, Y. Tanabe and N. Sugimoto

Nucleosides Nucleotides Nucleic Acids   25   397 - 416   2006.11

Joint Work

DNA logic gates based on structural polymorphism of telomere DNAs responding to chemical input signals

D. Miyoshi, M. Inoue and N. Sugimoto

Angew. Chem. Int. Ed.   45   7716 - 7719   2006.11

Joint Work

Characterization of Structure and Stability of Long Telomeric DNA G-Quadruplexes

H.Q. Yu, D. Miyoshi and N. Sugimoto

J. Am. Chem. Soc.   128   15461 - 15468   2006.11

Joint Work

Molecularly-Imprinted Polymeric Logic Gates Selective for Predetermined Chemical Input Species

J. Matsui, T. Sodeyama, K. Tamaki and N. Sugimoto

Chem. Comm.   14   3217 - 3219   2006

Joint Work

A DNA duplex with Extremely Enhanced Thermal Stability Based on Controlled Immobilization on Gold Nanoparticles

K. Akamatsu, M. Kimura, Y. Shibata, S. Nakano, D. Miyoshi, H. Nawafune and N. Sugimoto

Nano Lett.   6   491 - 495   2006

Joint Work

Effect of molecular crowding on DNA polymerase activity

Y. Sasaki, D. Miyoshi and N. Sugimoto

Biotech. J.   1   440 - 446   2006

Joint Work

Site-Selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside

S. Nakano, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto

J. Am. Chem. Soc.   127   518 - 519   2005.11

Joint Work

DNA base flipping by a base pair-mimic nucleoside

S. Nakano, Y. Uotani, K. Uenishi, M. Fujii and N. Sugimoto

Nucleic Acids Res.   33   7111 - 7119   2005.11

Joint Work

Roles of Mg2+ in TPP-dependent riboswitch

T. Yamauchi, D. Miyoshi, T. kubodera, A. Nishimura, S. Nakai and N. Sugimoto

FEBS Lett.   579   2583 - 2588   2005

Joint Work

An SPR Sensor Chip for Selective Detection of Small Molecules Using Molecularly Imprinted Polymer with Embedded Au Nanoparticles

J. Matsui, K. Akamatsu, N. Hara, D. Miyoshi, H. Nawafune, K. Tamaki and N.Sugimoto

Anal. Chem.   77   4282 - 4285   2005

Joint Work

DNA-based biosensor for monitoring pHin vitro and in living cells

T. Ohmichi, Y. Kawamoto, P. Wu, D. Miyoshi, H. Karimata and N. Sugimoto

Biochemistry   44   7125 - 7130   2005

Joint Work

Drastic effect of a single base difference between human and tetrahymena telomere sequences on their structures under molecular crowding conditions

D. Miyoshi, H. Karimata and N. Sugimoto

Angew. Chem. Int. Ed. Engl.   44   3740 - 3744   2005

Joint Work

Nucleic Acid with guanidium modification exhibits efficient cellular uptake

T. Ohmichi, M. Kuwahara, N. Sasaki, M. Hasegawa, T. Nishikata, H. Sawai and N. Sugimoto

Angew. Chem. Int. Ed. Engl.   44   6682 - 6685   2005

Joint Work

Synthesis of Water-soluble Porphyrine and the Corresponding Hughly Planar Benzoporphyrin without meso-Substituents

T. Murashima, S. Tsujimoto, T. Yamada, T. Miyazawa, H. Uno, N. Ono and N.Sugimoto

Tetrahedron Lett.   46   113 - 116   2005

Joint Work

Central Dogma for a Molecular Design Based on DNA: DNB (Databasing/Designable Nanobio) →　ENB (Engineering Nanobio) → FNB (Functional Nanobio)

S. Nakano and N. Sugimoto

Chemistry Letters   34   1206 - 1211   2005

Joint Work

Thermodynamic and Kinetic Analyses of Nucleic Acid Structures for Pharmacogenomics

D. Miyoshi and N. Sugimoto

Current Pharmacogenomics   3   217 - 236   2005

Joint Work

A nano-circular single-stranded DNA as a novel tool for SNPs detection

T. Ohmichi, A. Takashima and N. Sugimoto

Nucleosides Nucleotides Nucleic Acids   24   359 - 366   2005

Joint Work

Thermodynamic Analysis of Duplex Formation of the Heterochiral DNA with L-Deoxyadenosine

J. Kawakami, K. Tsujita and N. Sugimoto

Anal.Sci.   21   77 - 82   2005

Joint Work

Introduction of peptide functions into DNA by nucleic asid peptides,NAPs

J. Kawakami, Z.M. Wang, H. Fujiki, S. Izumi and N. Sugimoto

Chem. Lett   33   1554 - 1555   2004

Joint Work

The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability

S. Nakano, H. Karimata, T. Ohmichi, J. Kawakami and N. Sugimoto

J. Am. Chem. Soc.   126   14330 - 14331   2004

Joint Work

Duplex dissociation of telomere DNAs induced by molecular crowding

D. Miyoshi, S. Matsumura, S. Nakano and N. Sugimoto

J. Am. Chem. Soc.   126   165 - 169   2004

Joint Work

Influences of ribonucleotide on a duplex conformation and its thermal stability:Study with the chimeric RNA-DNA strands

