Original papers/ Reviews / Presentations / Patents
Original papers
*corresponding author
Chen, Q; Yamada, T; Murata, A; Sugai, A; Matsushita, Y; Nakatani, K.* A machine learning approach toward generating the focused molecule library targeting CAG repeat DNA. Digital Discovery. 2024, 3, 243–248.
https://doi.org/10.1039/D3DD00160A
Chen, Q; Yamada, T; Miyagawa, K; Murata, A; Shoji M; Nakatani, K.* A New Small Molecule DoNA Binding to CAG Repeat RNA. Bioorganic & Medicinal Chemistry, 2024, 98, 117580.
https://doi.org/10.1016/j.bmc.2023.117580
Fujino, Y; Ueyama, M; Ishiguro, T; Ozawa, D; Ito, H; Sugiki, T; Murata, A; Ishiguro, A; Gendron, T; Mori, K; Tokuda, E; Taminato, T; Konno, T; Koyama, A; Kawabe, Y; Takeuchi, T; Furukawa, Y; Fujiwara, T; Ikeda, M; Mizuno, T; Mochizuki, H; Mizusawa, H; Wada, K; Ishikawa, K; Onodera, O; Nakatani, K; Petrucelli, L; Taguchi, H; Nagai, Y.* FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA in C9orf72-linked ALS/FTD. eLife. 2023, 12: RP84338.
https://doi.org/10.7554/eLife.84338.3 Open Access
Ulhusna, A.; Murata, A.; Nakatani, K.* Inhibitory Effects of Mismatch Binding Molecules on the Repair Reaction of Uracil-Containing DNA. Biochemistry. 2022, 61 (22), 2522–2530.
https://doi.org/10.1021/acs.biochem.2c00344.
Takashima, Y.; Murata, A.*; Iida, K.; Sugai, A.; Hagiwara, M.; Nakatani, K.* Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding. ACS Chemical Biology. 2022, 17 (10), 2817–2827. On-line publication on Sep. 23, 2022. https://doi.org/10.1021/acschembio.2c00452 Open Access
Hsu, H.-T.; Murata, A.; Dohno, C.; Nakatani, K.; Chang, K.* Premature Translation Termination Mediated Non-ER Stress Induced ATF6 Activation by a Ligand-Dependent Ribosomal Frameshifting Circuit. Nucleic Acids Research. 2022, 50 (9), 5369–5383. https://doi.org/10.1093/NAR/GKAC257. Open Access
Das, B.; Nagano, K.; Kawai, G.; Murata, A.; Nakatani, K.* 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. Journal of Organic Chemistry. 2022, 87 (1), 340–350. https://doi.org/10.1021/acs.joc.1c02383.
Mukherjee, S.*; Murata, A.; Ishida, R.; Sugai, A.; Dohno, C.; Hamada, M.; Krishna, S.; Nakatani, K. HT-SELEX-Based Identification of Binding Pre-MiRNA Hairpin-Motif for Small Molecules. Molecular Therapy – Nucleic Acids. 2021, 27, 165–174. https://doi.org/10.1016/j.omtn.2021.11.021. Open Access
Ni, L.; Yamada, T.; Murata, A.; Nakatani, K.* Mismatch Binding Ligand Upregulated Back-Splicing Reaction Producing Circular RNA in a Cellular Model. Chemical Communications. 2022, 58 (22), 3629–3632. https://doi.org/10.1039/d1cc06936e.
Furuzono, T.; Murata, A.; Okuda, S.; Mizutani, K.; Adachi, T.; Nakatani, K.* Speeding Drug Discovery Targeting RNAs: An Iterative “RNA Selection-Compounds Screening Cycle“ for Exploring RNA-Small Molecule Pairs. Bioorganic and Medicinal Chemistry. 2021. 36, 116070–116076. https://doi.org/10.1016/j.bmc.2021.116070.
Das, B.; Murata, A.; Nakatani, K.* A Small-Molecule Fluorescence Probe ANP77 for Sensing RNA Internal Loop of C, U and A/CC Motifs and Their Binding Molecules. Nucleic Acids Research. 2021, 49 (15), 8462–8470. https://doi.org/10.1093/nar/gkab650. Open Access
Murata, A.; Mori, Y.; Di, Y.; Sugai, A.; Das, B.; Takashima, Y.; Nakatani, K.* Small Molecule-Induced Dimerization of Hairpin RNA Interfered with the Dicer Cleavage Reaction. Biochemistry 2021, 60 (4), 245–249. https://doi.org/10.1021/acs.biochem.0c00920.
