京都大学エネルギー理工学研究所
エネルギー構造生命科学研究分野 片平研究室 (K-12分野)
(京都大学大学院　エネルギー科学研究科
                 エネルギー基礎科学専攻　生体エネルギー科学分野(K-12))

(1999～2024）

2024

Sci. Rep, 2024, in press
"Recombinant mycobacterial DNA-binding protein 1 with post-translational modifications boosts IFN-gamma production from BCG-vaccinated individuals’ blood cells in combination with CpG-DNA"
Ozeki, Y., Yokoyama, A., Nishiyama, A., Yoshida, Y., Ohara, Y., Mashima, T., Tomoyama, C., Shaban, A., Takeishi, A., Osada-Oka, M., Yamaguchi, T., Tateishi, Y., Maeyama, J., Hakamata, M., Moro, H., Kikichi, T., Hayashi, D., Suzuki, F., Yamamoto, T., Iho, S., Katahira, M., Yamamoto, S. and Matsumoto, S.
DOI:   

Materials Advances, 2024, in press
"Reassembly of wood to plastic- and paper-like films via ultra-mild dissolution in formic acid"
Kobayashi, N., Hashizume, T., Kondo, K., Kitayama, K., Katahira, M.. and Watanabe, T.
DOI:   

ACS Sustain. Chem. & Eng., 2024, in press
"Structure-based characterization and improvement of an enzymatic activity of Acremonium alcalophilum feruloyl esterase"
Phienluphon, A., Kondo, K., Mikami, B., Teo, S. K. K., Saito, K., Watanabe, T., Nagata, T. and Katahira, M.
DOI:   

J. Phys. Chem. Lett., 2024, in press
"Fluoride ion in alcohols: isopropanol vs. hexafluoroisopropanol"
Yoneda, N., Iyama, H., Nagata, T., Katahira, M., Ishii, Y., Tada, K., Matsumoto, K. and Hagiwara, R.
DOI:   

Sustain. Energy & Fuels, 2024, in press
"Boosting Sugarcane Trash Decomposition: Synergistic action and proximity effect of Xylanase and Feruloyl Esterase co-displayed on the cell surface of Pichia pastoris (Komagataella phaffi)"
Phienluphon, A., Kondo, K., Okano, H., K., Watanabe, T., Nagata, T. and Katahira, M.
DOI:   

J. Agric. ＆ Food Chem., 2024, in press
"Enhancing bioethanol production from rice straw through environmentally-friendly delignification using versatile peroxidase"
Teo, S. K. K., Kondo, K., Khattab, S., Watanabe, T., Nagata, T. and Katahira, M.
DOI:   

Sustain. Chem. & Eng., 2024, in press
"Understanding manganese peroxidase-catalyzed conversion of the lignin structure and its application for the polymerization of Kraft lignin"
Teo, S. A. K., Kondo, K., Watanabe, T., Nagata, T. and Katahira, M.
DOI:   

2023

Holzforschung, 2023, in press
"Quantitative analysis of the β-1 structure in lignin by administration of [ring-1-13C] coniferin"
Imamura, S., Hosokawa, M., Matsushita, Y., Aoki, D., Fukushima, K., and Katahira, M.
DOI:   

Biophys. J., 2023, in press
"Direct inhibition of human APOBEC3 deaminases by HIV-1 Vif independent of the proteolysis pathway"
Kamba, K., Wan, L. Unzai, S., Morishita, R., Takaori, K. A., Nagata, T. and Katahira, M.
DOI:   

Biochem. Biophys. Res. Commun., 2023, 683, 149112, 2023
"NMR characterization of the structure of the intrinsically disordered region of human origin recognition complex subunit 1, hORC1, and its interaction with G-quadruplex DNAs"
Eladl, A., Yamaoki, Y., Kamba, K., Hoshina, S., Horinouchi, H., Kondo, K., Waga S., Nagata, T. and Katahira, M.
DOI: 10.1016/j.bbrc.2023.10.044   

Int. J. Biol. Macromol., 253, 5, 127188, 2023
"Structural insights into the molecular mechanisms of substrate recognition and hydrolysis by feruloyl esterase from Aspergillus sydowii"
Phienluphon, A., Kondo, K., Mikami, B., Nagata, T., and Katahira, M.
DOI: 10.1016/j.ijbiomac.2023.127188   

J. Appl. Microbiol., 134, 9, lxad199, 2023
"Enzymatic degradation of glucosaminoglucan and cellulase resistance of cellulose nanofiber coated with glucosaminoglucan"
Morita, H., Chida, S., Takato, M., Kondo, K., Katahira, M., Simao, L. and Takeda, M.
DOI: 10.1093/jambio/lxad199   

Green Chem., 25, 7682, 2023
"Enhanced depolymerization of beech wood lignin and its removal with peroxidases through continuous separation of lignin fragments"
KENNETH SZE KAI TEO, Kondo, K., Saito, K., Iseki, Y., Watanabe, T., Nagata, T., and Katahira, M.
DOI: 10.1039/D3GC01246H   

Int. J. Mol. Sci., 24 9069. 2023
"Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR"
Eladl, O., Yamaoki, Y., Kondo, K., Nagata, T., Katahira, M.
DOI: 10.3390/ijms24109069   

2022

Biosci. Biotech. Biochem., 87, 3, 256–266, 2022
"A heterodimeric hyaluronate lyase secreted by the activated sludge bacterium Haliscomenobacter hydrossis"
Mori, T., Masuzawa, N., Kondo, K., Nakanishi, Y., Chida, S., Uehara, D., Katahira, M.
and Takeda, M. DOI: 10.1093/bbb/zbac207   

Chem. Commun., 59, 102, 2023
"Detection of interaction between an RNA aptamer and its target compound in living human cells using 2D in-cell NMR"
Eladl, O., Yamaoki, Y., Kondo, K., Nagata, T., Katahira, M.
DOI: 10.1039/D2CC05576G   

Nat. Commun., 13, 7143, 2022
"Shedding light on the base-pair opening dynamics of nucleic acids in living human cells"
Yamaoki, Y., Nagata, T., Kondo, K., Sakamoto, T., Takami, S., Katahira, M.
DOI: 10.1038/s41467-022-34822-4   

Ind. Crops Prod., 190, 115849, 2022
"Microwave-accelerated glycerolysis of sugarcane trash using Lewis acid, AlK(SO₄)₂, for bioethanol production"
Chotirotsukon, C., Khattab, S., Kobayashi, N., Katahira, M., Laosiripojana, N., Champred, V., Watanabe, T.
DOI: 10.1016/j.indcrop.2022.115849   

Biomol. NMR Assign., 16, 615, 2022
"Chemical shift assignments of a fusion protein comprising the C-terminal-deleted hepatitis B virus X protein BH3-like motif peptide and Bcl-x L"
Kusunoki, H., Hamaguchi, I., Kobayashi, N., Nagata, T.
DOI: 10.1007/s12104-022-10104-4   

Polymers, 14, 12, 2401, 2022
"Degradation of Lignin by Infrared Free Electron Laser"
Kawasaki, T., Zen, H., Sakai, T., Sumitomo, Y., Nogami, K., Hayakawa, K., Yaji, T., Ohta, T., Nagata, T., Hayakawa, Y.
DOI: 10.3390/polym14122401   

