トップページ｜埼玉大学 根本研究室

Publications

2023年

• “A novel agonist for FGF receptor-1 based on homobivalent single domain antibodies binding to the receptor domain III functions as FGF2 ligand”, Ryo Yonehara, Shigefumi Kumachi, Kenji Kashiwagi, Kanako Wakabayashi-Nakao, Maiko Motohashi, Taihei Murakami, Teruhiko Yanagisawa, Hidenao Arai, Akikazu Murakami, Yukio Ueno, Naoto Nemoto, and Masayuki Tsuchiya, J Bio Chem, 299, 2, 102804 (2023)                                                         

2022年

2021年

• "Nasal delivery of single-domain antibodies improves symptoms of SARS-CoV-2 infection in an animal model” PLOS Pathogens, Haga K, Takai-Todaka R, Matsumura Y, Takano T, Tojo T, Nagami A, Ishida Y, Masaki H, Tsuchiya M, Ebisudani T, Sugimoto S, Sato T,  Yasuda H, Fukunaga K, Sawada A, Nemoto N, Song C, Murata K, Morimoto T, Katayama K, 17, e1009542 (2021) 
• ”Interleukin-17A Peptide Aptamers with an Unexpected Binding Moiety Selected by cDNA Display under Heterogenous Conditions”, ACS Medicinal Chemistry Letters, Anzai H, Terai T, Wakabayashi-Nakao K, Noguchi T, Kumachi S, Tsuchiya M, and Nemoto N, 12, 1427-1434 (2021)  
•  “cDNA Display-Mediated Immuno-PCR (cD-IPCR): An Ultrasensitive Immunoassay for Biomolecular Detection”, Chathuni Jayathilake and Naoto Nemoto, Methods in Molecular Biology "Proteomic Profiling", 2261, 307-321(2021)   
•   “高速進化技術で「抗体」デザイン・・・医薬品・診断薬への実用化へ”, 根本直人, 埼経協ニュース, 421号, 6,(2021)       
•   “膜タンパク質を標的とした高速人工ペプチドリガンドスクリーニングシステム”, 鈴木香絵、熊地重文、戸澤譲、根本直人, 細胞, 53, 5(2021)         

2020年

• “cDNA Display: A Stable and Simple Genotype-Phenotype Coupling Using a Cell-Free Translation System”,Arai H, Kumachi S, Nemoto N., Methods Mol Biol.,2070, 43-56, (2020)
• "In vitro selection of anti-gliadin single-domain antibodies from a naïve library for cDNA-display mediated immuno-PCR.", Jayathilake C, Kumachi S, Arai H, Motohashi M, Terai T, Murakami A, Nemoto N., Anal Biochem, 589, (2020)
• “In Vitro Construction of Large-scale DNA Libraries from Fragments Containing Random Regions using Deoxyinosine-containing Oligonucleotides and Endonuclease V.”, Yamamoto Y, Terai T, Kumachi S, Nemoto N., ACS Comb Sci.22 4, 165-171, (2020) 
• “Photocrosslinking of cDNA Display Molecules with Their Target Proteins as a New Strategy for Peptide Selection.”, Terai T, Koike T, Nemoto N., Molecules, 25, 6, E1472, (2020)

2019年

•   “Selection of Peptides that Associate with Dye-Conjugated Solid Surfaces in a pH-Dependent Manner Using cDNA Display” Terai, T., Anzai, H., Nemoto, N., ACS Omega, 4, 4,  7378-7384(2019)                                                                                                     
•  “A novel immuno-PCR method using cDNA display”, Anzai H, Terai T, Jayathilake C, Suzuki T, Nemoto N., Anal Biochem, 578, 1-6(2019)   
•    「ペプチドデザインと分子ロボティクス」根本直人, 分子ロボティクス研究会著　村田智編　CBI学会出版, 分子ロボティクス概論, 188-191(2019) 
•   “cDNA Display Mediated Immuno-PCR (cD-IPCR): A Novel PCR-based Antigen Detection Method” Jayathilake, C., Terai, T. and Nemoto, Bio-protocol, 9, 24,e3457(2019)    

