研究業績

論文 (Publications)

  • Kumagai, K., Kamba, K., Suzuki, T., Sekikawa, Y., Yuki, C., Hamada, M., Nagata, K., Takaori-Kondo, A., Wan, L., Katahira, M., Nagata, T., Sakamoto, T., Selection and characterization of aptamers targeting the Vif-CBFβ-ELOB-ELOC-CUL5 complex, J. Biochem., in press.
  • Umezawa, K., Ikeda, R., Sakamoto, T., Enomoto, Y., Nihashi, Y., Shinji, S., Shimosato, T., Kagami, H., Takaya, T., Development of the 12-Base Short Dimeric Myogenetic Oligodeoxynucleotide That Induces Myogenic Differentiation, BioTech, 13, 11 (2024).
  • Kusunoki, H., Sakamoto, T., Kobayashi, N., Kohno, T., Wakamatsu, K., Nagata, T., Structural insights into the interaction between the C-terminal-deleted BH3-like motif peptide of hepatitis B virus X protein and Bcl-xL, Biochemistry., 63, 632-643 (2024).
  • Kawai, G., Okada, K., Baba, S., Sato, A., Sakamoto, T., Kanai, A., Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus, J. Biochem., 175, 671-676 (2024).
  • Kumagai, K., Okubo, H., Amano, R., Kozu, T., Ochiai, M., Horiuchi, M., Sakamoto, T., Selection of aptamers using β-1,3-glucan recognition protein tagged proteins and curdlan beads. J. Biochem., 174, 433-440 (2023).
  • Takahashi, Y., Kakuta, K., Namioka, Y., Igarashi, A., Sakamoto, T., Hara, R.I., Sato, K., Wada, T., Synthesis of P-Modified DNA from Boranophosphate DNA as a Precursor via Acyl Phosphite Intermediates, J. Org. Chem., 88, 10617-10631 (2023).
  • 山岸賢司，坂本泰一，核酸アプタマーとターゲットの相互作用の熱力学的解析，Netsu Sokutei, 50, 96-102 (2023).
  • Nameki, N., Takizawa, M., Suzuki, T., Tani, S., Kobayashi, N., Sakamoto, T., Muto, Y., Kuwasako, K., Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1, Protein Sci., 31, e4437 (2022).
  • Minamisawa, M., Sato, Y., Ishiguro, E., Taniai, T., Sakamoto, T., Kawai, G., Saito, T., Saido, T.C., Amelioration of Alzheimer’s disease by gut–pancreas–liver–3 brain interaction in an App knock-in mouse model, Life, 12, 34 (2021).
  • Kusunoki, H., Tanaka, T., Ohshima, C., Sakamoto, T., Wakamatsu, K., Hamaguchi, I., The N93D mutation of the human T-cell leukemia virus type 1 envelope glycoprotein found in symptomatic patients enhances neuropilin-1 b1 domain binding, Biochim. Biophys. Acta, 1869, 140708 (2021).
  • Amano, R., Namekata, M., Horiuchi, M., Saso, M., Yanagisawa, T., Tanaka, Y., Ghani, F.I., Yamamoto, M., Sakamoto T., Specific Inhibition of FGF5-induced Cell Proliferation by RNA Aptamers, Sci. Reports, 11, 2976 (2021).
  • Fukunaga, J., Nomura, Y., Tanaka, Y., Torigoe, H., Nakamura, Y., Sakamoto, T., Kozu, T., A G-quadruplex-forming RNA aptamer binds to the MTG8 TAFH domain and dissociates the leukemic AML1-MTG8 fusion protein from DNA, FEBS Lett., 594, 3477-3489 (2020).
  • Raad, N.G., Ghattas, I.R., Amano, R., Watanabe, N., Sakamoto, T., Smith, C.A., Altered‐specificity mutants of the HIV Rev arginine‐rich motif‐RRE IIB interaction, Journal of Molecular Recognition, 33, e2833 (2020).
  • Yoshida H., Sato K., Ishikawa T., Sakamoto T., Yamagishi K., Binding interaction analysis of RNA aptamer-Fc region of human Immunoglobulin G using fragment molecular orbital calculation, Chem. Phys. Lett. 738, 136854 (2020).
  • 石井 清一郎, 関口 真裕, 吉田 尚恵, 増川 恵介, 石川 岳志, 坂本 泰一, 山岸 賢司，分子動力学計算によるRNAアプタマーとヒト抗体の複合体形成におけるCa2+の役割の解析，Journal of Computer Chemistry, Japan, 18, 208-210 (2019).
  • Maeda, Y., Hara, R.I., Nishina, K., Yoshida-Tanaka, K., Sakamoto, T., Yokota, T., Wada, T., Artificial cationic peptides that increase nuclease resistance of siRNA without disturbing RNAi activity, Nucleosides Nucleotides and Nucleic Acids, 38, 338-348 (2019).
  • Takahashi, D., Suzuki, K., Sakamoto, T., Iwamoto, T. Murata, T., Sakane, F., Crystal structure and calcium-induced conformational changes of diacylglycerol kinase α EF-hand domains, Protein Sci,. 28, 694-706 (2019).