Data in Brief, 42, 108285, 2022
"Small-angle X-ray scattering data of a guanine-rich DNA derived from the promoter region of c-MYC gene in solution"
Miyauchi, K., Imamura, H., Yamaoki, Y., Kato, M.
DOI: 10.1016/j.dib.2022.108285   

Biomol. NMR Assign., 16, 297, 2022
"¹H, ¹³C and ¹⁵N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis"
Kuwasako, K., Suzuki, S., Nameki, N., Takizawa, M., Takahashi, M., Tsuda, K., Nagata, T., Watanabe, S., Tanaka, A., Kobayashi, N., Kigawa, T., Güntert, P., Shirouzu, M., Yokoyama, S., Muto, Y.
DOI: 10.1007/s12104-022-10094-3   

2021

ACS Sustain. Chem. Eng.,10, 2, 923–934, 2021
"Functional and structural characterization of a lytic polysaccharide monooxygenase, which cooperates synergistically with cellulases, from Ceriporiopsis subvermispora"
Nguyen, H., Kondo, K., Yagi, Y., Iseki, Y., Okuoka, N., Watanabe, T., Mikami, B., Nagata, T., Katahira, M.
DOI: 10.1021/acssuschemeng.1c06810   

ACS Sustain. Chem. Eng., 9, 49, 16651–16658, 2021
"Natural organic ultraviolet absorbers from lignin"
Mikame, K., Ohashi, Y., Naito, Y., Nishimura, H., Katahira, M., Sugawara, S., Koike, K., Watanabe, T.
DOI: 10.1021/acssuschemeng.1c05415   

Biomol. NMR Assign., 16, 41–49, 2021
"¹H, ¹³C and ¹⁵N resonance assignments and solution structures of the two RRM domains of Matrin-3"
He, F., Kuwasako, K., Takizawa, M., Takahashi, M., Tsuda, K., Nagata, T., Watanabe, S., Tanaka, A., Kobayashi, N., Kigawa, T., Guntert, P., Shirouzu, M., Yokoyama, S., Muto, Y.
DOI: 10.1007/s12104-021-10057-0   

J. Electrochem. Soc., 168, 090521, 2021
"Glyme-Lithium bis(trifluoromethylsulfonyl)amide super-concentrated electrolytes: Salt addition to alovate ionic liquids lowers iconicity but liberates Lithium ions"
Kitada, A., Koujin, Y., Shimizu, M., Kawata, K., Yoshinaka, C., Saimura, M., Nagata, T., Katahira, M., Fukami, K. and Murase, K.
DOI: 10.1149/1945-7111/ac239c   

Chem. Commun., 57, 6364-6367, 2021
"Detection of parallel and antiparallel DNA triplex structures in living human cells using in-cell NMR"
Sakamoto, T., Yamaoki, Y., Nagata, T., and Katahira, M.
DOI: 10.1039/D1CC01761F
Selected as a HOT article and a inside front cover.
  

Int. J. Biol. Macromol., 183, 992-1001, 2021
"Structural determination of the sheath-forming polysaccharide of Sphaerotilus montanus using thiopeptidoglycan lyase which recognizes the 1,4 linkage between α-d-GalN and β-d-GlcA"
Kashiwabara, D., Kondo, K., Usami, R., Kan, D., Kawamura, I., Kawasaki, Y., Sato, M., Nittami, T., Suzuki, I., Katahira, M., and Takeda, M.
DOI: 10.1016/j.ijbiomac.2021.05.001   

Sci. Rep., 11, 9523, 2021
"Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner"
Hamad, N., Yoneda, R., So, M., Kurokawa, R., Nagata, T., and Katahira, M.
DOI: 10.1038/s41598-021-89075-w   

Int. J. Mol. Sci., 22, 3481, 2021
"Investigation of the interaction of human origin recognition complex subunit 1 with G-quadruplex DNAs of human c-myc promoter and telomere regions"
Eladl, A., Yamaoki, Y., Hoshina, S., Horinouchi, H., Kondo, K., Waga, S., Nagata, T., and Katahira, M.
DOI: 10.3390/ijms22073481   

J. Electrochem. Soc., 168, 26515, 2021
"An ammonium solvate ionic liquid"
Kawata, K., Kitada, A., Fukami, K., Saimura, M., Nagata, T., Katahira, M., and Murase, K.
DOI: 10.1149/1945-7111/abe512   

J. Electrochem. Soc., 168, 016506, 2021
"Ligand exchange conduction of lithium ion in a pentaglyme-lithium bis(trifluoromethylsulfonyl)amide super-concentrated electrolyte"
Kitada, A., Kawata, K., Shimizu, M., Saimura, M., Nagata, T., Katahira, M., Fukami, K. and Murase, K.
DOI: 10.1149/1945-7111/abda03   

2020

Phys. Chem. Chem. Phys., 23, 449-456, 2020
"Proton conduction in hydronium solvate ionic liquids affected by ligand shape"
Kawata, K., Kitada, A., Tsuchida, N., Saimura, M., Nagata, T., Katahira, M., Fukami, K. and Murase, K.
DOI:   

Biotech. Biofuels, 13, 164, 2020
"NMR elucidation of nonproductive binding sites of lignin models with carbohydrate-binding module of cellobiohydrolase I"
Tokunaga, Y., Nagata, T., Kondo, K., Katahira, M., and Watanabe, T.
DOI: 10.21203/rs.3.rs-36005/v2   

J. Fluorine Chem., 239, 109637, 2020
"Structural evaluation and protium-deuterium exchange in 1-ethyl-3-methylimidazolium halide-ethylene glycol mixtures"
Chen, Z., Tonouchi, Y., Matsumoto, K., Tsuzuki, S., Nagata, T., Katahira, M., and Hagiwara, R.
DOI: 10.1016/j.jfluchem.2020.109637   

Nucleic Acid Therapeutics, 30, 414-421, 2020
"Improved anti-prion nucleic acid aptamers by incorporation of chemical modifications"
Amato, J., Mashima, T., Kamatari, Y. O., Kuwata, K., Novellino, E., Randazzo, A., Giancola, C., Katahira, M., and Pagano, B.
DOI: 10.1089/nat.2020.0899   

Holzforschung, 75, 379-389, 2020
"Complete NMR assignment and analysis of molecular structural changes of β-O-4 lignin oligomer model compounds in organic media with different water content"
Tokunaga, Y., Nagata, T., Kondo, K., Katahira, M., and Watanabe, T.
DOI: 10.1515/hf-2020-0039   

Chem. Commun., 56, 9134–9137, 2020.
"Direct visualization of the conformational change of FUS/TLS upon binding to promoter-associated non-coding RNA"
Hamad, N., Watanabe, H., Uchihashi, T., Kurokawa, R., Nagata, T. and Katahira, M.
DOI: 10.1039/D0CC03776A   

Biosci. Biotech. Biochem., 84, 2085-2095, 2020
"Aggregability of β(1→4)-linked glucosaminoglucan originating from a sulfur-oxidizing bacterium Thiothrix nivea"
Takeda, M., Kondo, K., Tomonaga, R., Mori, H., Kato, M., Usami, R., Murakami, T., Ueda, K., Suzuki, I. and Katahira, M.
DOI: 10.1080/09168451.2020.1785838   

