Faculty Information - Gota Kawai

1.	2019/08～2024/03	The Chem-Bio Informatics Society
2.	2010/01～	The Japanese Society of Polyamine Research
3.	2010/01～	∟ Councilor
4.	2025/01	∟ Chairperson

■ Acquisition patent

1.	2006/05/02	Oligonucleotides labeled with Stable Isotopes and Method for detecting the same
2.	2006/03/09	Oligonucleotides labeled with Stable Isotopes and Method for detecting the same

■ Works

1.	Book	Essential Structural Biology (Collaboration) 2018/02
2.	Book	Experimental Approaches of NMR spectroscopy (Collaboration) 2018/01
3.	Article	Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of the bulged residues J. Biochem. 178,pp.229-236 (Collaboration) 2025
4.	Article	Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and IL-33 regulation via Alu elements JCI Insight 10,pp.e187172 (Collaboration) 2025
5.	Article	NMR analysis of interaction between RNA structure elements and small molecules J. Biochem. 178,pp.1-9 (Collaboration) 2025
6.	Article	Polyamines enhance repeat-associated non-AUG translation from CCUG repeats by stabilizing the tertiary structure of RNA J. Biol. Chem. 301,pp.108251 (Collaboration) 2025
7.	Article	Specific Interaction between a Fluoroquinolone Derivative, KG022, and RNAs with a Single Bulge Biochemistry (Collaboration) 2025
8.	Article	The role of spatial arrangement of aromatic rings on the binding of N,N'-diheteroaryl guanidine ligands to the G2C4/G2C4 motif DNA Phys Chem Chem Phys. 27,pp.3341-3350 (Collaboration) 2025
9.	Article	NMR analysis of a loop-bulge structure of UUCGA pentaloop Biochemical and Biophysical Research Communications 691,pp.149327 (Collaboration) 2024/01
10.	Article	Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus J. Biochem. 175,pp.675-680 (Collaboration) 2024
11.	Article	Cis-Allosteric Regulation of HIV-1 Reverse Transcriptase by Integrase Viruses 15,pp.31 (Collaboration) 2023
12.	Article	Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8 Acta Cryst. F F79,pp.278-284 (Collaboration) 2023
13.	Article	Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3ʹ adjacent to the bulged residues Front. Mol. Biosci. 10,pp.1145528 (Collaboration) 2023
14.	Article	Non-coding RNAs and functional RNA elements in Thermus thermophilus, J. Gen. Appl. Microbiol. 69 (Collaboration) 2023
15.	Article	Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins J. Am. Chem. Soc 145(37),pp.20432-20441 (Collaboration) 2023
16.	Article	2-Amino-1,8-naphthyridine Dimer (ANP77), a High-Affinity Binder to the Internal Loops of C/CC and T/CC Sites in Double-Stranded DNA The Journal of Organic Chemistry 87,pp.340-350 (Collaboration) 2022
17.	Article	Dye-Conjugated Spinach RNA by Genetic Alphabet Expansion Chem. Eur. J. 28,pp.e202104396 (Collaboration) 2022
18.	Article	Interaction between a fluoroquinolone derivative and RNAs with a single bulge J. Biochem. 171,pp.239-244 (Collaboration) 2022
19.	Article	T-hairpin structure found in the RNA element involved in piRNA biogenesis RNA 28,pp.541-550 (Collaboration) 2022
20.	Article	Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes Int. J. Mol. Sci. 22,pp.9708 (Collaboration) 2021
21.	Article	Identification of a short form of a Caenorhabditis elegans Y RNA homolog Cel7 RNA BBRC 557,pp.104-109 (Collaboration) 2021
22.	Article	Influence of the 5’‑terminal sequences on the 5’‑UTR structure of HIV‑1 genomic RNA Scientific Reports 11,pp.10920 (Collaboration) 2021
23.	Article	Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model Nature Communications 12,pp.236 (Collaboration) 2021
24.	Article	Cytotoxic Mechanism of Excess Polyamines Functions through Translational Repression of Specific Proteins Encoded by Polyamine Modulon Int. J. Mol. Sci. 21,pp.2406 (Collaboration) 2020
25.	Article	Epigenetic TET Catalyzed Oxidative Products of 5-Methylcytosine Impede Z-DNA Formation of CG Decamers ACS Omega 5,pp.8056-8064 (Collaboration) 2020
26.	Article	Impact of 5'-end nucleotide modifications of HIV-1 genomic RNA on reverse transcription Biophysical Research Communications 516(4),pp.1145-1151 (Collaboration) 2019/09/03