S. Nakano, T. Kanzaki and N. Sugimoto

J. Am. Chem. Soc.   126   1088 - 1095   2004

Joint Work

Composite of Au Nanoparticles and molecularly imprinted polymer as a sensing material

J. Matsui, K. Akamatsu, S. Nishiguchi, D. Miyoshi, H. Nawafune, K. Tamaki and N. Sugimoto

Anal. Chem.   76   1310 - 1315   2004

Joint Work

Mechanical force analysis of peptide interactions using atomic force microscopy

C. Nakamura, S. Takeda, M. Kageshima, M. Ito, N. Sugimoto, K. Sekizawa and J. Miyake

Biopolymers (Peptide Science)   76   48 - 54   2004

Joint Work

Synthetic cinchonidine receptors obtained by cross-linking linear poly(methacrylic acid) derivertives as an alternative molecular imprinting technique

J. Matsui, N. Minamimura, K. Nishimoto, K. Tamaki and N. Sugimoto

J. Chromatogr.   804   223 - 229   2004

Joint Work

An oligopeptide containing the C-terminal sequence of RNase A has a potent RNase A binding property

S. Nakano and N. Sugimoto

J. Am. Chem. Soc.   125   8728 - 8729   2003.11

Joint Work

Effect of putrescine and PEG on a structural transition of DNA G-quadruplex

D. Miyoshi, A. Nakao and N. Sugimoto

Nucleosides, Nucleotides Nucleic Acids   22   1591 - 1594   2003

Joint Work

Structural polymorphism of telomeric DNA regulated by pH and divalent cation

D. Miyoshi, S. Matsumura, W. Li and N. Sugimoto

Nucleosides, Nucleotides Nucleic Acids   22   203 - 221   2003

Joint Work

Large stabilization of a DNA duplex by the deoxyadenosine derivatives tethering an aromatic hydrocarbon group

S. Nakano, Y. Uotani, S. Nakashima, Y. Anno, M. Fujii and N. Sugimto

J. Am. Chem. Soc.   125   8086 - 8087   2003

Joint Work

Structural competition involving G-quadruplex DNA and its complement

W. Li, D. Miyoshi, S. Nakano and N. Sugimoto

Biochemistry   42   11736 - 11744   2003

Joint Work

Factors that contribute to efficient catalytic activity of a small Ca2+-dependent deoxyribozyme in relation to its RNA cleavage function

Y. Okumoto, Y. Tanabe and N. Sugimoto

Biochemistry   42   2158 - 2165   2003

Joint Work

Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+

D. Miyoshi, A. Nakao and N. Sugimoto

Nucleic Acids Res.   31   1156 - 1163   2003

Joint Work

Molecular crowding regulates the structural switch of the DNA G-quadruplex

D. Miyoshi, A. Nakao and N. Sugimoto

Biochemistry   41   15017 - 15024   2002

Joint Work

Immobilized small deoxyribozyme to distinguish RNA secondary structures

Y. Okumoto, T. Ohmichi and N. Sugimoto

Biochemistry   41   2769 - 2773   2002

Joint Work

Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation

P. Wu, S. Nakano and N. Sugimoto

Eur. J. Biochem.   269   2821 - 2830   2002

Joint Work

Effect of divalent cations and cytosine protonation on thermodynamic properties of intermolecular DNA double and triple helices

P. Wu, Y. Kawamoto, H. Hara and N. Sugimoto

J. Inorg. Biochem.   91   277 - 285   2002

Joint Work

Molecular imprinting in alcohols: utility of a pre-polymer based strategy for synthesizing stereoselective artificial receptor polymers in hydrophilic media

J. Matsui, K. Tamaki and N. Sugimoto

Anal. Chem. Acta.   466   11 - 15   2002

Joint Work

Characterization and thermodynamic properties of quadruplex/duplex competition.

W. Li, P. Wu, T. Ohmichi and N. Sugimoto

FEBS Lett.   526   77 - 81   2002

Joint Work

Long RNA dangling end has large energetic contribution to duplex stability

T. Ohmichi, S. Nakano, D. Miyoshi and N. Sugimoto

J. Am. Chem. Soc.   124   10367 - 10372   2002

Joint Work

Quartz crystal microbalance sensor targeting low molecular weight compounds using oligopeptide binder and peptide-immobilized latex beads

C. Nakamura, S. H. Song, S. M. Change, N. Sugimoto and J. Miyake

Anal. Chim. Acta.   469   183 - 188   2002

Joint Work

pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes

N. Sugimoto, P. Wu, H. Hara and Y. Kawamoto

Biochemistry   40   9396 - 9405   2001

Joint Work

A stable DNA tetraloop and its structural tolerance for modification

J. Kawakami, M. Yoneyama, D. Miyoshi and N. Sugimoto

Chem. Lett.     258 - 259   2001

Joint Work

Effect of extending the CD reference spectra to 168 nm on the prediction of protein secondary structures

