Shigeyoshi Matsumura Publications

2025
(44) Abe, S., Aburaya, S., Koyama, T., Usui, T., Yoshino, J., Matsumura, S., & Ikawa, Y.
        Biochemical characterization of a non-G4-type RNA aptamer that lights up a GFP-like fluorogenic ligand.
        Molecules, 30, 1777 (2025) [Link]
(43) Miyazaki, Y., Nakane, R., Tanishi, S., Matsumura, S., & Ikawa, Y.
        Catalytic cleavage of an RNA substrate that bypasses the reorganization of its secondary structure during substrate recognition by a trans-acting VS ribozyme.
        Nucleosides Nucleotides Nucleic Acids, (2025) published online [PubMed]

2023
(42) Siddika, Mst. A., Oi, H., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        Structural expansion of catalytic RNA nanostructures through oligomerization of a cyclic trimer of engineered ribozymes.
        Molecules, 28, 6465 (2023) [PubMed]
(41) Ueda, T., Nishimura, K., Nishiyama, Y., Tominaga, Y., Miyazaki, Y., Furuta, H., Matsumura, S., & Ikawa, Y.
        Pairwise engineering of tandemly aligned self-splicing group I introns for analysis and control of their alternative splicing.
        Biomolecules, 13, 654 (2023) [PubMed]

2022
(40) Siddika, Mst. A., Yamada, T., Aoyama, R., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        Catalytic RNA oligomers formed by co-oligomerization of a pair of bimolecular RNase P ribozymes.
        Molecules, 27, 8298 (2022) [PubMed]
(39) Islam, Md. D., Hidaka, K., Suzuki, Y., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers.
        J. Biosci. Bioeng., 134, 195-202 (2022) [PubMed]
(38) Yu, K., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers.
        ChemBioChem, 23, e202100573 (2022) [PubMed]

2021
(37) Islam, Md. D., Rahman, Md. M, Matsumura, S., & Ikawa, Y.
        Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module.
        Nucleosides Nucleotides Nucleic Acids, 40,867-883 (2021) [PubMed]
(36) Mori, Y., Oi, H., Suzuki, Y., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        Flexible assembly of engineered Tetrahymena ribozymes forming polygonal RNA nanostructures with catalytic ability.
        ChemBioChem, 22, 2168-2176 (2021) [PubMed]
(35) Akagi, J., Yamada, T., Hidaka, K., Fujita, Y., Saito, H., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        An RNA triangle with six ribozyme units can promote a trans-splicing reaction through trimerization of unit ribozyme dimers.
        Applied Sciences, 11, 2583 (2021) [Link]

2020
(34) Matsumura, S.
        マイクロ流体デバイスで迫るレプリケーターの進化と細胞の関係
        極限環境生物学会誌,18, 19-24 (2020) [Link]
(33) Kiyooka, R., Akagi, J., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures.
        J. Biosci. Bioeng., 130, 253-259 (2020) [PubMed]
(32) Rahman, Md. S., Gulshan, Mst. A, Matsumura, S., & Ikawa, Y.
        Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes.
        Nucleosides Nucleotides Nucleic Acids, 39, 715-729 (2020) [PubMed]
(31) Rahman, Md. S., Matsumura, S., & Ikawa, Y.
        Effects of external molecular factors on adaptation of bacterial RNase P ribozymes to thermophilic conditions.
        Biochem. Biophys. Res. Commun., 523, 342-347 (2020) [PubMed]

2019
(30) Nozawa, Y., Hagihara, M.,Rahman, Md. S., Matsumura, S., & Ikawa, Y.
        Rational design of an orthogonal pair of bimolecular RNase P ribozymes through heterologous assembly of their modular domains.
        Biology, 8, pii: E65 (2019) [PubMed]
(29) Tsuruga, R., Uehara, N., Suzuki, Y., Furuta, H., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA-RNA interface between two structural modules.
        J. Biosci. Bioeng., 128, 410-415 (2019) [PubMed]