Nakamori, M.; Panigrahi, G. B.; Lanni, S.; Gall-Duncan, T.; Hayakawa, H.; Tanaka, H.; Luo, J.; Otabe, T.; Li, J.; Sakata, A.; Caron, M.-C.; Joshi, N.; Prasolava, T.; Chiang, K.; Masson, J.-Y.; Wold, M. S.; Wang, X.; Lee, M. Y. W. T.; Huddleston, J.; Munson, K. M.; Davidson, S.; Layeghifard, M.; Edward, L.-M.; Gallon, R.; Santibanez-Koref, M.; Murata, A.; Takahashi, M. P.; Eichler, E. E.; Shlien, A.; Nakatani, K.; Mochizuki, H.; Pearson, C. E.* A Slipped-CAG DNA-Binding Small Molecule Induces Trinucleotide-Repeat Contractions in Vivo. Nature Genetics. 2020, 52 (2), 146–159. https://doi.org/10.1038/s41588-019-0575-8.
Takei, F.; Akiyama, M.; Murata, A.; Sugai, A.; Nakatani, K.; Yamashita, I.* RT-Hpro-PCR: A MicroRNA Detection System Using a Primer with a DNA Tag. ChemBioChem. 2020, 21 (4), 477–480. https://doi.org/10.1002/cbic.201900382.
Matsumoto, J.; Nakamori, M.; Okamoto, T.; Murata, A.; Dohno, C.; Nakatani, K. The Dimeric Form of 1,3-Diaminoisoquinoline Derivative Rescued the Mis-Splicing of Atp2a1 and Clcn1 Genes in Myotonic Dystrophy Type 1 Mouse Model. Chemistry – A European Journal.2020, 26 (63), 14305–14309. https://doi.org/10.1002/chem.202001572.
Mukherjee, S.; Blaszczyk, L.; Rypniewski, W.; Falschlunger, C.; Micura, R.; Murata, A.; Dohno, C.; Nakatani, K.; Kiliszek, A.* Structural Insights into Synthetic Ligands Targeting A-A Pairs in Disease-Related CAG RNA Repeats. Nucleic Acids Research. 2019, 47 (20), 10906–10913. https://doi.org/10.1093/nar/gkz832. Open Access
Murata, A.; Nakamori, M.; Nakatani, K.* Modulating RNA Secondary and Tertiary Structures by Mismatch Binding Ligands. Methods. 2019, 167, 78–91. https://doi.org/10.1016/j.ymeth.2019.05.006.
Otabe, T.; Nagano, K.; Kawai, G.; Murata, A.; Nakatani, K.* 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. 2019, 27 (10), 2140–2148. https://doi.org/10.1016/j.bmc.2019.03.031.
Matsumoto, S.; Caliskan, N.; Rodnina, M. V; Murata, A.*; Nakatani, K.* Small Synthetic Molecule-Stabilized RNA Pseudoknot as an Activator for –1 Ribosomal Frameshifting. Nucleic Acids Research. 2018, 46 (16), 8079–8089. https://doi.org/10.1093/nar/gky689. *corresponding authors Open Access
Li, J.; Nakamori, M.; Matsumoto, J.; Murata, A.; Dohno, C.; Kiliszek, A.; Taylor, K.; Sobczak, K.; Nakatani, K.* A Dimeric 2,9-Diamino-1,10-Phenanthroline Derivative Improves Alternative Splicing in Myotonic Dystrophy Type 1 Cell and Mouse Models. Chemistry – A European Journal. 2018, 24 (68), 18115–18122. https://doi.org/10.1002/chem.201804368.
Nakatani, K.*; Natsuhara, N.; Mori, Y.; Mukherjee, S.; Das, B.; Murata, A. Synthesis of Naphthyridine Dimers with Conformational Restriction and Binding to DNA and RNA. Chemistry – An Asian Journal. 2017, 12 (23), 3077–3087. https://doi.org/10.1002/asia.201701293.
Matsumoto, S.; Iida, K.; Murata, A.; Denawa, M.; Hagiwara, M.; Nakatani, K.* Synthetic Ligand Promotes Gene Expression by Affecting GC Sequence in Promoter. Bioorganic Medicinal Chemistry Letters. 2017, 27 (15), 3391–3394. https://doi.org/10.1016/j.bmcl.2017.06.006.
Li, J.; Matsumoto, J.; Bai, L.-P.; Murata, A.; Dohno, C.; Nakatani, K. A Ligand That Targets CUG Trinucleotide Repeats. Chemistry – A European Journal. 2016, 22 (42), 14881–14889. https://doi.org/10.1002/chem.201602741.
Murata, A.; Otabe, T.; Zhang, J.; Nakatani, K. BzDANP, a Small-Molecule Modulator of Pre-MiR-29a Maturation by Dicer. ACS Chemical Biology. 2016, 11 (10), 2790–2796. https://doi.org/10.1021/acschembio.6b00214.