  • Yamaguchi, K., Asakura, K., Imamura, M., Kawai, G., Sakamoto, T., Furihata, T., Linhardt, R.J., Igarashi, K., Toida, T., Higashi, K., Polyamines stimulate the CHSY1 synthesis through the unfolding of the RNA G-quadruplex at the 5'-untraslated region, Biochem. J., 475, 3797-3812 (2018)
  • Koizumi, K., Maeda, Y., Kano, T., Yoshida, H., Sakamoto, T., Yamagishi, K., Ueno, Y., Synthesis of 4'-C-aminoalkyl-2'-O-methyl modified RNA and their biological properties, Bioorg. Med. Chem., 26, 3521-3534 (2018).
  • Sakamoto, T., Ennifar, E., Nakamura, Y., Thermodynamic study of aptamers binding to their target proteins, Biochimie, 145, 91-97 (2018).
  • Takada, K., Amano, R., Nomura, Y., Tanaka, Y., Sugiyama, S., Nagata, T., Katahira, M., Nakamura, Y., Kozu, T., Sakamoto, T., Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses, FEBS Open Bio, 8, 264-270 (2018).
  • Nomura, Y., Yamazaki, K., Amano, R., Takada, K., Nagata, T., Kobayashi, N., Tanaka, Y., Fukunaga, J., Katahira, M., Kozu, T., Nakamura, Y., Haishima, Y., Torigoe, H., Sakamoto, T., Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain, J. Biochem. 162, 432-436 (2017).
  • Sakamoto, T., NMR study of aptamers, Aptamers, 1, 13-18 (2017).
  • Amano, R., Aoki, K., Miyakawa, S., Nakamura, Y., Kozu, T., Kawai, G., Sakamoto, T., NMR monitoring of the SELEX process to confirm enrichment of structured RNA, Sci. Reports 7, 283 (2017).
  • Minagawa, H., Onodera, K., Fujita, H., Sakamoto, T., Akitomi, J., Kaneko, N., Shiratori, I., Kuwahara, M., Horii, K., Waga, I., Selection, characterization and application of artificial DNA aptamer containing appended bases with sub-nanomolar affinity for a salivary biomarker, Sci. Reports 7, 42716 (2017).
  • Hara, R.I., Maeda, Y., Sakamoto, T., Wada, T., Double-stranded RNA-binding artificial cationic oligosaccharides stabilizing siRNAs with low N/P ratio, Org. Biomol. Chem. 15, 1710-1717 (2017).
  • Kuwasako, K., Nameki, N., Tsuda, K., Takahashi, M., Sato, A., Tochio, N., Inoue, M., Terada, T., Kigawa, T., Kobayashi, N., Shirouzu, M., Ito, T., Sakamoto, T., Wakamatsu, K., Güntert, P., Takahashi, S., Yokoyama S., Muto, Y., Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment, Protein Sci. 26, 280-291 (2017).
  • Oguro, A., Yanagida, A., Fujieda, Y., Amano, R., Otsu, M., Sakamoto, T., Kawai, G., Matsufuji, S., Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding, J. Biochem. 161, 197-206 (2017).
  • Amano, R., Takada, K., Tanaka, Y., Nakamura, Y., Kawai, G., Kozu, T., Sakamoto, T., Kinetic and thermodynamic analyses of interaction between a high-affinity RNA aptamer and its target protein, Biochemistry, 55, 6221-6229 (2016).
  • Ohuchi, S.J., Sagawa, F., Sakamoto, T., Inoue, T., Altering the orientation of a fused protein to the RNA-binding ribosomal protein L7Ae and its derivatives through circular permutation, Biochem. Biophys. Res. Commun. 466, 388-392 (2015).
  • Ohuchi, S.J., Sagawa, F., Sakamoto, T., Inoue, T., A trifunctional, triangular RNA-protein complex, FEBS Lett. 589, 2424-2428 (2015).
  • Iwashita, S., Suzuki, T., Yasuda, T., Nakashima, K., Sakamoto, T., Kohno, T., Takahashi, I., Kobayashi, T., Ohono-Iwashita, Y., Imajoh-Oomi, S., Song, Si-Y., Dohmae, N., Mammalian Bcnt/Cfdp1, a potential epigenetic factor characterized by an acidic stretch in the disordered N-terminal and S250 phosphorylation in the conserved C-terminal regions, Biosci. Rep. 35, e00228 (2015).
  • Nomura, Y., Tanaka, Y., Fukunaga, J., Fujiwara, K., Chiba, M., Iibuchi, I., Tanaka, T., Nakamura, Y., Kawai, G., Kozu, T., and Sakamoto, T., Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain. J. Biochem. 154, 513-519 (2013).
  • Fukunaga J., Nomura Y.,Tanaka Y., AmanoR., Tanaka T.,Nakamura Y., Kawai G., Sakamoto T., and KozuT., The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element, RNA, 19, 927-936 (2013).
  • Nomura Y., Sugiyama S., Sakamoto T., Miyakawa S., Adachi H., Takano K., Murakami S., Inoue T., Mori Y., Nakamura Y., Matsumura H., Conformational plasticity of RNA for target recognition as revealed by the 2.15 Å crystal structure of a human IgG-aptamer complex, NucleicAcids Res. 38, 7822-7829 (2010).