27.	Article	Crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus with an extra C-terminal domain Acta Crystallographica Section F 75,pp.450-454 (Collaboration) 2019/06
28.	Article	Inhibition of pre-miRNA-136 processing by Dicer with small molecule BzDANP suggested the formation of ternary complex of pre-miR-136–BzDANP–Dicer Bioorganic & Medicinal Chemistry 27,pp.2140-2148 (Collaboration) 2019/05/15
29.	Article	Distinct RNA recognition mechanisms in closely related LINEs from zebrafish Nucleosides, Nucleotides, and Nucleic Acids 38(4),pp.294-304 (Collaboration) 2019/04/03
30.	Article	Conformational Changes in HIV-1 Reverse Transcriptase that Facilitate Its Maturation Structure 27,pp.1581-1593 (Collaboration) 2019
31.	Article	Synthesis of a protected ribonucleoside phosphoramidite-linked spin label via an alkynyl chain at the 5' position of uridine Synthetic Communications 49(1),pp.136-145 (Collaboration) 2019
32.	Article	Polyamines stimulate the CHSY1 synthesis through the unfolding of the RNA G-quadruplex at the 50-untraslated region Biochemical Journal 475(23),pp.3797-3812 (Collaboration) 2018/12
33.	Article	NMR monitoring of the SELEX process to confirm enrichment of structured RNA Scientific Reports 7 (Collaboration) 2017
34.	Article	RNomics of Thermus themophilus HB8 by DNA microarray and next-generation sequencing Journal of Biochemistry (Collaboration) 2017
35.	Article	Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish Journal of Biochemistry (Collaboration) 2017
36.	Article	Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding Journal of Biochemistry 161,pp.197-206 (Collaboration) 2017
37.	Article	Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus Journal of Biochemistry 159,pp.313-321 (Collaboration) 2016
38.	Article	Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii Acta Crystallographica Section F 72,pp.627-635 (Collaboration) 2016
39.	Article	Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein Biochemistry 55,pp.6221-6229 (Collaboration) 2016
40.	Article	Sequence and structure analysis of a mirror tRNA located upstream of the cytochrome oxidase I mRNA in mouse mitochondria Journal of Biochemistry 159,pp.341-350 (Collaboration) 2016
41.	Article	Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase Acta Crystallographica Section F 72,pp.507-515 (Collaboration) 2016
42.	Article	A new role for PGA1 in inhibiting hepatitis C virus-IRES-mediated translation by targeting viral translation factors Antiviral Research 117,pp.1-9 (Collaboration) 2015
43.	Article	Fate of HIV-1 cDNA intermediates during reverse transcription is dictated by transcription initiation site of virus genomic RNA Scientific Reports 5,pp.17680 (Collaboration) 2015
44.	Article	In NMR tube transcription for rapid screening of RNA conformation Nucleosides, Nucleotides, and Nucleic Acids 34,pp.103-113 (Collaboration) 2015
45.	Article	Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing Genomics 106,pp.122-128 (Collaboration) 2015
46.	Article	Fabrication and BSA adsorption/desorption properties of titania/silica composite films modified with silane coupling agents JOURNAL OF OLEO SCIENCE 63,pp.1077-1083 (Collaboration) 2014
47.	Article	Microtubule-associated protein (MAP) 4 interacts with microtubules in an intrinsically disordered manner Bioscience, Biotechnology, and Biochemistry 78,pp.1864-1870 (Collaboration) 2014
48.	Article	The Characteristic Structure of Anti-HIV Actinohivin in Complex with Three HMTG D1 Chains of HIV-gp120 Chembiochem 15,pp.2766-2773 (Collaboration) 2014
49.	Article	Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain J. Biochem. 154,pp.513-519 (Collaboration) 2013
50.	Article	The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element RNA 19,pp.927-936 (Collaboration) 2013
51.	Article	Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq Nucleic Acids Reseasch 40,pp.1856-1867 (Collaboration) 2012
52.	Article	Crystal Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8 Acta Crystallography F 68,pp.14-19 (Collaboration) 2012