Li, J.; Sakata, A.; He, H.; Bai, L. P.; Murata, A.; Dohno, C.; Nakatani, K.* Naphthyridine-Benzoazaquinolone: Evaluation of a Tricyclic System for the Binding to (CAG)n Repeat DNA and RNA. Chemisty – An Asian Journal. 2016, 11 (13), 1971–1981. https://doi.org/10.1002/asia.201600527.
Sato, S. I.; Watanabe, M.; Katsuda, Y.; Murata, A.; Wang, D. O.; Uesugi, M.* Live-Cell Imaging of Endogenous MRNAs with a Small Molecule. Angewangewandte chemie international edition. 2015, 54 (6), 1855–1858. https://doi.org/10.1002/anie.201410339.
Fukuzumi, T.; Murata, A.; Aikawa, H.; Harada, Y.; Nakatani, K.* Exploratory Study on the RNA-Binding Structural Motifs by Library Screening Targeting Pre-MiRNA-29a. Chemistry – A European Journal. 2015, 21 (47), 16859–16867. https://doi.org/10.1002/chem.201502913.
Hirata, N.†; Nakagawa, M.†; Fujibayashi, Y.†; Yamauchi, K.†; Murata, A.†; Minami, I.; Tomioka, M.; Kondo, T.; Kuo, T. F.; Endo, H.; Inoue, H.; Sato, S. I.; Ando, S.; Kawazoe, Y.; Aiba, K.; Nagata, K.; Kawase, E.; Chang, Y. T.; Suemori, H.; Eto, K.; Nakauchi, H.; Yamanaka, S.; Nakatsuji, N.; Ueda, K.; Uesugi, M.* A Chemical Probe That Labels Human Pluripotent Stem Cells. Cell Rep. 2014, 6 (6), 1165–1174. https://doi.org/10.1016/j.celrep.2014.02.006. †Equal contribution Open Access
Fukuzumi, T.; Aikawa, H.; Harada, Y.; Sugai, A.; Murata, A.; Nakatani, K.* Synthesis of 8-Substituted Adenine and Adenosine Libraries and the Binding to Pre-MiR-29a. Bulletin of the Chemical Society of Japan. 2014, 87 (9), 1013-1015. https://doi.org/10.1246/bcsj.20140137.
Hong, C. F.; Otabe, T.; Matsumoto, S.; Dohno, C.; Murata, A.; Hagihara, M.; Nakatani, K.* Formation of a Ligand- Assisted Complex of Two RNA Hairpin Loops. Chemistry – A European Journal. 2014, 20 (18), 5282–5287. https://doi.org/10.1002/chem.201304683.
Murata, A.; Harada, Y.; Fukuzumi, T.; Nakatani, K.* Fluorescent Indicator Displacement Assay of Ligands Targeting 10 MicroRNA Precursors. Bioorganic Medicinal Chemistry. 2013, 21 (22), 7101–7106. https://doi.org/10.1016/j.bmc.2013.09.007.
Murata, A.; Fukuzumi, T.; Umemoto, S.; Nakatani, K.* Xanthone Derivatives as Potential Inhibitors of MiRNA Processing by Human Dicer: Targeting Secondary Structures of Pre-MiRNA by Small Molecules. Bioorganic Medicinal Chemistry Letters. 2013, 23 (1), 252–255.
Matsumoto, S.; Hong, C.; Otabe, T.; Murata, A.; Nakatani, K.* Ligand-Inducible Formation of RNA Pseudoknot. Bioorganic Medicinal Chemistry Letters. 2013, 23 (12), 3539–3541. https://doi.org/10.1016/J.BMCL.2013.04.037.
Umemoto, S.; Im, S.; Zhang, J.; Hagihara, M.; Murata, A.; Harada, Y.; Fukuzumi, T.; Wazaki, T.; Sasaoka, S. I.; Nakatani, K.* Structure-Activity Studies on the Fluorescent Indicator in a Displacement Assay for the Screening of Small Molecules Binding to RNA. Chemistry – A European Journal. 2012, 18 (32), 9999–10008. https://doi.org/10.1002/chem.201103932.
Sato, S. I.; Murata, A.; Orihara, T.; Shirakawa, T.; Suenaga, K.; Kigoshi, H.; Uesugi, M.* Marine Natural Product Aurilide Activates the Opa1-Mediated Apoptosis by Binding to Prohibitin. Chemistry & Biology. 2011, 18 (1), 131–139. https://doi.org/10.1016/j.chembiol.2010.10.017.
Murata, A.; Ichi Sato, S.; Kawazoe, Y.; Uesugi, M.* Small-Molecule Fluorescent Probes for Specific RNA Targets. Chemical Communications. 2011, 47 (16), 4712–4714. https://doi.org/10.1039/c1cc10393h.