J. Zou and N. Sugimoto

J. Biochem. Mol. Biol. Biophy   5   15 - 24   2001

Joint Work

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

N. Sugimoto

Biopolymers (Peptide Science)   55   416 - 424   2001

Single Work

Effect of divalent cations on antiparallel G-quartet structure of d(G4T4G4)

D. Miyoshi, A. Nakao, T. Toda and N. Sugimoto

FEBS Lett.   496   128 - 133   2001

Joint Work

Cu2+ inhibits the aggregation of amyloid b-peptide(1-42) in vitro

J. Zou, K. Kajita and N. Sugimoto

Angew. Chem. Int. Ed. Engl.   40   2274 - 2277   2001

Joint Work

Utilization of ribozymes for loss-of-function analyses of the early development of the ascidian Ciona intestinalis

M. Katano, A. Yamada, K. Tanaka, J. Murakami, K. Taira, J. Kawakami, N. Sugimoto and T. Nishikata

Mem. Konan Univ., Sci. Eng. Ser.   48   11 - 20   2001

Joint Work

Stabilization factors affecting duplex formation of peptide nucleic acid with DNA

N. Sugimoto, N. Satoh, K. Yasuda and S. Nakano

Biochemistry   40   8444 - 8451   2001

Joint Work

Detection of porphyrin using a short peptide immobilized on a surface plasmon resonance sensor chip

C. Nakamura, Y. Inuyama, K. Shirai, N. Sugimoto and J. Miyake

Biosensors & Bioelectronics   16   1095 - 1100   2001

Joint Work

Thermodynamic stability of base pairs between 2-hydroxyadenine and incoming nucleotides as a determinant of nucleotide incorporation specificity during replication

J. Kawakami, H. Kamiya, K. Yasuda, H. Fujiki, H. Kasai and N. Sugimoto

Nucleic Acids Res.   29   3289 - 3296   2001

Joint Work

Transition characteristics and thermodynamic analysis of DNA duplex formation: a quantitative consideration for the extent of duplex association

杉本　直己

Nucleic Acids Res., 28     4762 - 4768   2000.11

Single Work

In vitro selection of aptamers that act with Zn2+

J. Kawakami, H. Imanaka, Y. Yokota and N. Sugimoto

J. Inorg. Biochem.   82   197 - 206   2000

Joint Work

Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes

N. Sugimoto, M. Nakano and S. Nakano

Biochemistry   39   11270 - 11281   2000

Joint Work

A role of the Trp-His interaction in the conformational switch between a-helix and b-sheet in short alanine-based peptides

J. Zou and N. Sugimoto

J. Chem. Soc., Perkin Trans.   2   2135 - 2140   2000

Joint Work

Effects of metal ions and catalytic loop sequences on the complex formation of a deoxyribozyme and its RNA substrate

Y. Okumoto and N. Sugimoto

J. Inorg. Biochem.   82   189 - 195   2000

Joint Work

Ribozyme-metal ion interaction

N. Sugimoto and T. Ohmichi

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

Joint Work

Kinetic property of bulged helix formation: analysis of kinetic behavior using nearest-neighbor parameters

T. Ohmichi, H. Nakamuta, K. Yasuda and N. Sugimoto

J. Am. Chem. Soc.   122   11286 - 11294   2000

Joint Work

Development of small peptides recognizing a monosaccharide by combinatorial chemistry

N. Sugimoto, D. Miyoshi and J. Zou

Chem. Commun.     2295 - 2296   2000

Joint Work

Complexation of peptide with Cu2+ responsible to inducing and enhancing the formation of a-helix conformation

J. Zou and N. Sugimoto

BioMetals   13   349 - 359   2000

Joint Work

RNA cleavage by a short catalytic DNA

杉本　直己

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

Single Work

Nucleic acid duplex stability: influence of base composition on cation effects

S. Nakano, M. Fujimoto, H. Hara and N. Sugimoto

Nucleic Acids Res.   27   2957 - 2965   1999

Joint Work

A selection of short peptides that interact with a porphyrin as a small target by immobilized phage display

J. Kawakami, T. Kitano, and N. Sugimoto

Chem. Commun.     1765 - 1766   1999

Joint Work

Development of new biotechnology for the 21st century (I) role of side-chain interactions of peptides in some neurodegenerative diseases

J. Zou and N. Sugimoto

Mem. Konan Univ., Sci. Ser.   46   49 - 60   1999

Joint Work

Development of new biotechnology for the 21st century (II) structural and thermodynamic studies of PNA/DNA hybrids containing single bulge nucleotides