J. Inorg. Chem., 59, 6631–6639, 2020
"Fluoride Ion Interactions in Alkali Metal Fluoride-Diol Complexes"
Tonouchi, Y., Matsumoto, K., Nagata, T., Katahira, M., and Hagiwara, R.
DOI: 10.1021/acs.inorgchem.0c00783   

Sci. Rep., 10, 4934, 2020
"Development and structural determination of an anti-PrP^C aptamer that blocks pathological conformational conversion of prion protein"
Mashima, T., Lee, J. H., Kamatari, Y. O., Hayashi, T., Nagata, T., Nishikawa, F., Nishikawa, S., Kinoshita, M., Kuwata, K. and Katahira, M.
DOI: 10.1038/s41598-020-61966-4   

J. Electrochem. Soc., 167, 046508, 2020
"Suppression of fast proton conduction by dilution of a hydronium solvate ionic liquid: Localization of ligand exchange"
Kawata, K., Kitada, A., Tsuchida, N., Saimura, M., Nagata, T., Katahira, M., Fukami, K. and Murase, K.
DOI: 10.1149/1945-7111/ab75fc   

Sci. Rep., 10, 2629, 2020
"RNA sequence and length contribute to RNA-induced conformational change of TLS/FUS"
Hamad, N., Mashima, T., Yamaoki, Y., Kondo, K., Yoneda, R., Oyoshi, T., Kurokawa, R., Nagata, T. and Katahira, M.
DOI: 10.1038/s41598-020-59496-0   

2019

J. Chem. Inform. & Model, 59, 3533-3544, 2019
"How does the recently discovered peptide MIP exhibit much higher binding affinity than an anticancer protein p53 for an oncoprotein MDM2?"
Yamada, T., Hayashi, T., Hikiri, S., Kobayashi, N., Yanagawa, H., Ikeuchi, M., Katahira, M., Nagata, T., Kinoshita, M.
DOI: 10.1021/acs.jcim.9b00226   

Holzforschung, 73, 1083–1092, 2019
"Evaluation of ring-5 structures of guaiacyl lignin in Ginko biloba L. using solid- and liquid-state ¹³C NMR difference spectroscopy"
Aoki, D., Nomura, K., Hashiura, M., Imamura, Y., Miyata, S., Terashima, N., Mstsushita, Y., Nishimura, H., Watanabe, T., Katahira, M. and Fukushima, K.
DOI: 10.1515/hf-2019-0011   

Biochim. Biophys. Acta, pii: S0304-4165(19)30088-1, 2019
"An insight into the dependence of the deaminase activity of human APOBEC3F on the length of single-stranded DNA, which is affected by the concentrations of APOBEC3F and single-stranded DNA"
Wan, L., Kamba, K., Nagata, T. and Katahira, M.
DOI: 10.1016/j.bbagen.2019.04.011   

Int. J. Biol. Macromol., 132, 222-229, 2019
"Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis"
Wan Osman, W. H., Mikami, B., Saka, N., Kondo, K., Lin, M. I., Nagata, T. and Katahira, M.
DOI: 10.1016/j.ijbiomac.2019.03.199   

FEBS J., 286, 2355-2365, 2019
"The anti-prion RNA aptamer R12 disrupts the Alzheimer’s disease-related complex between prion and amyloid β"
Iida, M., Mashima, T., Yamaoki, Y., So, M., Nagata, T. and Katahira, M.
DOI: 10.1111/febs.14819   

Biochem. Biophys. Res. Commun., 510, 177-183, 2019
"Structure of a serine-type glutathione S-transferase of Ceriporiopsis subvermispora and identification of the enzymatically important non-canonical residues by functional mutagenesis"
Wan Osman, W. H., Mikami, B., Saka, N., Kondo, K., Nagata, T. and Katahira, M.
DOI: 10.1016/j.bbrc.2019.01.076   

2018

J. Phys. Chem. Lett., 9, 6662-6667, 2018
"Partially naked fluoride in solvate ionic liquids"
Chen, Z., Tonouchi, Y., Matsumoto, K., Saimura, M., Atkin, R., Nagata, T., Katahira, M. and Hagiwara, R.
DOI: 10.1021/acs.jpclett.8b03117   

PLoS ONE, 13, e0204160, 2018
"Significance of a histone-like protein with its native structure for the diagnosis of asymptomatic tuberculosis"
Ohara, Y., Ozeki, Y., Tateishi, Y., Mashima, T., Arisaka, F., Tsunaka, Y., Fujiwara, Y., Nishiyama, A., Yoshida, Y., Kitadokoro, K., Kobayashi, H., Kaneko, Y., Najagawa, I., Maekura, R., Yamamoto, S., Katahira, M. and Matsumoto, S.
DOI: 10.1371/journal.pone.0204160   

ChemBioChem, 19, 2268-2272, 2018
"Analysis of interaction between telomeric i-motif DNA and a cyclic tetraoxazole compound"
Masoud, S.S., Yamaoki, Y., Ma, Y., Marchand, A., Winnerdy, F.R., Gabelica, V., Phan, A.T., Katahira, M. and Nagasawa, K.
DOI: 10.1002/cbic.201800425   

Appl. Microbiol. Biotech., 102, 9635-9645, 2018
"Classification of fungal glucuronoyl esterases (FGEs), and characterization of two new FGEs from Ceriporiopsis subvermispora and Pleurotus eryngii"
Lin, M.I., Hiyama, A., Kondo, K., Nagata, T. and Katahira, M.
DOI: 10.1007/s00253-018-9318-5   

Arch. MicroBiol., 200, 1257-1265, 2018
"Identification and characterization of the S-layer formed on the sheath of Thiothrix nivea"
Kawasaki, Y., Kurosaki, K., Kan, D., Borges, I. K., Satake, A., Sato, M., Kondo, K., Katahira, M., Suzuki, I. and Takeda, M.
DOI: 10.1007/s00203-018-1543-x   

J. Electrochem. Soc., 165, H496-H499, 2018
"A hydronium solvate ionic liquid: Ligand exchange conduction driven by labile solvation"
Kitada, A., Kintsu, K., Takeoka, S., Fukami, K., Saimura, M., Nagata, T., Katahira, M. and Murase, K.
DOI: 10.1149/2.0971809jes   

Sci. Rep., 8, 6538, 2018
"Direct evidence for a ether linkage between lignin and carbohydrates in wood cell walls"
Nishimura, H., Kamiya, A., Nagata, T., Katahira, M. and Watanabe, T.
DOI: 10.1038/s41598-018-24328-9   

Int. J. Biol. Macromol, 113, 1158-1166, 2018
"Characterization of the glutathione S-transferases that belong to the GSTFuA class in Ceriporiopsis subvermispora: Implications in intracellular detoxification and metabolism of wood-derived compounds"
Wan Osman, W. H., Lin, M.I., Kondo, K., Nagata, T. and Katahira, M.
DOI: 10.1016/j.ijbiomac.2018.03.029   

Phys. Chem. Chem. Phys., 20, 9167-9180, 2018
"Mechanism of protein-RNA recognition: Analysis based on statistical mechanics of hydration"
Hayashi, T., Matsuda, T. Nagata, T., Katahira, M. and Kinoshita, M.
DOI: 10.1039/C8CP00155C   