  • Kanai A., Sato A., Fukuda Y., Okada K., Matsuda T., Sakamoto T., MutoY.,Yokoyama S., Kawai G,.Tomita M., Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus, RNA 15, 420-431 (2009).
  • Sugiyama S, Nomura Y, Sakamoto T,Kitatani T, Kobayashi A, Miyakawa S, Takahashi Y, Adachi H, Takano K, Murakami S, Inoue T, Mori Y, Nakamura Y, Matsumura H., Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment, Acta Crystallogr Sect F Struct Biol Cryst Commun 64, 942-944 (2008).
  • Miyakawa S., Nomura Y., Sakamoto T., Yamaguchi Y., Kato K., Yamazaki S., Nakamura Y., Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G, RNA, 14, 1154-1163 (2008).
  • Nomura, Y., Kajikawa, M., Baba, S., Nakazato, S., Imai, T., Sakamoto, T., Okada, N., and Kawai, G., Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2, Nucleic Acids Res. 34, 5184-5193 (2006).
  • Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kanai, A. and Kawai, G., 1H, 13C and 15N resonance assignments of the 2´-5´ RNA ligase-like protein from Pyrococcus furiosus, J. Biomol. NMR 36, 16 (2006).
  • Okada, K., Takahashi, M., Sakamoto, T., Nakamura, K., Kanai, A. and Kawai, G., Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus, Nucleosides, Nucleotides and Nucleic Acids 25, 383-395 (2006).
  • Kashida, H., Tanaka, M., Baba, S., Sakamoto, T., Kawai, G., Asanuma, H. and *Komiyama, M., Covalent Incorporation of Methyl Red Dyes into Double-Stranded DNA for Their Ordered Clustering, Chem. Eur. J. 12, 777-784 (2006).
  • 野村祐介，坂本泰一，河合剛太，NMR法によるRNAの構造解析におけるRDCを用いた二段階精密化の効果，分光研究, 55, 252-258 (2006).
  • Sakamoto, T., Oguro, A., Kawai,G., Ohtsu, T., Nakamura, Y., NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A, Nucleic Acids Res., 33, 745-754 (2005).
  • Someya, T., Sakamoto, T., Takasu, A., Kawai, G., 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, 691-700 (2004).
  • 馬場清喜，清宮恭子，木村友美，冨士原和也，染谷龍彦，坂本泰一，河合剛太, NMR法によるRNAの立体構造解析における残余双極子相互作用の効果，分光研究，53, 171-176 (2004).
  • Liang, X., Asanuma, H., Kashida, H., Takasu, A., Sakamoto, T., Kawai, G., Komiyama, M., 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, 16408-16415 (2003).
  • Sakamoto, T., Morita, S., Tabata, K., Nakamura, K., Kawai, G., Solution structure of a SRP19 binding domain in human SRP RNA, J. Biochem., 132, 177-182 (2002).
  • Tanaka, Y., Tagaya, M.,Hori, T., Sakamoto, T., Kurihara, Y., Katahira, M., Uesugi, S.,Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change, Genes Cells, 7, 567-579 (2002).
  • Tanaka, Y., Hori, T., Tagaya, M., Sakamoto, T., Kurihara, Y., Katahira, M., Uesugi, S., 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., 30, 766-774 (2002).
  • Nakamura, K., Miyamoto, H., Suzuma, S., Sakamoto, T., Kawai, G., Yamane, K., Minimal functional structure of Escherichia coli 4.5S RNA required for binding EF-G, J. Biol. Chem., 276, 22844-22849 (2001).
  • Sakamoto T., Tanaka T., Ito Y., Rajesh S., Iwamoto-Sugai M., Kodera Y., Tsuchida N., Shibata T., Kohno T., An NMR analysis of Ubiquitin recognition by Yeast Ubiquitin Hydrolase: Evidence for novel substrate recognition by a cysteine protease, Biochemistry 38, 11634-11642 (1999).
  • Rajesh S., Sakamoto T., Iwamoto-Sugai M., Shibata T., Kohno T., Ito Y., Ubiquitin binding Interface mapping on Yeast Ubiquitin Hydrolase by NMR chemical shift perturbation, Biochemistry 38, 9242-9253 (1999).
  • Sakamoto T., Kawai G., Katahira M., Kim M.H., Tanaka Y., Kurihara Y., Kohno T., Watanabe S., Yokoyama S., Watanabe K., Uesugi S., 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 which is not of side-by-side type, J. Biochem. 122, 556-562 (1997).
  • Sakamoto T., Tanaka Y., Kuwabara T., Kim M.H., Kurihara Y., Katahira M., Uesugi S., Properties of an HDV ribozyme which consists of three RNA oligomer strands, J. Biochem. 121, 1123-1128 (1997).
  • Sakamoto T., Kim M.H., Kurihara Y., Sasaki N., Noguchi T., Katahira M., Uesugi S., Properties of a hammerhead ribozyme with deletion of stem II, J. Biochem. 121, 288-294 (1997)