K. Yasuda, J. Kawakami and N. Sugimoto

Mem. Konan Univ., Sci. Ser.   46   61 - 69   1999

Joint Work

Stabilization of the a-helix conformation of short peptides

J. Zou and N. Sugimoto

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

Joint Work

Fishing out tryptophan selective peptides from combinatorial library

N. Sugimoto and H. Kazuta

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

Joint Work

Thermodynamic stabilities of the short PNA/DNA hybrid duplexes

N. Sugimoto and N. Sato

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

Joint Work

Effect of DNA sequences on its catalytic activity for porphyrin metallation

N. Sugimoto and T. Toda

Rep. Prog. Poly. Phys. Jpn.   42   573 - 576   1999

Joint Work

Effect of copper ion on conformations of short alanine-based peptides with single Trp/His stacking interactions

J. Zou and N. Sugimoto

Protein and Peptide Lett.   6   373 - 378   1999

Joint Work

a-b structural transition of short oligopeptides by water/organic solvent titration

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

Chem. Lett.     637 - 638   1999

Joint Work

A novel screening method for combinatorial chemistry for low affinity interactions

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

Chem. Commun.     677 - 678   1999

Joint Work

Effect of metal ions and sequence of deoxyribozymes on their RNA cleavage activity

N. Sugimoto, Y. Okumoto and T. Ohmichi

J. Chem. Soc., Perkin Trans.   2   1381 - 1386   1999

Joint Work

Selection of peptides that recognize tryptophan by combinatorial chemistry

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

Peptide Science     281 - 284   1999

Joint Work

Effect of substrate RNA sequence on the cleavage reaction by a short ribozyme

T. Ohmichi, Y. Okumoto and N. Sugimoto

Nucleic Acids Res.   26   5655 - 5661   1998

Joint Work

生命関連分子の微視的相互作用 (4)　ミスマッチを含む RNA/DNA ハイブリッドの安定性に及ぼすミスマッチの隣接塩基対の影響

杉本直己

甲南大学紀要、理学編   45   135 - 143   1998

Single Work

生命関連分子の微視的相互作用 (3)　RNA鎖を切断するデオキシリボザイムと金属イオンの関係

奥本泰秀, 川上純司, 杉本直己

甲南大学紀要、理学編   45   125 - 133   1998

Joint Work

Single-stranded DNA recognition of a 24-mer peptide derived from RecA protein

S. Nakano and N. Sugimoto

Bull. Chem. Soc. Jpn.   71   2205 - 2210   1998

Joint Work

Reaction field for efficient porphyrin metallation catalysis produced by self-assembly of a short DNA oligonucleotide

N. Sugimoto, T. Toda and T. Ohmichi

Chem. Commun.     1533 - 1534   1998

Joint Work

Thermodynamic stability of DNA triple helixes

N. Sugimoto and K. Aoki

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

Joint Work

Stability of internal single A・A mismatches in RNA/DNA hybrids

N. Sugimoto and M. Fujimoto

Rep. Prog. Poly. Phys. Jpn.   41   659 - 662   1998

Joint Work

Model reaction between TAR RNA and Tat protein in HIV

N. Sugimoto, I. Hirai and T. Ohmichi

Rep. Prog. Poly. Phys. Jpn.   41   663 - 666   1998

Joint Work

In vitro selection of aptamers that recognize a monosaccharide

J. Kawakami, Y. Kawase and N. Sugimoto

Anal. Chem. Acta.   365   95 - 100   1998

Joint Work

Effect of Cu2+ on complex formation between a deoxyribozyme and its substrates

N. Sugimoto and N. Wakizaka

Nucleosides & Nucleotides   17   565 - 574   1998

Joint Work

生命関連分子の微視的相互作用 (II)　ペプチドの分子内αヘリックスと分子間bシートの構造遷移

杉本　直己

甲南大学紀要、理学編, 44     17 - 26   1997.11

Single Work

Role of Nd3+ and Pb2+ on the RNA cleavage reaction by a small ribozyme

T. Ohmichi and N. Sugimoto

Biochemistry   36   3514 - 3521   1997

Joint Work

Roles of 2’-hydroxyls of leadzyme on an RNA cleavage

T. Ohmichi and N. Sugimoto

Bull. Chem. Soc. Jpn.   70   2743 - 2747   1997

Joint Work

Sandwiching interaction of peptides with a porphyrin

N. Sugimoto and S. Nakano

Chem. Lett.     939 - 940   1997

Joint Work

A 24 mer peptide derived from RecA protein can discriminate a single-stranded DNA from a double-stranded DNA

N. Sugimoto and S. Nakano

Chem. Commun.     2125 - 2126   1997

Joint Work

Stability of internal G・T mismatches in RNA/DNA hybrids

N. Sugimoto and M. Fujimoto

Rep. Prog. Poly. Phys. Jpn.   40   665 - 668   1997

Joint Work

Stability of the duplexes between a peptide nucleic acid and DNA

N. Sugimoto and Y. Okumoto

Rep. Prog. Poly. Phys. Jpn.   40   661 - 664   1997

Joint Work

Effect of cation concentration on stability of short DNA triplexes

N. Sugimoto and K. Aoki

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

Joint Work

Stability of long dangling ends on RNA double helices

杉本　直己

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

Single Work

Stability of long RNA/DNA hybrids

杉本　直己

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

Single Work

Interactions of 5-(1-pyrenyl)-10,15,20-tris(4-methylpyridinium)porphine with double-helix and triple-helix nucleic acids