J. Electrochem. Soc., 165, H121-H127, 2018
"A Hydronium Solvate Ionic Liquid: Facile Synthesis of Air-Stable Ionic Liquid with Strong Bronsted Acidity"
Kitada, A., Takeoka, S., Kintsu, K., Fukami, K., Saimura, M., Nagata, T., Katahira, M. and Murase, K.
DOI: 10.1149/2.0481803jes   

Sci. Rep., 8, 2864, 2018
"Plastic roles of phenylalanine and tyrosine residues of an RGG motif of TLS/FUS in binary and ternary complex formation with the G-quadruplex structures of telomeric DNA and TERRA"
Kondo, K., Mashima, T., Oyoshi, T., Yagi, R., Kurokawa, R., Kobayashi, N., Nagata, T. and Katahira, M.
DOI: 10.1038/s41598-018-21142-1   

Protein Expr. Pur., 145, 45-52, 2018
"High yield production of fungal manganase peroxidases by E. coli through soluble expression, and examination of the activities"
Lin, M. I., Nagata, T. and Katahira, M.
DOI: 10.1016/j.pep.2017.12.012   

Nucleic Acids Res., 46, 1059-1068, 2018
"Selective alkylation of T-T mismatched DNA using vinyldiaminotriazine-acridine conjugate"
Onizuka, K., Usami, A., Yamaoki, Y., Kobayashi, T., Hazemi, M., Chikuni, T., Sato, N., Sasaki, K., Katahira, M. and Nagatsugi, F.
DOI: 10.1093/nar/gkx1278   

Int. J. Biol. Macromol., 109, 323-328, 2018
"Enzymatic degradation of β-1,4-linked N-acetylglucosaminoglucan prepared from Thiothrix nivea"
Takeda, M., Kondo, K., Sanda, S., Kan, D., Borges, I. K., Suzuki, I. and Katahira, M.
DOI: 10.1016/j.ijbiomac.2017.12.065   

FEBS Open Bio., 8, 264-270, 2018
"Characterisation of an aptamer against Runt domain of AML1 (RUNX1) by NMR and mutational analyses"
Takada, K., Amano, R., Nomura, Y., Tanaka, Y., Sugiyama, S., Nagata, T., Katahira, M., Nakamura, Y., Kozu, T. and Sakamoto, T.
DOI: 10.1002/2211-5463.12368   

RSC Phys. Chem. Chem. Phys., 20, 2982-2985, 2018
"The first successful observation of in-cell NMR signals of DNA and RNA in living human cells"
Yamaoki, Y., Kiyoishi, A., Miyake, M., Kano, F., Murata, M., Nagata, T. and Katahira, M.
DOI: 10.1039/c7cp05188c   

RSC Phys. Chem. Chem. Phys., 20, 2976-2981, 2018
"The C-terminal cytidine deaminase domain of APOBEC3G itself undergoes intersegmental transfer for a target search, as revealed by real-time NMR monitoring"
Kamba, K., Nagata, T. and Katahira, M.
DOI: 10.1039/c7cp05171a   

RSC Phys. Chem. Chem. Phys., 20, 3109-3117, 2018
"Influence of the DNA sequence/length and pH on deaminase activity, as well as the roles of the amino acid residues around the catalytic center of APOBEC3F"
Wan, L., Nagata, T. and Katahira, M.
DOI: 10.1039/c7cp04477a   

2017

Molecules, 22, E1991., 2017
"DNA G-wire formation using an artificial peptide is controlled by protease activity"
Usui, K., Okada, A., Sakashita, S., Shimooka, M., Tsuruoka, T., Nakano, S., Miyoshi, D., Mashima, T., Katahira, M. and Hamada, Y.  

ACS Chem. Biol., 12, 2704-2708, 2017
"Observation by real-time NMR, and interpretation of length- and location-dependent deamination activity of APOBEC3B"
Wan, L., Nagata, T., Morishita, R., Takaori-Kondo, A. and Katahira, M.  

Biomol. NMR Assign., 11, 265-268, 2017
"Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA"
Iwaoka, R., Nagata, T., Tsuda, K., Imai, T., Okano, H., Kobayashi, N. and Katahira, M.  

Molecules, 22, E1207, 2017
"Structural insight into recognition of r(UAG) by Musashi-1 RBD2, and construction of a model of Musashi-1 RBD1-2 bound to the minimum target RNA"
Iwaoka, R., Nagata, T., Tsuda, K., Imai, T., Okano, H., Kobayashi, N. and Katahira, M.  

J. Biochem., 162, 431-436, 2017
"Conjugating two RNA aptamers improves binding affinity for AML1 Runt domain"
Nomura, Y., Yamazaki, K., Amano, R., Takada, K., Nagata, T., Kobayashi, N., Tanaka, Y., Fukunaga, J., Katahira, M., Kozu, T., Nomura, Y., Haishima, Y., Torigoe, H. and Sakamoto, T.   

Chem. Commun., 53, 7056-7059, 2017
"Development of an RNA aptamer that acquires binding capacity against HIV-1 Tat protein via G-quadruplex formation in response to potassium ions."
Yamaoki, Y., Nagata, T., Mashima, T. and Katahira, M.   

Cell Rep., 18, 2651-2663, 2017
"Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5."
Obayashi E, Luna RE, Nagata T, Martin-Marcos P, Hiraishi H, Singh CR, Erzberger JP, Zhang F, Arthanari H, Morris J, Pellarin R, Moore C, Harmon I, Papadopoulos E, Yoshida H, Nasr ML, Unzai S, Thompson B, Aube E, Hustak S, Stengel F, Dagraca E, Ananbandam A, Gao P, Urano T, Hinnebusch AG, Wagner G, Asano K.   

2016

Biochemistry, 55, 2553-66, 2016
"Structure, Dynamics, and Interaction of p54(nrb)/NonO RRM1 with 5' Splice Site RNA Sequence."
Duvignaud JB, Bédard M, Nagata T, Muto Y, Yokoyama S, Gagné SM, Vincent M.   

Int. J. Biol. Macromol., 95, 1280-1288., 2016
"Elongation pattern and fine structure of the sheaths formed by Thiothrix nivea and Thiothrix fructosivorans"
Kawasaki, Y., Endo, T., Fujiwara, A., Kondo, K., Katahira, M., Nittani, T., Sato, M. and Takeda, M.   

Biochem. Biophys. Res. Commun., 482, 335-340, 2016
"NMR elucidation of reduced B-Z transition activity of PKZ protein kinase at high NaCl concentration"
Lee, A., Seo, Y., Choi, S., Ryu, K., Cheong, H., Lee, S., Katahira, M., Park, C. and Lee, J.   

Front. Microbiol., 7, 587, 2016
"Characterization of the deamination coupled with sliding along DNA of anti-HIV factor APOBEC3G on the basis of the pH-dependence of deamination revealed by real-time NMR monitoring"
Kamba, K., Nagata, T. and Katahira, M..   

Sci. Rep., 6, 21742, 2016
"Accurate and molecular-size-tolerant NMR quantitation of diverse components in solution"
Okamura, H., Nishimura, H., Nagata, T., Kigawa, T., Watanabe, T. and Katahira, M..   