53.	Article	Solution structure of S-DNA formed by covalent base pairing involving a disulfide bond Organic & Biomolecular Chemistry 10,pp.7327-7333 (Collaboration) 2012
54.	Article	Crystal Structures of Glycinamide Ribonucleotide Synthetase, PurD, from Thermophilic Eubacteria J. Biochem. 148,pp.429-438 (Collaboration) 2010/10
55.	Article	Crystal Structures of Hypoxanthine-Guanine Phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8 Acta Cryst. F66,pp.893-898 (Collaboration) 2010/08
56.	Article	Expression, crystallization and preliminary crystallographic analysis of RNA binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer Acta Cryst. F66,pp.563-566 (Collaboration) 2010/05
57.	Article	Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus RNA 15,pp.420-431 (Collaboration) 2009/03
58.	Article	Modeling the Chain Entropy of Biopolymers: Unifying Two Different Random Walk Models under One Framework J. Comput. Sci. Syst. Biol. 2,pp.1-23 (Collaboration) 2009/02
59.	Article	Selective structural change of bulged-out region of double-stranded RNA containing bulged nucleotides by spermidine Biochem. Biophys. Res. Commun 370,pp.572-577 (Collaboration) 2008/06
60.	Article	Recognition of a bulged RNA by peptides derived from the influenza NS1 protein J. Biochem. 143,pp.339-347 (Collaboration) 2008/03
61.	Article	Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding PLoS ONE 2,pp.e905 (Collaboration) 2007/09
62.	Article	Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2 Nucleic Acids Res. 34,pp.5184-5193 (Collaboration) 2006/09
63.	Article	Structural Analysis of a Mutant of the HIV-1 Integrase Zinc Finger Domain that Forms a Single Conformation J. Biochem. 139,pp.753-759 (Collaboration) 2006/04
64.	Article	A method for finding optimal RNA secondary structures using a new entropy model (vsfold) Nucleosides, Nucleotides and Nucleic Acids 25,pp.171-189 (Collaboration) 2006/01
65.	Article	¹H, ¹³C and ¹⁵N resonance assignments of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus J. Biomol. NMR 36,pp.16 (Collaboration) 2006
66.	Article	Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus Nucleosides, Nucleotides and Nucleic Acids 25,pp.383-395 (Collaboration) 2006
67.	Article	Interaction analysis between tmRNA and SmpB from Thermus Thermophilus J. Biochem. 138,pp.729-739 (Collaboration) 2005/12
68.	Article	Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers J. Biochem. 138,pp.583-592 (Collaboration) 2005/11
69.	Article	Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2 RNA 10,pp.1380-1387 (Collaboration) 2004/09
70.	Article	Analysis of local convergence in NMR structure calculation for RNA by a classification system for nucleic acid structure, CSNA Nucleosides, Nucleotides and Nucleic Acids 23,pp.691-700 (Collaboration) 2004/06
71.	Article	NMR study on the Photo-responsive DNA Tethering an Azobenzene. Assignment of the Absolute Configuration of Two Diastereomers and Structure Determination of their Duplexes in the trans-Form J. Am. Chem. Soc. 125,pp.16408-16415 (Collaboration) 2003/12
72.	Article	Role of the Zinc Fingers of HIV-1 Nucleocapsid Protein for Maturation of Genomic RNA J. Biochem. 134,pp.637-639 (Collaboration) 2003/12
73.	Article	RNA LEGO: Magnesium-dependent formation of specific RNA assemblies through kissing interactions Chem. & Biol. 10,pp.645-654 (Collaboration) 2003/07
74.	Article	Conformational properties of 2',5' linked Rp- and Sp-phosphorothioate oligoadenylates studied by circular dichroism and NMR Biopolymers 72,pp.48-58 (Collaboration) 2003/01
75.	Article	Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus FEBS lett. 535,pp.94-100 (Collaboration) 2003/01
76.	Article	Polyamines Enhance Synthesis of the RNA polymerase sigma-38 Subunit by Suppression of an Amber Termination Codon in the Open Reading Frame J. Biol. Chem. 277,pp.37139-37146 (Collaboration) 2002/10
77.	Article	Binding of ribosome recycling factor (RRF) to ribosomes - Comparison with tRNA J. Biol. Chem. 277,pp.35847-35852 (Collaboration) 2002/09
78.	Article	Classification of RNA Structures Based on Hydrogen Bond and Base-Base Stacking Patterns: Application for NMR structures J. Biochem. 132,pp.211-215 (Collaboration) 2002/08