杉本　直己

Nucleosides & Nucleotides, 15     743 - 747   1996.11

Single Work

The stability of DNA and RNA G-quartets

杉本　直己

Nucleosides & Nucleotides, 15     559 - 567   1996.11

Single Work

A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme

杉本　直己

Biochemistry, 35     648 - 658   1996.11

Single Work

Site-specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions

杉本　直己

FEBS Lett., 393     97 - 100   1996.11

Single Work

Stability of G・A mismatches in RNA/DNA hybrids and DNA double helices

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 39     675 - 678   1996.11

Single Work

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes

N. Sugimoto, S. Nakano, M. Yoneyama and K. Honda

Nucleic Acids Res.   24   4501 - 4505   1996

Joint Work

生命関連分子の微視的相互作用 (I)　バルジを含むDNA二重らせんの熱力学的安定性に及ぼすイノシン置換の影響

楢木泰俊彦, 川上純司, 杉本直己

甲南大学紀要、理学編   43   37 - 47   1996

Joint Work

Energetics of oligodeoxyribonucleotides with a bulge

杉本　直己

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

Single Work

核酸の機能と構造に関する微視的相互作用XI　DNAの一本鎖部位の安定性とペプチド認識における役割

杉本　直己

甲南大学紀要、理学編, 42     37 - 43   1995.11

Single Work

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes

杉本　直己

Biochemistry, 34     11211 - 11216   1995.11

Single Work

Influence of a-deoxyadenosine on the stability and structure of DNA. Thermodynamic and molecular mechanics studies

杉本　直己

Biochemistry, 34     6947 - 6955   1995.11

Single Work

On the mechanism of preferential incorporation of dAMP at abasic sites in translational DNA synthesis. Role of proofreading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site

杉本　直己

Nucleic Acids Res., 23     123 - 129   1995.11

Single Work

Energetics of oligodeoxyribonucleotides with 5-methylcytosine

杉本　直己

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

Single Work

RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs have identical stability

杉本　直己

FEBS Lett., 354     74 - 78   1994.11

Single Work

The study of biomodel solution containing various salts: fourier transform infrared attenuated total reflectance (FTIR ATR) spectrometry of phosphate-family solution

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 37     815 - 818   1994.11

Single Work

Application of the thermodynamic parameters of DNA stability prediction to double-helix formation of deoxyribooligonucleotides

杉本　直己

Nucleosides & Nucleotides, 13     1311 - 1317   1994.11

Single Work

核酸の構造と機能に関する微視的相互作用X　連続配列をもつ核酸の特異的構造とその安定性

杉本　直己

甲南大学紀要、理学編, 41     23 - 30   1994.11

Single Work

Effect of Na+ and K+ ions on the stability of DNA G-quartet

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 37     823 - 824   1994.11

Single Work

Thermodynamic study of RNA・DNA hybrids, (rA)8・(dT)8 and (dA)8・(rU)8

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 37     819 - 822   1994.11

Single Work

FTIR ATR法による無電解パラジウム リン合金めっき浴中の浴成分のモニタリング

杉本　直己

表面技術, 45     85 - 87   1994.11

Single Work

核酸の構造と機能に関与する微視的相互作用IX　RNAの二次構造安定性へのダングリング・エンドとヘアピン・ループ部位の寄与

杉本　直己

甲南大学紀要、理学編, 40     83 - 92   1993.11

Single Work

Secondary structures of wild-type and mutant hairpin ribozymes

杉本　直己

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

Single Work

Relationship between catalytic activity and secondary structure of a hammerhead ribozyme: a study using thermodynamic parameters for RNA structure prediction

杉本　直己

Supramol. Chem., 2     99 - 102   1993.11

Single Work

Effect of GA and AA mismatches on RNA double helix

杉本　直己

Chemistry Express, 8     309 - 312   1993.11

Single Work

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

杉本　直己

Chemistry Express, 8     137 - 140   1993.11

Single Work

Effect of berenil on stability of double-helix of octamers of deoxyriboadenylic and deoxyribothymidylic acids

杉本　直己

Chemistry Express, 8     313 - 316   1993.11

Single Work

Effect of GA and AA mismatches on interaction between substrate RNA and active site of ribozyme

杉本　直己

Chemistry Express, 8     613 - 616   1993.11

Single Work

Kinetics of double-helix melting of self-complementary deoxyribooctanucleotid d(TATGCATA)

杉本　直己

Chemistry Express, 7     325 - 328   1992.11

Single Work

Melting kinetics of self-complementary double-helix by a fluorescent oligonucleotide AUGCAUeA

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 35     745 - 746   1992.11

Single Work

Effects of dimidium and ethidium on melting of double-helix by octamers of deoxyriboadenylic and deoxyribothymidylic acids

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 35     741 - 744   1992.11

Single Work

Stability of right-handed and left-handed double-helices of self-complementary hexanucleotide CGCGCG