J. Exp. Med., 213, 605-619, 2016
"Arid5a regulates naïve CD4+ T-cell fate through selective stabilization of Stat3 mRNA"
Masuda, K., Ripley, B., Nyati, K., Dubey, P., Zaman, M., Hanieh, H., Hoga, M., Yamashita, K., Standley, D., Mashima, T., Katahira, M., Okamoto, T., Matsuura, Y., Takeuchi, O., Kishimoto, T.   

Cell & Biosci., 6, 4, 2016
"The binding specificity of translocated in liposarcoma/fused in sarcoma with lncRNA transcribed from the promoter region of cyclin D1"
Yoneda, R., Suzuki, S., Mashima, T., Kondo, K., Nagata, T., Katahira, M. and Kurokawa, R.   

Internat. J. Biol. Macromol., 82, 772-779, 2016
"Presence of N-L-lactyl-D-perosamine residue in the sheath-forming polysaccharide of Thiothrix fructosivorans"
Kawasaki, Y., Kondo, K., Narizuka, R., Endo, T., Katahira, M., Kawamura, I., Sato, M. and Takeda, M.   

2015

Biochem. Biophys. Res. Commun., 468, 27-31, 2015
"K+-responsive off-to-on switching of hammerhead ribozyme through dual G-quadruplex formation requiring no heating and cooling treatment"
Yamaoki, Y., Nagata, T., Mashima, T. and Katahira, M.   

Chem. Eur. J., 21, 14713-14716, 2015
Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases Both through Hydrogen Bonding and Metal Coordination
Takezawa, Y., Nishiyama K., Mashima T., Katahira, M. and Shionoya, M.   

Nucleic Acids Res., 43, 7717-7730, 2015
Crosslinking Reactions of 4-Amino-6-oxo-2-vinylpyrimidine (AOVP) with Guanine Derivatives and Structural Analysis of the Adducts
Kusano, S., Ishiyama, S., Lam, S. L., Mashima, T., Katahira, M., Miyamoto, K., Aida, M. and Nagatsugi, F.   

PLOS ONE, 10, e0124142, 2015
Catalytic analysis of APOBEC3G involving real-time NMR spectroscopy reveals nucleic acid determinants for deamination
Kamba, K., Nagata, T. and Katahira M.   

Chem. Commun., 51, 5898-5901, 2015
Boosting of activity enhancement of K⁺-responsive quadruplex hammerhead ribozyme
Yamaoki Y, Mashima T, Nagata T, and Katahira M.   

2014

PLos One., e109163, volume 9(Issue10), 2014.
Structural Basis for Inhibition of the MDM2:p53 Interaction by an Optimized MDM2-Binding Peptide Selected with mRNA Display
Nagata T, Shirakawa K, Kobayashi N, Shiheido H, Tabata N, Sakuma-Yonemura Y, Horisawa K, Katahira M, Doi N, Yanagawa H.   

Nucleic Acids Res., 42, 6861-6875, 2014.
Binding of an RNA aptamer and a partial peptide of a prion protein: Crucial importance of water entropy in molecular recognition
Hayashi, T., Oshima, H., Mashima, T., Nagata, T., Katahira, M. and Kinoshita, M.   

ChemBioChem, 15, 794-798, 2014.
RNA-directed amino acid coupling as a model reaction for primitive coded translation
Harada, K., Aoyama, S., Matsugami, A., Kumar, P.K.R.,  Katahira, M.,  Kato, N. and Ohkanda, J.

Angew. Chem., Int. Ed., 53, 2349-2352, 2014.
Quantitative analysis of the location- and sequence-dependent deamination by APOBEC3G using real-time NMR
Furukawa, A., Sugase, K., Morishita, R., Nagata, T., Kodaki, T., Takaori, A.,
Ryo, A. and  Katahira, M. 

2013

Holzforschung, 2013, 67, 835-841.
Multistep degradation method for β-O-4 linkage in lignins: γ-TTSA method. Part 3: Degradation of milled wood lignin (MWL) from Eucalyptus Globulus
Ando, D., Nakatsubo, F., Takano, T., Nishimura, H.,  Katahira, M.  and Yano, H.

Internat. J. Biol. Macromol., 2013 Apr 12. pii: S0141-8130(13)00184-0.
Structure of perosamine-containing polysaccharide, a component of the sheath of Thiothrix fructosivorans
Kondo, K., Umezu, T., Shimura, S., Narizuka, R., Koizumi, J., Mashima, T.,  Katahira, M.  and Takeda, M.

 

Holzforschung, 2013 67:249-256.
Multistep degradation method for β-O-4 linkage in lignins: γ-TTSA method. Part 2: reaction of lignin model polymer (DHP)
Ando, D., Nakatsubo, F., Takano, T., Nishimura, H.,  Katahira, M.  and Yano, H.
  Link to this paper

Nucleic Acids Res., 2013 Jan;41(2):1355-62.
Anti-prion activity of an RNA aptamer and its structural basis
Mashima, T., Nishikawa, F., Kamatari, YO., Fujiwara, H., Saimura, M., Nagata, T., Kodaki, T., Nishikawa, S., Kuwata, K.and  Katahira, M. 
 

2012

Carbohydrate Research, 2012 Oct 1;360:102-8.
Conformational analysis of an extracellular polysaccharide produced by Sphaerotilus natans
Kondo, K., Takeda, M., Mashima, T., Katahira, M ., Koizumi, J. and Ueda, K.
 

Biochem. Biophys. Res. Commun., 2012 Aug 24;425(2):284-9.
NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir
Furukawa, A., Okamura, H., Morishita, R., Matsunaga, S., Kobayashi, N., Kodaki, T., Takaori, A., Ryo, A., Nagata, T. and  Katahira, M. 
 

FEBS Lett., 2012, Jul 30;586(16):2548-54.
Conformational dynamics of yeast calmodulin in the Ca²⁺-bound state probed using NMR relaxation dispersion
Ogura, K., Okamura, H.,  Katahira, M. , Katoh, E. and Inagaki, F.
 

J. Proteomics, 2012 Aug 3;75(15):4863-73.
Molecular and enzymatic characterization of XMRV protease by a cell-free proteolytic analysis
Matsunaga, S., Sawasaki, T., Ode, H., Morishita, R., Furukawa, A., Sakuma, R., Sugiura, W., Sato, H.,  Katahira, M. , Takaori, A., Yamamoto, N. and Ryo, A
 

FEBS J.,2012 Apr; 279(8), 1456-1463.
'Intelligent' ribozyme whose activity is altered in response to K⁺ as a result of quadruplex formation
Nagata, T., Sakurai, Y., Hara, Y., Mashima, T., Kodaki, T., and Katahira, M.
 

Internat. J. Biol. Macromol.,2012 Jan; 50(1), 236-244.
Presence of alternating glucosaminoglucan in the sheath of Thiothrix nivea
Takeda, M., Kondo, K., Ymamada, M., Sumikawa, M., Koizumi, J., Mashima, T. and Katahira, M. 
 

Nucleic Acids Res., 2012 Apr; 40(7), 3218-3231.
Structure of Musashi1 in a complex with target RNA: The role of aromatic stacking interactions
Ohyama, T., Nagata, T., Tsuda, K., Kobayashi, N., Imai, T., Okano, H., Yamazaki, T. and Katahira, M.
 