2018年

• "In Vitro Selection of Single-Domain Antibody (VHH) Using cDNA Display.", Nemoto N, Kumachi S, Arai H., Methods in Molecular Biology, 1827, 269-285(2018)
• "Anti-survivin single-domain antibodies derived from an artificial library including three synthetic random regions by in vitro selection using cDNA display.", Suzuki T, Mochizuki Y, Kimura S, Akazawa-Ogawa Y, Hagihara Y, Nemoto N., Biochemical and Biophysical Research Communications, 503, 3, 2054-2060(2018)
• "High-throughput Selection of Pore-forming Peptides Assembling in Liposome Membranes by Combining cDNA Display Method with Cell Sorter System", Hiroki Miyajima and Naoto Nemoto,Peptide Science 2017 (Edited by Ikuo Fujii), 30-31(2018)
• "A Study to Select pH-dependent Phenolphthalein-binding Peptide Aptamers by cDNA Display Method", Hiroki Anzai, Takuya Terai, and Naoto Nemoto, Peptide Science 2017 (Edited by Ikuo Fujii), 54-55(2018)

2017年

• ”In vitro Selection of Random Peptides against Artificial Lipid Bilayers: A Potential Tool to Immobilize Molecules on Membranes”, Shota Kobayashi, Takuya Terai, Yuki Yoshikawa, Ryoya Ohkawa, Mika Ebihara, Masahito Hayashi, Kingo Takiguchi, and Naoto Nemoto, ChemComm, 53, 3458-3461(2017)
• ”Enhanced mRNA-protein fusion efficiency of a single-domain antibody by selection of mRNA display with additional random sequences in the terminal translated regions”, Kazuki Takahashi, Masato Sunohara, Takuya Terai, Shigefumi Kumachi and Naoto Nemoto, Biophysics and Physicobiology, 14, 23-28(2017)
• "ｃDNAディスプレイ法によるペプチドスクリーニング技術", 寺井琢也、熊地重文、根本直人,「ペプチド医薬品のスクリーニング・安定化・製剤化技術」,40-49(2017)
• "Iodoacetyl-functionalized pullulan: A supplemental enhancer for single-domain antibody-polyclonal antibody sandwich enzyme-linked immunosorbent assay for detection of survivin", Matsushita T, Arai H, Koyama T, Hatano K, Nemoto N, Matsuoka K.,Bioorg Med Chem Lett.,27,21,4844-4848(2017)

2016年

• “試験管内進化を加速するcDNA display システム”, 熊地重文、根本直人, 酵素工学ニュース, 76, 21-25 (2016)
• ”An RNA Binding Peptide Consisting of Four Types of Amino Acid by in Vitro Selection Using cDNA Display”, Shigefumi Kumachi, Yuzuru Husimi, and Naoto Nemoto, ACS Omega, 1, 52–57 (2016)
• 「cDNAディスプレイによる機能性ペプチドアプタマーの創出」根本直人,生物学会誌,94(8).481-484(2016)        

2015年

• ” A versatile puromycin-linker using cnvK for high-throughput in vitro selection by cDNA display”, Yuki Mochizuki, Takeru Suzuki, Kenzo Fujimoto, Naoto Nemoto, J Biotech. ,212, 174-180 (2015)
• ” Functional Analysis of Liposome Anchoring Peptide Selected by Complementary DNA display (cDNA display)”, Naoto Nemoto, Yuki Yoshikawa, Toshiki Miyajima, and Shota Kobayashi, Peptide Science 2014 (Edited by Akira Otaka), 71-72 (2015)
• ”Easy and rapid binding assay for functional analysis of disulfide-containing peptides by a pull-down method using a puromycin-linker and a cell-free translation system”, Tanemura Y, Mochizuki Y, Kumachi S, Nemoto N., Biology (Basel), 4, 161-172  (2015)
• ” Detection of ultra-low levels of DNA changes by drinking water: epidemiologically important finding.”, Kumari P, Kamiseki M, Biyani M, Suzuki M, Nemoto N, Aita T, Nishigaki K., J Biochem., 157, 113-119 (2015)
• “An RI-nondependent high-sensitivity method for measuring the activity of glioblastoma-related O(6)-methylguanine-DNA methyltransferase (MGMT).” Hongo A, Gu R, Suzuki M, Nemoto N, Nishigaki K., Anal Biochem., 480, 82-84        (2015)