杉本　直己

Chemistry Express, 7     493 - 496   1992.11

Single Work

Stability of double-helix by deoxyribooligonucleotides containing 5-trifluoro-methyluracil and 5-cyanouracil

杉本　直己

Chemistry Express, 7     405 - 408   1992.11

Single Work

Melting behavior and stability of (dA)8・(dT)8 double helix

杉本　直己

Nucleosides & Nucleotides, 11     515 - 520   1992.11

Single Work

Thermodynamics of triple-helix and double-helix formations by octamers of deoxyriboadenylic and deoxyribothymidylic acids

杉本　直己

Bull. Chem. Soc. Jpn., 65     535 - 540   1992.11

Single Work

核酸の構造と機能に関与する微視的相互作用VIII　GC塩基対からなるRNA・DNAキメラ体の特性

杉本　直己

甲南大学紀要、理学編, 39     189 - 204   1992.11

Single Work

核酸の構造と機能に関与する微視的相互作用VII　RNA-DNAハイブリッド型オクタヌクレオチドr(CU)4・d(AG)4の二重らせんの性質

杉本　直己

甲南大学紀要、理学編, 39     29 - 35   1992.11

Single Work

Temperature and pressure effects on equilibrium of double-helix to single-strands by octamers of deoxyriboadenylic and deoxyribothymidylic acids

杉本　直己

Chemistry Express, 7     273 - 276   1992.11

Single Work

Effect of base-triplet formation on binding of tetrakis(1-methyl-4-pyridyl)porphine with poly(A)・poly(U)

杉本　直己

Chemistry Express, 7     61 - 64   1992.11

Single Work

Salt effects on binding of propidium with poly(A)・poly(U) and poly(I)・poly(C)

杉本　直己

Chemistry Express, 7     57 - 60   1992.11

Single Work

Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops

杉本　直己

Biochemistry, 30     6428 - 6436   1991.11

Single Work

Double-helix melting of octamers of deoxyriboadenylic and deoxyribothymidylic acids in the presence of ethidium

杉本　直己

Chem. Lett     9 - 12   1991.11

Single Work

Ab initio MO calculations of model molecules for ribozyme reaction including an Mg2+ ion

杉本　直己

Chem. Lett.,     2119 - 2122   1991.11

Single Work

Relationship between catalytic activity and stability of a hammerhead ribozyme with/without a hairpin

杉本　直己

Chemistry Express, 6,     691 - 694   1991.11

Single Work

The effect of actinomycin D on the transition of poly(dG-dMeC) from right-handed to left-handed form

杉本　直己

Chemistry Express, 6,     507 - 510   1991.11

Single Work

Stabilization energy of the catalytic core of the Tetrahymena ribozyme

杉本　直己

Chem. Lett     345 - 348   1991.11

Single Work

核酸の構造と機能に関与する微視的相互作用VI　DNAオリゴマーの三重らせん形成

杉本　直己

甲南大学紀要、理学編, 38,     99 - 114   1991.11

Single Work

Self-complementary double-helix formation of d(TCATGA) and d(TGATCA)

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 34,     647 - 648   1991.11

Single Work

Triple-helix formation of (dA)8 and (dT)8

杉本　直己

Rep. Prog. Poly. Phys. Jpn.   34   643 - 646   1991.11

Single Work

Effect of unpaired terminal nucleotides of substrate RNAs on the RNA ligation with T4 RNA ligase

杉本　直己

Bull. Chem. Soc. Jpn., 64,     2978 - 2982   1991.11

Single Work

Effect of dangling ends on the double-helix melting of ribooligonucleotides at different Na+ concentrations

杉本　直己

Chem. Lett.     1291 - 1294   1991.11

Single Work

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

杉本　直己

Chem. Lett.     1287 - 1290   1991.11

Single Work

核酸の構造と機能に関与する微視的相互作用V　非塩基対部位をもつRNA二重らせんの異常な融解挙動

杉本　直己

甲南大学紀要、理学編, 38     43 - 52   1991.11

Single Work

Influence of cis-diamminedichloroplatinum (II) on the reaction of propidium with RNAs

杉本　直己

Chemistry Express, 6     209 - 212   1991.11

Single Work

Influence of mononucleotides on the reaction of tetrakis(4-N-methylpyridyl)porphine with RNAs

杉本　直己

Chemistry Express, 6     205 - 208   1991.11

Single Work

Application of energy parameters of RNA stability to the reaction of hammerhead ribozymes

杉本　直己

Chemistry Express, 5,     585 - 588   1990.11

Single Work

Stability of oligonucleotide YAUGCAU helices

杉本　直己

Chemistry Express, 5,     581 - 584   1990.11

Single Work

Binding behavior of tetrakis(4-N-methylpyridyl)porphine with DNA in ethanol-buffer solution

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 33,     733 - 734   1990.11

Single Work

Double-helix formation of CGCAGCG

杉本　直己

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

Single Work

Salt effects on equilibrium and kinetics of the reaction of tetrakis(1-methyl-4-pyridinio)porphine with DNA