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2011

J. Am. Chem. Soc., 2011 Mar; 133(12), 4567-4579.
Structural aspects for the recognition of ATP by ribonucleopeptide receptors
Nakano, S., Mashima, T., Matsugami, A., Inoue, M., Katahira, M. and Morii, T.
 

Biochem Biophys Res Commun. 2011 Jan 14;404(2):634-7. Epub 2010 Dec 10.

A novel strictly NADPH-dependent Pichia stipitis xylose reductase constructed by site-directed mutagenesis.

Khattab SM, Watanabe S, Saimura M, Kodaki T.


J. Biol. Chem. 286, 10051-10057. 

Heat shock protein 70 inhibits HIV-1 Vif-mediated ubiquitination and degradation of APOBEC3G

Sugiyama, R., Nishitsuji, H., Furukawa, A., Katahira, M., Habu, Y., Takeuchi, H., Ryo, A. and Takaku, H.

Internat. J. of Biolog. Macromol., 48, 256-262

Study of a novel glycoconjugate, thiopeptidoglycan, and a novel polysaccharide lyase, thiopeptidoglycan lyase

2010

Proteins. 2010 Nov;78(14):3033-47.

Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1, implying a mechanism for an increase in DNA-binding affinity through phosphorylation

Int. J. Biol. Macromol. 2010 Mar;46(2):206-11.

Solubilization and structural determination of a glycoconjugate which is assembled into the sheath of Leptothrix cholodnii

Biochem. Biophys. Res. Commun. 2010 Jan;391(1):118-22.

Biomolecular response of oxanine in DNA strands to T4 polynucleotide kinase, T4 DNA ligase, and restriction enzymes.

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2009

　

EMBO J. 2009 Feb;28(4):440-51.

Structure, interaction, and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G.

　

Nucleic Acids Res. 2009 Oct;37(18):6249-58.

Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein.

　

Bioorg. Medici. Chem. 2009 Mar;17(5):1870-5.

The orientation of the ends of G-quadruplex structures investigated using end-extended oligonucleotides.

　

Oligonucleotides 2009 Jun;19(2):179-90.

Structural studies of an RNA aptamer containing GGA repeats under ionic conditions using microchip electrophoresis, circular dichroism and 1D-NMR

　

Nucleic Acids Symp. Ser. 2009 No. 53, 87-8.

Structure and real-time monitoring of the enzymatic reaction of APOBEC3G which is involved in anti-HIV activity

　

Nucleic Acids Symp. Ser. 2009 No. 53, 259-260.

Structural aspects for the function of ATP-binding ribonucleopeptide receptors

　

Nucleic Acids Symp. Ser. 2009 No. 53, 267-8.

Structural analysis of ribonucleopeptide aptamer against ATP

　

Appl. Microbiol. Biotechnol. 2009 Aug;84(1):37-53.

Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives.

Appl. Environment. Microbiol. 2009 Jun;75(11):3818-22.

Efficient bioethanol production by a recombinant flocculent Saccharomyces cerevisiae strain with a genome-integrated NADP+-dependent xylitol dehydrogenase gene.

J. Biochem. 2009 Aug;146(2):201-8.

Reinvestigation of the molecular influence of hypoxanthine on the DNA cleavage efficiency of restriction endonucleases BglII, EcoRI and BamHI.

J. Biotechnol. 2009 Mar;140(3-4):242-5.

Stabilization of the immobilized linkers and DNA probes for DNA microarray fabrication by end-capping of the remaining unreacted silanol on the glass.

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2008

Nucleic Acids Res. 2008 Dec;36(21):6816-6824.

Elucidation of the mode of interaction in the UP1-telomerase RNA-telomeric DNA ternary complex which serves to recruit telomerase to telomeric DNA and to enhance the telomerase activity.

　

Nucleic Acids Res. 2008 Aug;36(14):4754-67. Epub 2008 Jul 19.

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition. 

　

J. Biochem. 2008 Oct;144(4):513-21.

N- and C-terminal Fragments of A Globular Protein Constructed by Elongation of Modules as A Units Associated for Functional Complementation. 

　

Nucleic Acids Symp. Ser. 2008 No. 52, 183-184.

NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase

　

Nucleic Acids Symp. Ser. 2008 No. 52, 171-172.

Orientation of ends of G-quadruplex structure investigated with end-extended oligonucleotides

　

Nucleic Acids Symp. Ser. 2008 No. 52, 193-194.

Structural analysis of Musashi-RNA complex on the basis of long-range structural information

　

Nucleic Acids Symp. Ser. 2008 No. 52, 179-180.

Structural analysis of r(GGA)4 found in RNA aptamer for prion protein

　

Nucleic Acids Symp. Ser. 2008 No. 52, 217-218.

Interactions between antitumor drugs and vault RNA

　

Nucleic Acids Res. 2008 Apr;36(6):1805-12.

Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease-resistance

　

Appl. Microbiol. Biotechnol. 2008 Nov;81(2):243-55.

Expression of protein engineered NADP+-dependent xylitol dehydrogenase increases ethanol production from xylose in recombinant Saccharomyces cerevisiae.

Nucleic Acids Symp. Ser. 2008 No. 52, 567-8.

Reactive oxygen species generation through NADH oxidation by pterin derivatives.

Nucleic Acids Symp. Ser. 2008 No. 52, 473-4.

Temperature-gradient dependent detection of target DNA oligomers using DNA-immobilized open tubular capillary column.

Nucleic Acids Symp. Ser. 2008 No. 52, 441-2.

Reactivity of oxanine: efficient fabrication of DNA microarray by using oxanine-containing DNA oligomer as probe molecule.

Nucleic Acids Symp. Ser. 2008 No. 52, 277-8.

Efficient preparation of xanthine-containing oligodeoxynucleotide from oxanine-containing oligodeoxynucleotide, catalyzed by N alpha-acetyl-L-histidine.

J. Biosci. Bioeng. 2008 Mar;105(3):296-9.

Bioethanol production from xylose by recombinant Saccharomyces cerevisiae expressing xylose reductase, NADP+-dependent xylitol dehydrogenase, and xylulokinase.

J. Gene Med. 2008 Mar;10(3):316-24.

Construction of X-ray inducible promoters through cis-acting element elongation and error-prone polymerase chain reaction.

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2007

　

Biosci. Biotechnol. Biochem. 2007 Dec 23;71(12):2992-2998. Epub 2007 Dec 7.

Structural Analysis of the Fundamental Polymer of the Sheath Constructed by Sphaerotilus natans.

　

Nucleic Acids Symp. Ser. 2007 No. 51, 141-2.

Structure of 4'-thioDNA which exhibits endonuclease resistance.

　

Nucleic Acids Symp. Ser. 2007 No. 51, 77-8.

Interactions with RNA/DNA of proteins involved in the regulation of transcription, translation and telomere elongation.

　

FEBS J. 2007 Jul;274(14):3545-56.

Structure of a human telomeric DNA sequence stabilized by 8-bromoguanosine substitutions, as determined by NMR in a K+ solution.

　

Biol. Pharm. Bull. 2007 Nov;30(11):2181-4.

Inhibitory effect of 6-formylpterin on HIF-1alpha protein accumulation.

Nucleic Acids Symp. Ser. 2007;(51):451-2.

Comparison of enzymatic recognition of DNA-duplexes containing NO-induced lesions by DNA-relevant enzymes.