2014年

• “架橋ペプチドの進化工学とその応用”根本直人, 化学工業,  65(12), 13-18 (2014)
• “Familial clustering of mice consistent to known pedigrees enabled by the genome profiling (GP) method” Harshita Sharma, Fumihito Ohtani, Parmila Kumari, Deepti Diwan, Naoko Ohara, Tetsuya Kobayashi, Miho Suzuki, Naoto Nemoto, Yoshibumi Matsushima, Koichi Nishigaki, Biophysics, 10, 55-62 (2014)
• “Establishment of a reborn MMV-microarray technology: realization of microbiome analysis and other hitherto inaccessible technologies” Sharma H, Kinoshita Y, Fujiu S, Nomura S, Sawada M, Ahmed S, Shibuya M, Shirai　K, Takamatsu S, Watanabe T, Yamazaki H, Kamiyama R, Kobayashi T, Arai H, Suzuki M, Nemoto N, Ando K, Uchida H, Kitamura K, Takei O, Nishigaki K, BMC Biotechnol., 14(1), 78 (2014)    
• “Versatile C-terminal specific biotinylation of proteins using both a puromycin-linker and a cell-free translation system for studying high-throughput protein-molecule interactions” Nemoto N, Fukushima T, Kumachi S, Suzuki M, Nishigaki K, Kubo T., Anal Chem., 86(17), 8535-8540 (2014)
• “Amino group binding peptide aptamers with  double disulphide-bridged loops selected by in vitro selection using cDNA display” Mochizuki Y, Nishigaki K, Nemoto N., Chem Commun. 50(42), 5608-5610 (2014)
• “Functional analysis of peptide aptamers against survivin selected from a novel  three-finger scaffold library by cDNA display” Takeru Suzuki, Yuki Mochizuki, Yuya Yotsumoto, Miho Suzuki, Koichi Nishigaki, Tai Kubo, Naoto Nemoto, Peptide Science 2013: Y. Nishiuchi and T. Teshima (Eds), 175-176 (2014)
• “Optimal terminal sequences for continuous or serial isothermal amplification of dsRNA with norovirus RNA replicase” Hidenao Arai, Koichi Nishigaki, Naoto Nemoto, Miho Suzuki and Yuzuru Husimi, Biophysics, 10, 15-23 (2014)
• “Systematic genome sequence differences among leaf cells within individual trees” Diwan D, Komazaki S, Suzuki M, Nemoto N, Aita T, Satake A, Nishigaki K., BMC Genomics., 15(1),  142 (2014)                                      

2013年

• “Characterization of Norovirus RNA replicase for in vitro amplification of RNA”, Arai H, Nishigaki K, Nemoto N, Suzuki M, Husimi Y., BMC Biotechnol., 13, 85 (2013)
• “遺伝子型－表現型対応付け技術” 根本直人,『進化分子工学－高速分子進化によるタンパク質・核酸の開発－』第２編第３章, (NTS), 161-170 (2013)
• “cDNA displayによる分子デザイン　－mRNA display(in vitro virus)からcDNA displayへ－” 根本直人、望月佑樹、上野真吾、生物物理, 53(5), 250-253 (2013)
• “Increasing the library size in cDNA display by optimizing purification procedures” Mochizuki Y, Kumachi S, Nishigaki K, Nemoto N., Biol Proced Online, 15(1), 7 (2013)
• “A pull-down method with a biotinylated bait protein prepared by cell-free translation using a puromycin-linker” Yuki Mochizuki, Fumiaki Kohno, Koichi Nishigaki, Naoto Nemoto, Analytical Biochemistry, 434, 93-95 (2013)