Sato, S. ichi; Murata, A.; Shirakawa, T.; Uesugi, M.* Biochemical Target Isolation for Novices: Affinity-Based Strategies. Chemistry & Biology. 2010, 17 (6), 616–623. https://doi.org/10.1016/j.chembiol.2010.05.015.
Murata, A.; Wada, T.* A Novel Linker for Solid-Phase Synthesis Cleavable under Neutral Conditions. Tetrahedron Letters. 2006, 47 (13), 2147–2150. https://doi.org/10.1016/j.tetlet.2006.01.135.
Murata, A.; Wada, T.* Synthesis of a Novel Ester Analog of Nucleic Acids Bearing a Serine Backbone. Bioorganic Medicinal Chemistry Letters. 2006, 16 (11), 2933–2936. https://doi.org/10.1016/j.bmcl.2006.02.076.
Reviews
マイクロRNA前駆体を標的とする低分子化合物の探索研究.
村田亜沙子, 化学工業集「次世代を担う女性研究者」, 2016, 67, 39–44.
In Vitro Selection of RNA Aptamers for a Small-Molecule Dye.
Murata, A.; Sato, S. Methods. Mol. Biol.: Artificial Riboswitches, 2014, 1111, 17–28.
顕在化した創薬標的マイクロRNA（miRNA）
村田亜沙子, 中谷和彦, 実験医学増刊32, 2014, 160–165.
生理活性物質による創薬標的同定のコツ
佐藤慎一, 村田亜沙子, 白川貴詩, 上杉志成, 実験医学別冊 創薬研究のためのタンパク質・プロテオミクス解析, 2010, 141–146.
海洋天然物のケミカルジェネティクス
佐藤慎一, 村田亜沙子, 上杉志成, 細胞工学28 特集ケミカルジェネティクス, 2009, 332–337.
iPS細胞作製を効率化する化合物
村田亜沙子, 上杉志成, 現代化学452, 2008, 37–39.
Identification of the Cardiac Beta-Adrenergic Receptor Protein: Solubilization and Purification by Affinity Chromatography
佐藤慎一, 村田亜沙子, 上杉志成, 蛋白質核酸酵素, 2007, 52, 1782–1783.
生物医学研究を加速するケミカルゲノミクス
村田亜沙子, 佐藤慎一, 上杉志成, 最新医学62 臨床遺伝学’07, 2007, 2205–2213.
Presentations
Comprehensive analysis of small molecule-target RNA pairs toward profiling small-molecule binders of RNA.
Asako Murata, Yusuke Takashima, Ayumu Asai, Kazuhiko Nakatani, The 44th Annual Meeting of the Molecular Biology Society of Japan, December 1–3, 2021. (ワークショップでの依頼講演)
RNAを標的とする低分子の探索と応用
村田亜沙子, 核酸化学若手フォーラム2021, オンライン, 2021年11月10日（フォーラムでの依頼講演）
Comprehensive Analysis of Dicer Substrates by High-Throughput Sequencing Identified New Target RNA Motifs for Small Molecules.
Asako Murata, Yusuke Takashima, Kei Iida, Ayako Sugai, Masatoshi Hagiwara, Kazuhiko Nakatani, The 43th Annual Meeting of the Molecular Biology Society of Japan (MBSJ2020, Online), December 2–4, 2020. (ワークショップでの依頼講演)
小分子による−1リボソーマルフレームシフト誘起とタンパク質の輸送・局在制御への応用.
村田亜沙子, 松本咲, 洪昌峰, 中谷和彦, 第38回分子生物学会年会 第88回日本生化学会 合同大会, 2015年12月1~4日 (ワークショップでの依頼講演)
RNAの構造・機能を制御する小分子化合物の開発.
村田亜沙子, 日本化学会第94春季年会, 名古屋, 2014年3月27~30日 (シンポジウムでの依頼講演)
Fluorescent indicator displacement assay for the discovery of RNA-binding ligands.
Asako Murata, Yasue Harada, Takeo Fukuzumi, Shiori Umemoto, Seongwang Im, Masaki Hagihara, Kazuhiko Nakatani, The 34th Annual Meeting of the Molecular Biology Society of Japan, December 13–16, 2011. (ワークショップでの依頼講演)
Patents
多能性細胞を選別するための方法, 特許第6246125号, 登録年月: 2017年12月13日
発明者: 上杉志成, 平田直, 村田亜沙子, チャンヨンテ, 中辻憲夫, 末盛博文, 川瀬栄八郎, 山内香織, 植田和光, 藤林悠人, 山中伸弥, 中川誠人