Nucleic Acids Symp. Ser. 2007 No. 51, 327-8.

Development of stable DNA microarray platforms suitable for quantitative analysis.

Nucleic Acids Symp. Ser. 2007 No. 51, 227-8.

Chemical natures of 6-formylpterin nucleoside analogs.

Nucleic Acids Symp. Ser. 2007 No. 51, 53-4.

Functional reactivity of oxanine: its biological meanings and biotechnological applications.

Nucleosides, Nucleotides & Nucleic Acids. 2007;26(10-12):1589-93.

Biophysical stability and enzymatic recognition of oxanine in DNA.

Nucleic Acids Res. 2007 35(17):e110.

Direct immobilization of DNA oligomers onto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine.

Org. Biomol. Chem. 2007 Oct;5(20):3314-9.

Synthesis of 6-fromylpterin nucleoside analogs and their ROS generation activities in the presence of NADH in the dark.

Anal. Bioanal. Chem. 2007 Jun;388(4):919-28.

Base sequence- and T m-dependent DNA oligomer separation by open tubular capillary columns carrying complementary DNA oligomers as probes.

Chem. Lett. 2007 36:322-323.

Additional alkylsilanization of aminosilane-modified glass slide: Effect of alkylsilane structure for enhancing surface amine functionality.

Kamisetty N.K., Pack S.P., Nonogawa M., Devarayapalli K.C., Kodaki T., and Makino K

Biosci. Biotechnol. Biochem. 2007 May;71(5):1365-9.

The positive effect of the decreased NADPH-preferring activity of xylose reductase from Pichia stipitis on ethanol production using xylose-fermenting recombinant Saccharomyces cerevisiae.

Microbiology. 2007 Sep;153(Pt 9):3044-54.

Ethanol production from xylose by recombinant Saccharomyces cerevisiae expressing protein-engineered NADH-preferring xylose reductase from Pichia stipitis.

J. Biotechnol. 2007 Jun;130(3):316-9.

Ethanol production from xylose by recombinant Saccharomyces cerevisiae expressing protein engineered NADP+-dependent xylitol dehydrogenase.

Biotechniques. 2007 May;42(5):628-33.

Construction of strong mammalian promoters by random cis-acting element elongation.

J. Biotechnol. 2007 May;129(4):717-22.

Thermostabilization of Pichia stipitis xylitol dehydrogenase by mutation of structural zinc-binding loop.

Anal. Bioanal. Chem. 2007 Mar;387(6):2027-35.

Efficient preparation of amine-modified oligodeoxynucleotide using modified H-phosphonate chemistry for DNA microarray fabrication.

Biochem. Biophys. Res. Commun. 2007 Feb;353(4):1105-10.

Reactive oxygen species generation through NADH oxidation by 6-formylpterin derivatives in the dark.

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2006

　

Nucleic Acids Symp. Ser. 2006 No. 50, 237-8.

Structural analysis of DNA containing (6-4) photoproduct in complex with distamycin A by NMR. 

　

Nucleic Acids Symp. Ser. 2006 No. 50, 45-6.

The new models of the human telomere DNA in K+ solution revealed by NMR analysis assisted by the incorporation of 8-bromoguanines.

　

Biosci. Biotechnol. Biochem.. 2006 May;70(5):1265-8. 

Identification of 2-(cysteinyl)amido-2-deoxy-D-galacturonic acid residue from the sheath of Leptothrix cholodnii.

　

Nucleosides, Nucleotides & Nucleic Acids, 2006 25(4-6):417-425.

Structural property of DNA that migrates faster in gel electrophoresis, as deduced by CD spectroscopy

　

Biosci. Biotechnol. Biochem.. 2006 May;70(5):1265-8.

Identification of 2-(cysteinyl)amido-2-deoxy-D-galacturonic acid residue from the sheath of Leptothrix cholodnii. 

　

Mutat. Res. 2006 Jun;598(1-2):120-31.

Molecular mechanisms for maintenance of G-rich short tandem repeats capable of adopting G4 DNA structures.

　

Zoolog. Sci.. 2006 Jan;23(1):9-21.

Unichrom, a novel nuclear matrix protein, binds to the ars insulator and canonical Mars.

　

Nucleic Acids Symp. Ser. 2006 No. 50, 297-8.

Chemical natures and application of 6-formylpterin derivatives.

Nucleic Acids Symp. Ser. 2006 No. 50, 281-2.

Site-directed mutagenesis of a yeast gene for improvement of enzyme thermostability.

Nucleic Acids Symp. Ser. 2006 No. 50, 279-80.

Construction of various mutants of xylose metabolizing enzymes for efficient conversion of biomass to ethanol.

Nucleic Acids Symp. Ser. 2006 No. 50, 209-10.

Development of DNA-arrayed column for sensitive and selective analysis of DNA.

Nucleic Acids Symp. Ser. 2006 No. 50, 171-2.

Synthesis and application of new amine- modified oligonucleotides using H-phosphonate chemistry.

Nucleic Acids Symp. Ser. 2006 No. 50, 97-8.

Structural property and enzymatic response of oxanine in DNA strands.

Anal. Bioanal. Chem. 2006 Nov;386(6):1649-55.

Development of an efficient amine-functionalized glass platform by additional silanization treatment with alkylsilane.

J. Biol. Chem. 2006 Nov;281(44):33521-36.

Identification and characterization of L-arabonate dehydratase, L-2-keto-3-deoxyarabonate dehydratase, and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism. Novel evolutionary insight into sugar metabolism.

J. Biol. Chem. 2006 Sep;281(39):28876-88.

A Novel α-Ketoglutaric Semialdehyde Dehydrogenase. Evolutionary Insight into an Alternative Pathway of Bacterial L-Arabinose Metabolism.

Org. Biomol. Chem. 2006 May;4(9):1811-6.

Novel 6-Formylpterin Derivatives: Chemical Synthesis and O2 to ROS Conversion Activities.

Biosci. Biotechnol. Biochem. 2006 Mar;70(3):646-53.

Identification of genes affecting lipid content using transposon mutagenesis in Saccharomyces cerevisiae.

J. Biol. Chem. 2006 Feb;281(5):2612-23.

Cloning, Expression and Characterization of Bacterial L-Arabinose 1-Dehydrogenase Involved in an Alternative Pathway of L-Arabinose Metabolism.

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2005

　

Genes Cells. 2005 Oct;10(10):953-62.

Unfolding of higher DNA structures formed by the d(CGG) triplet repeat by UP1 protein

　

Nucleic Acids Res. 2005 Sep;33(15):4874-81.

Human vault-associated non-coding RNAs bind to mitoxantrone, a chemotherapeutic compound.

　

J. Biol. Chem.. 2005 May;280(19):18862-70.

Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D. 

　

Nucleic Acids Res. Suppl.. 2005 5:69-70.

Structure of RNA aptamer complexed with an RNA-binding peptide of Tat with aid of residue-specific 13C, 15N labeling.

　

Frontiers in Organic Chemistry 2005 1:343-355.

Reaction of NO with nucleic acid bases and its biological implication.

Pack S.P., Suzuki T., Ide H., Kodaki T., and Makino K

Nucleic Acids Res. 2005 Oct;33(18):5771-80.

Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides.

Nucleic Acids Symp. Ser. 2005 No. 49, 311-2.