杉本　直己

Bull. Chem. Soc. Jpn., 63,     1641 - 1646   1990.11

Single Work

核酸の構造と機能に関与する微視的相互作用III　塩基対逐次形成モデルのDNAオリゴマーへの適用

杉本　直己

甲南大学紀要、理学編, 37,     77 - 86   1990.11

Single Work

Salt and pressure effects on reaction of drugs binding to nucleic acids

杉本　直己

Review of Physical Chemistry of Japan, Special issue,     39 - 48   1990.11

Single Work

Thermodynamics and kinetics of propidium binding to poly(A)・poly(U) in aqueous solution

杉本　直己

Bull. Chem. Soc. Jpn., 63,     697 - 701   1990.11

Single Work

Double-helix formation by oligodeoxyriboadenylic and oligodeoxyribothymidylic acids

杉本　直己

Chemistry Express,   5   765 - 768   1990.11

Single Work

Activation parameters for the proton-transfer reaction of 1,8-bis(dimethylamino) naphthalene in micellar solution

杉本　直己

Chemistry Express, 5,     41 - 44   1990.11

Single Work

Cationic micellar effect upon the protonation of 2,4-dimethyl-3-ethylpyrrole

杉本　直己

Chemistry Express, 5,     925 - 928   1990.11

Single Work

Melting of double-helix of the decamers of deoxyriboadenylic and deoxyribothymidylic acids in the presence of ethidium

杉本　直己

Chemistry Express, 5,     677 - 680   1990.11

Single Work

Stability of oligonucleotide GGCGUC and CGGCUG helices

杉本　直己

Chemistry Express, 5,     673 - 676   1990.11

Single Work

核酸の構造と機能に関与する微視的相互作用IV　核酸ポリマーと薬物の反応

杉本　直己

甲南大学紀要、理学編, 37,     163 - 175   1990.11

Single Work

Reactions of tetrakis(4-N-methylpyridyl)porphine and propidium with poly(A)・poly(U) and poly(I)・poly(C)

杉本　直己

Chemistry Express, 5,     399 - 402   1990.11

Single Work

Salt effect on double-helix formation of AUGCAU

杉本　直己

Chemistry Express, 5,     249 - 252   1990.11

Single Work

Double-helix melting of octamers of deoxyriboguanylic and deoxyribocytidylic acids

杉本　直己

Chemistry Express, 5,     765 - 768   1990.11

Single Work

Inhibition of deoxyribooligonucleotides on the circle opening reaction of the intervening sequence from Tetrahymena thermophila

杉本　直己

Chem. Lett.,     747 - 748   1990.11

Single Work

核酸の構造と機能に関与する微視的相互作用I　RNAの二重らせん形成

杉本　直己

甲南大学紀要、理学編, 36,     41 - 50   1989.11

Single Work

Effect of a-cyclodextrin inclusion on kinetics of complex formation between Co(II) Ion and pyridine-2-azo-p-dimetylaniline

杉本　直己

Chemistry Express, 4,     475 - 478   1989.11

Single Work

Ethanol and salts effects on the reaction of azure B with poly(A)poly(U) and poly(dA)poly(dT)

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 32,     715 - 718   1989.11

Single Work

Mg2+ contribution to a formation of active form of ribozyme

杉本　直己

Rep. Prog. Poly. Phys. Jpn., 32,     711 - 714   1989.11

Single Work

Behaviors of AA, CA, GA, terminal mismatches and UA terminal base-pair in ribooligonucleotide

杉本　直己

Chemistry Express, 4,     401 - 404   1989.11

Single Work

Propidium binding to DNA and tRNA in solution

杉本　直己

Chemistry Express, 4,     385 - 388   1989.11

Single Work

Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: evidence for substrate and Mg2+ binding interactions

杉本　直己

Nucleic Acids Res., 17,     355 - 371   1989.11

Single Work

Inclusion kinetics of crystal violet into g-cyclodextrin

杉本　直己

Chemistry Express, 4,     65 - 68   1989.11

Single Work

Binding of pyridine-2-azo-p-dimethylaniline to DNA in ethanol-water solution

杉本　直己

Chemistry Express, 4,     29 - 32   1989.11

Single Work

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

杉本　直己

Chem. Lett.,     2223 - 2226   1989.11

Single Work

Ethanol effect on the reactions of DNA with actinomycin D and tetrakis(4-N-methylpyridyl)porphine

杉本　直己

Chemistry Express, 4,     661 - 664   1989.11

Single Work

核酸の構造と機能に関与する微視的相互作用II　テトラヒメナ・リボザイムの活性位の構造

杉本　直己

甲南大学紀要、理学編, 36,     89 - 97   1989.11

Single Work

Application of improved free-energy parameters of RNA stability to codon-anticodon interactions

杉本　直己

Bull. Chem. Soc. Jpn., 62,     3745 - 3747   1989.11

Single Work

Thermodynamic parameters for melting of the stem regions in the self-splicing intervening sequence from Tetrahymena