2012年

• “A pull-down method with a biotinylated bait protein prepared by cell-free translation using a puromycin-linker” Mochizuki, Y., Kohno, F., Nishigaki, K., Nemoto, N. Anal. Biochem. (accepted)
• “Evolutionary Molecular Engineering to Efficiently Direct in vitro Protein Synthesis” Biyani, M., Biyani, M., Nemoto, N. and Husimi. H. “Cell-free Protein Synthesis” (Edited by M. Biyani) 51-62 (2012)
• “Improvement of a puromycin-linker to extend the selection target varieties in cDNA display method.” Ueno S, Kimura S, Ichiki T, Nemoto N. J Biotechnol. 162, 299? 302 (2012)
• “Photoassisted Recovery of DNA Molecules for On-chip Directed Evolution” Ueno, S., Ono, A., Kobayashi, R., Tanaka, Y., Sato, S., Biyani, M., Nemoto, N., and Ichiki, T. J. Photopolym. Sci. Technol. 25, 67-72 (2012)
• "In vitro selection of a peptide antagonist of growth hormone secretagogue receptor using cDNA display" Ueno, S., Yoshida, S., Mondal, M., Nishina, K., Koyama, M., Sakata, I., Miura, K., Hayashi, Y., Nemoto, N., Nishigaki, K., and Sakai, K. Proc Natl Acad Sci U S A. 109, 11121-11126 (2012)
• “Antagonistic effect of disulfide-rich peptide aptamers selected by cDNA display on interleukin-6-dependent cell proliferation” Nemoto N, Tsutsui C, Yamaguchi J, Ueno S, Machida M, Kobayashi T, Sakai T. Biochem Biophys Res Commun. 421, 129-133 (2012)
• “In vitro Selection of Peptide Aptamers against Acetylcholine-binding Protein (AChBP) from Disulfide-rich Peptide Library by cDNA Display” Nemoto, N., Kimura, S., Kumachi, S., Cai, W., Suzuki, M., Nishigaki, K., and Kubo, T., Peptide Science 2011: K. Sakaguchi (Ed.), 89-90 (2012)
• “Evolution of Disulfide-Rich Peptide Aptamers Using cDNA Display” Y. Mochizuki and N. Nemoto Methods in Mol. Biol. “Ribosome Display and Related Technologies” Douthwaite, Julie A.; Jackson, Ronald H. (Eds.), 805, 237-250 (2012）
• “cDNA Display: Rapid Stabilization of mRNA Display” S. Ueno and N. Nemoto, Methods in Mol. Biol. “Ribosome Display and Related Technologies” Douthwaite, Julie A.; Jackson, Ronald H. (Eds.), 805, 113-135 (2012）

2011年

• “One-Pot Preparation of mRNA/cDNA Display by a Novel and Versatile Puromycin-Linker DNA” Y. Mochizuki, M. Biyani, S. Tsuji-Ueno, M. Suzuki, K. Nishigaki, Y. Husimi, and N. Nemoto, ACS comb Sci. 13, 5, 478-485 (2011)
• “Microintaglio Printing of Biomolecules and Its Application to In situ Production of Messenger Ribonucleic Acid Display Microarray” M. Biyani, T. Osawa, N. Nemoto, T. Ichiki Applied Physics Express, 4, 4, 041101 (2011)
• “Novel High-affinity Aβ-binding Peptides Identified by an Advanced In Vitro Evolution, Progressive Library Method” S. Tsuji-Ueno, M. Komatsu, K. Iguchi, M. Takahashi, S. Yoshino, M. SuzukiN. Nemoto, Nishigaki K. Protein Pept Lett. 18, 642-650 (2011)
• “Directed evolution of a three-finger neurotoxin by using cDNA display yields antagonists as well as agonists of interleukin-6 receptor signaling” M. Naimuddin, S. Kobayashi, C. Tsutsui, M. Machida, N. Nemoto, T. Sakai, T. Kubo, Mol. Brain, 4, 2 (2011)

2010年

• “Gel shift selection of translation enhancer sequences using messenger RNA display” M. Biyani, M. Biyani, N. Nemoto, T. Ichiki, K. Nishigaki, Y. Husimi, Anal. Biochem. 409, 105-111 (2010)
• “DNA-linked protein array for high-throughput proteomics: from spatially unknown DNA arrays to identifiable protein arrays” Biyani, M., Nemoto, N. and Ichiki, T., Nano LIFE, 1, 33-43 (2010)
• “In vitro Selection of Cysteine-rich Peptide Aptamers against the IL-6 Receptor using cDNA display” N. Nemoto, J. Yamaguchi, M. Naimuddin, M. Machida and Y. Husimi, Peptide Science 2009: K. Okamoto (Ed.), 115-118 (2010)

2009年

• “cDNA display: a novel screening methods for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA-protein fusions.” Yamaguchi, J., Naimuddin, M., Biyani, M., Sasaki, T., Machida, M., Kubo, T., Funatsu, T., Husimi, Y. and Nemoto, N. Nucleic Acids Res. 37, e108 (2009)
• “Development of systemic in vitro evolution and its application to generation of peptide-aptamer-based inhibitors of cathepsin E.” Kitamura, K., Yoshida, C., Kinoshita, Y., Kadowaki, T., Takahashi, Y., Tayama, T., Kawakubo,T., Naimuddin, M., Salimullah, M., Nemoto, N., Hanada, K., Husimi, Y., Yamamoto, K. and Nishigaki,K. J Mol Biol. 387, 1186-1198 (2009)
• “Host-parasite relations of bacteria and phages can be unveiled by oligostickiness, a measure of relaxed sequence similarity” Ahmed, S., Saito, A., Suzuki, M., Nemoto, N. and Nishigaki K.　 Bioinformatics, 25, 563-570 (2009)