Hydrogen bond removal of pterin derivative whose structure is similar to nucleic acid bases.

Nucleic Acids Symp. Ser 2005 No. 49, 309-10.

L-Arabinose 1-dehydrogenase: a novel enzyme involving in bacterial L-arabinose metabolism.

Nucleic Acids Symp. Ser. 2005 No. 49, 225-6.

Fabrication of efficient DNA microarray by additional surface modification and functional probe design.

Nucleic Acids Symp. Ser. 2005 No. 49, 95-6.

Biophysical and biochemical properties of oxanine-containing oligodeoxynucleotide.

J. Colloid. Interface Sci. 2005 Sep;289(1):125-31.

A novel method for synthesis of silica nanoparticles.

J. Biotechnol. 2005 Feb;115(3):239-48.

Generation of a strong promoter for Escherichia coli from eukaryotic genome DNA.

J. Biol. Chem. 2005 Mar;280(11):10340-9.

Complete reversal of coenzyme specificity of xylitol dehydrogenase and increase of thermostability by the introduction of structural zinc.

Nitric Oxide-Biol. and Chem. 2004 11:55.

DNA-Protein Cross-link Formation Mediated by Oxanine, a NO-Induced Damaged Base.

Makino K., Nakano T., Pack S.P., Kodaki T., and Ide H

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2004

　

Nucleic Acids Res.. 2004 Sep;32(17):5113-8.

Method for direct discrimination of intra- and intermolecular hydrogen bonds, and characterization of the G(:A):G(:A):G(:A):G heptad, with scalar couplings across hydrogen bonds. 

　

Nucleic Acids Res. Suppl.. 2004;(4):277-8.

Structure, stability and application to functional DNA/RNA of unique quadruplex.

　

Nucleic Acids Res. Suppl.. 2004;(4):111-2.

Structure of RNA aptamer for HIV Tat complexed with Tat-derived peptide.

　

Nucleic Acids Symp. Ser. 2004 No. 48, 249-50.

Chemical synthesis of oxanine-contained oligodeoxynucleotides.

Nucleic Acids Symp. Ser. 2004 No. 48, 197-8.

Various mutations by using yeast gene for protein-engineering.

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2003

　

J. Biol. Chem. 2003 Oct;278(42):41309-15. Epub 2003 Aug 7.

Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, Musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials and backbone dynamics.

　

J. Biol. Chem.. 2003 Jul 25;278(30): 28147-53.

Intramolecular higher order packing of parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad of GGA triplet repeat DNA.

　

Structure 2003 May Vol 11(5): 533-545.

Structural Basis of the Highly Efficient Trapping of the HIV Tat Protein by an RNA Aptamer.

　

Nucleic Acids Res. Suppl.. 2003;(3):51-2. 

RNA and DNA, which contain two GGAGG segments connected with UUUU or TTTT sequences, form entirely different quadruplex structures

　

Nucleic Acids Res. Suppl.. 2003;(3):231-2.

Enokizono Y, Matsugami A, Uesugi S, Fukuda H, Tsuchiya N, Sugimura T, Nagao M, Nakagama H,Katahira M.

　

Org. Lett. 2003 Sep;5(18):3173-6.

Nitration of 2'-deoxyguanosine by a NO/O2 gas mixture: identification and characterization of N2-nitro-2'-deoxyguanosine.

Nucleic Acids Res. Suppl. 2003;(3):303-4.

Differential transcriptional regulation of two distinct S-adenosylmethionine synthetase genes (SAM1 and SAM2) of Saccharomyces cerevisiae.

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2002

　

Nucleosides, Nucleotides & Nucleic Acids. 2002 Nov-Dec;21(11-12):785-801.

A comparison of the properties and the solution structure for RNA and DNA quadruplexes which contain two GGAGG sequences joined with a tetranucleotide linker.

　

J. Mol. Biol. 2002 Oct;322(5):955-970.

A Dimeric RNA Quadruplex Architecture Comprised of Two G:G(:A):G:G(:A) Hexads, G:G:G:G Tetrads and UUUU Loops.

　

Proc. Natl. Acad. Sci. USA.. 2002 Oct;99(20):12685-12690.

Unfolding of quadruplex structure in the G-rich strand of the minisatellite repeat by the binding protein UP1. 

　

Genes Cells 2002 Jun;7(6):567-79.

Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change. 

　

Nucleic Acids Res.. 2002 Feb;30(3):766-74.

Imino proton NMR analysis of HDV ribozymes: nested double pseudoknot structure and Mg2+ ion-binding site close to the catalytic core in solution.

　

Nucleic Acids Res. Suppl.. 2002;(2):177-8.

Quadruplex structures of RNA 14-mer, r(GGAGGUUUUGGAGG) and DNA 14-mer, d(GGAGGTTTTGGAGG).

　

Nucleic Acids Res. Suppl.. 2002;(2):49-50.

Unique quadruplex structures of d(GGA)4 (12-mer) and d(GGA)8 (24-mer)--direct evidence of the formation of non-canonical base pairs and structural comparison.

　
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2001

　

J. Mol. Biol. 2001 Oct;313(2):255-269. 

An Intramolecular Quadruplex of (GGA)4 Triplet Repeat DNA with a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad, and its Dimeric Interaction. 

　

J. Mol. Biol. 2001 Aug;311(5):973-88. 

Structure of the C-terminal RNA-binding Domain of hnRNP D0 (AUF1), its Interactions with RNA and DNA, and Change in Backbone Dynamics upon Complex Formation with DNA. 

　

J. Mol. Biol. 2001 Feb;306(2):213-25.

Interaction of the C-terminal domain of the E. coli RNA polymerase alpha subunit with the UP element: recognizing the backbone structure in the minor groove surface. 

　

Nucleic Acids Res. Suppl.. 2001;(1):271-2.

New quadruplex structure of GGA triplet repeat DNA--an intramolecular quadruplex composed of a G:G:G:G tetrad and G(:A):G(:A):G(:A):G heptad, and its dimerization. 

　
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2000

　

Genes Cells. 2000 May;5(5):371-88. 

A novel RNA motif that binds efficiently and specifically to the Tat protein of HIV and inhibits the trans- activation by Tat of transcription in vitro and in vivo. 

　

Nucleic Acids Symp. Ser.. 2000;(44):285-6.

NMR analysis of tertiary interactions in HDV ribozymes,

　

Nucleic Acids Symp. Ser.. 2000;(44):65-6.

NMR study of a novel RNA quadruplex structure,

　
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1999

　

Biochem. Biophys. Res. Commun.. 1999 Oct;264(2):327-33. 

Intramolecular quadruplex formation of the G-rich strand of the mouse hypervariable minisatellite Pc-1. 

　

J. Mol. Biol. 1999 Mar 26;287(2):315-30 

Structure, backbone dynamics and interactions with RNA of the C-terminal RNA-binding domain of a mouse neural RNA-binding protein, Musashi1. 

　

J. Mol. Biol. 1999 Mar;287(2):221-37 

Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0. 

　

Nucleic Acids Symp. Ser. 1999;(42):269-70.

Structural study of an RNA aptamer for a Tat protein complexed with ligands.

　

Nucleic Acids Symp. Ser. 1999;(42):221-2.

Design and NMR analysis of HDV ribozymes for structural investigation.

 
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