杉本　直己

Chemistry Express, 4,     613 - 616   1989.11

Single Work

Salt effect on the reactions of DNA with actinomycin D and tetrakis(4-N-methylpyridyl)porphine

杉本　直己

Chemistry Express, 4,     609 - 612   1989.11

Single Work

Reaction of a circularized intervening sequence with the dinucleotide CU at high temperatures

杉本　直己

Chemistry Express, 4,     405 - 408   1989.11

Single Work

Hydrogen bonding and stacking contributions to nucleic acid stability

杉本　直己

Structure and Expression (R. H. Sarma and M. H. Sarma, Eds.), Adenine Press, NY, 1,     249 - 259   1988.11

Single Work

核酸の構造と機能に及ぼす非塩基対部位の影響

杉本　直己

甲南大学紀要、理学編, 35,     103 - 114   1988.11

Single Work

Pressure effect on ethidium binding to DNA

杉本　直己

Chemistry Express, 3,     487 - 490   1988.11

Single Work

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

杉本　直己

Chemistry Express, 3,     483 - 486   1988.11

Single Work

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

杉本　直己

Biochemistry, 27,     6384 - 6392   1988.11

Single Work

Micellar effect on rate of proton-transfer reaction of 1,8-bis(dimethylamino) naphthalene in aqueous solution

杉本　直己

Chemistry Express, 3,     407 - 410   1988.11

Single Work

Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic Acid

杉本　直己

Biochemistry, 26,     4554 - 4558   1987.11

Single Work

Free energy increments for hydrogen bonds in nucleic acid base pairs

杉本　直己

J. Am. Chem. Soc., 109,     3783 - 3785   1987.11

Single Work

Improved parameters for prediction of RNA structure

杉本　直己

Cold Spring Harbor Symposia on Quantitative Biology, 52,     123 - 133   1987.11

Single Work

Sequence dependence for the energetics of terminal mismatches in ribooligonucleotides

杉本　直己

Biochemistry, 26,     4559 - 4562   1987.11

Single Work

Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: An empirical estimate of the energetics of hydrogen bonds in nucleic acids

杉本　直己

Biochemistry, 25,     3214 - 3219   1986.11

Single Work

Improved free-energy parameters for predictions of RNA duplex stability

杉本　直己

Proc. Natl. Acad. Sci. USA, 83,     9373 - 9377   1986.11

Single Work

Energetics of internal GU mismatches in ribooligonucleotide helixes

杉本　直己

Biochemistry, 25,     5755 - 5759   1986.11

Single Work

Kinetic hydrogen isotope effects in the reaction between 2,4,6-trinitrotoluene and 1-ethylpiperidine in acetonitrile. The effect of pressure

杉本　直己

J. Chem. Soc., Faraday Trans. 1,81,     2959 - 2966   1985.11

Single Work

Substituent effects on proton tunnelling. Reaction between 2,4,6-trinitrotoluene and 1-substituted piperidines in acetonitrile

杉本　直己

J. Chem. Soc., Faraday Trans. 1, 81,     1441 - 1445   1985.11

Single Work

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

    1985.03

Single Work

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

杉本　直己

J. Chem. Soc., Perkin Trans. 2,     655 - 659   1984.11

Single Work

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

杉本　直己

Bull. Chem. Soc. Jpn.,57,     366 - 369   1984.11

Single Work

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

杉本　直己

J. Am. Chem. Soc., 105,     7676 - 7680   1983.11

Single Work

Kinetics and tunneling in the proton- and deuteron-transfer reaction between 2,4,6,-trinitrotoluene and 1,8-diazabicyclo[5.4.0]undec-7-ene in some aprotic solvents

杉本　直己

J. Phys. Chem.   86   3418 - 3423   1982.11

Single Work

Pressure effect on proton/deuteron transfer reactions of 4-nitrophenylnitromethane + N,N,N’,N’-tetramethylguanidine (TMG), 2,4,6-trinitorotoluene (TNT) + TMG, and TNT + 1,8-diazabicyclo[5.4.0]undec-7-ene in some aprotic solvents

杉本　直己

High Pressure in Research and Industry,2,     676 - 679   1982.11

Single Work

Influence of pressure on primary kinetic isotope effects of the proton-transfer reaction between 4-nitrophenylnitromethane and 1,1’,3,3’-tetramethylguanidine in toluene and dichloromethane

杉本　直己

Bull. Chem. Res., Kyoto Univ., 59,     63 - 71   1981.11

Single Work

Pressure effect on rate constants of proton-transfer reactions from 2,4,6-trinitrotoluene to N,N,N’,N’-tetramethylguanidine and 1,8-diazabicyclo[5.4.0]undec-7-ene in acetonitrile and dichloromethane

杉本　直己

Bull. Chem. Soc. Jpn., 54,     2598 - 2602   1981.11

Single Work

High-pressure stopped-flow kinetics of proton-transfer reaction between 4-nitrophenylnitromethane and 1,1’,3,3’-tetramethylguanidine in aprotic solvents

杉本　直己

Chem. Lett     887 - 890   1980.11

Single Work