79.	Article	Solution structure of a SRP19 binding domain in human SRP RNA J. Biochem. 132,pp.177-182 (Collaboration) 2002/08
80.	Article	30. Redox-coupled Conformational Alternations in Cytochrome c₃ from D. vulgaris Miyazaki F on the Basis of its Reduced Solution Structure J. Mol. Biol. 319,pp.767-778 (Collaboration) 2002/07
81.	Article	Analysis of Relative Positions of Ribonucleotide Bases in a Crystal Structure of Ribosome Nucleosides, Nucleotides and Nucleic Acids 21,pp.449-462 (Collaboration) 2002/06
82.	Article	Solution Structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the Tetrahymena group I intron RNA 8,pp.440-451 (Collaboration) 2002/04
83.	Article	Inhibition of human immunodeficiency virus type 1 activity in vitro by a new self-stabilized oligonucleotide with guanosine-thymidine quadruplex motifs J. Virology 76,pp.3015-3022 (Collaboration) 2002/03
84.	Article	Two basic regions of NCp7 are sufficient for conformational conversion of HIV-1 dimerization initiation site from kissing-loop dimer to extended-duplex dimer J. Biol. Chem. 276,pp.31274-31278 (Collaboration) 2001/08
85.	Article	Minimal functional structure of Escherichia coli 4.5S RNA required for binding EF-G J. Biol. Chem. 276,pp.22844-22849 (Collaboration) 2001/06
86.	Article	Polyamine enhancement of the synthesis of adenylate cyclase at the translational level and the consequential stimulation of the synthesis of the RNA polymerase sigma-28 subunit J. Biol. Chem. 276(19),pp.16289-16295 (Collaboration) 2001/05
87.	Article	Self-cleavage of p2Sp1 RNA with Mg²⁺ and non-ionic detergent (Brij 58). J. Inorg. Biochem. 82,pp.215-219 (Collaboration) 2000/11
88.	Article	Interactions of a didomain fragment of the Drosophila Sex-lethal protein with single-stranded uridine-rich oligonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective [5-²H]uridine substitutions J. Biomol. NMR 17(2),pp.153-165 (Collaboration) 2000/06
89.	Article	NMR analysis on intra- and inter-molecular stems in the dimerization initiation site of the HIV-1 genome J. Biochem. 127(4),pp.681-639 (Collaboration) 2000/04
90.	Article	Structural Requirement for the Two-Step Dimerization of Human Immunodeficiency Virus Type-1 Genome RNA 6(1),pp.96-102 (Collaboration) 2000/01
91.	Article	Polyamine Stimulation of the Synthesis of Oligopeptide-binding Protein (OppA): Involvement of a structural change of the Shine-Dalgarno sequence and the initiation codon AUG in OppA mRNA J. Biol. Chem. 274,pp.22723-22728 (Collaboration) 1999/12
92.	Article	The stem hairpin loop structure of p2Sp1 RNA is required for RNA-cleaving activity Biochem. Biophys. Acta 1489,pp.374-382 (Collaboration) 1999/12
93.	Article	Formation of a Complex Containing ATP, Mg²⁺, and Spermine: Structural Evidence and Biological Significance J. Biol. Chem. 273,pp.30939-30944 (Collaboration) 1998/04
94.	Article	Paramagnetic Inversion of the Sign of the Interference Contribution to the Transverse Relaxation of the Imido Protons of the Coordinated Imidazoles in the Uniformly ¹⁵N-Labeled Cytochrome c₃ J. Magn. Reson. 131,pp.367-372 (Collaboration) 1998/04
95.	Article	Hairpin Structure of an RNA 28-mer, Which Contains a Sequence of the Enzyme Component of a Hammerhead Ribozyme System: Evidence for Tandem G:A Pairs That Are Not of Side-by-Side Type J. Biochem. 122(2),pp.556-562 (Collaboration) 1997/09
96.	Article	Regional Polysterism in the GTP-Bound Form of the Human c-Ha-Ras Protein Biochemistry 36(30),pp.9109-9119 (Collaboration) 1997/07
97.	Article	GNA Trinucleotide Loop Sequences Producing Extraordinary Stable DNA Minihairpins Biochemistry 36,pp.4761-4767 (Collaboration) 1997/04
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■ Research topic, funded research, and department laboratory expense

1.	2002/07～2006/03	Functional analysis of proteins from thermophiles (Key Word : )
2.	2002/06～2005/03	Discovery and application of functional non-coding RNAs (Key Word : )
3.	1997/06～2002/03	Structural biology of RNA (Key Word : )

■ Home Page

https://cit-lifescience.jp/kawai/index.html