2018
(28) Nozawa, Y., Hagihara, M., Matsumura, S., & Ikawa, Y.
        Modular architecture of bacterial RNase P ribozymes as a structural platform for RNA nanostructure design.
        CHIMIA, 72, 882-887 (2018) [PubMed]
(27) Rahman, Md. M., Matsumura, S., & Ikawa, Y.
        Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers.
        Biochem. Biophys. Res. Commun.,507, 136-141 (2018) [PubMed]
(26) Gulshan, Mst. A., Tsuji, K., Matsumura, S., Higuchi, T., Umezawa, N., & Ikawa, Y.
        Distinct modulation of group I ribozyme activity among stereoisomers of a synthetic pentamine with structural constraints.
        Biochem. Biophys. Res. Commun., 504, 698-703 (2018) [PubMed]
(25) Rahman, Md. M., & Matsumura, S., & Ikawa, Y.
        Oligomerization of a bimolecular ribozyme modestly rescues its structural defects that disturb interdomain assembly to form the catalytic site.
        J. Mol. Evol., 86, 431-442 (2018) [PubMed]
(24) Gulshan, Mst. A., Matsumura, S., Higuchi, T., Umezawa, N., & Ikawa, Y.
        Comparative study of polyethylene polyamines as activator molecules for a structurally unstable group I ribozyme.
        Biosci. Biotech. Biochem., 82, 1404-1407 (2018) [PubMed]
(23) Inuzuka, S., Kakizawa, H., Nishimura, K., Naito, T., Miyazaki, K., Furuta, H., Matsumura, S., & Ikawa, Y.
        Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain.
        Genes to Cells, 23, 435-447 (2018) [PubMed]
(22) Ikawa, Y., & Matsumura, S.,
        Engineered group I ribozymes as RNA-based modular tools to control gene expression.
        Applied RNA Bioscience (Springer), Chapter 13, p203-p220 (2018) [Link]
(21) Gulshan, Mst. A., Rahman Md. M., Matsumura, S., Higuchi, T., Umezawa, N., Ikawa, Y.
        Biogenic triamine and tetraamine activate core catalytic ability of Tetrahymena group I ribozyme in the absence of its large activator module.
        Biochem. Biophys. Res. Commun., 496, 594-600 (2018) [PubMed]

2017
(20) Rahman, Md. M., Matsumura, S., & Ikawa, Y.
        Artificial RNA motifs expand the programmable assembly between RNA modules of a bimolecular ribozyme leading to application to RNA nanostructure design.
        Biology, 6, pii: E37 (2017) [PubMed]
(19) Tanaka, T., Hirata, Y., Tominaga, Y., Furuta, H., Matsumura, S., & Ikawa, Y.
        Heterodimerization of group I ribozymes enabling exon recombination through a pair of cooperative trans-splicing reactions.
        ChemBioChem, 18, 1659-1667 (2017) [PubMed]
(18) Tanaka, T., Ikawa, Y., & Matsumura, S.
        Rational engineering of a modular group I ribozyme to control its actvity by self-dimerization.
        Methods in Molecular Biology (RNA Nanostructures), 1632, 325-340 (2017) [PubMed]
(17) Matsumura, S., & Ikawa, Y.
        リボザイムの研究動向と安全性評価
        先端医療技術の実用化と開発戦略（技術科学協会）1章8節, p.61-p.65 (2017) [Link]
(16) Oi, H., Fujita, D., Suzuki, Y., Sugiyama, H., Endo, M., Matsumura, S., & Ikawa, Y.
        Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes.
        J. Biochem., 161, 451-462 (2017) [PubMed]

2016
(15) Matsumura, S., Kun, A., Ryckelynck, M., Coldren, F., Szilagyi, A., Jossinet, F., Rick, C., Nghe, P., Szathmary, E., & Griffiths, A.
        Transient compartmentalization of RNA replicators prevents extinction due to parasites.
        Science, 354, 1293-1296 (2016) [Link], [日本語解説]
(14) Furukawa, A., Tanaka, T., Furuta, H., Matsumura, S. & Ikawa, Y.
        Use of a fluorescent aptamer RNA as an exonic sequence to analyze self-splicing ability of a group I intron from structured RNAs.
        Biology, 5, pii: E43 (2016) [PubMed]
(13) Inuzuka, S., Nishimura, K., Kakizawa, H., Fujita, Y., Furuta, H., Matsumura, S., & Ikawa, Y.
        Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism.
        J. Biochem., 160, 153-162 (2016) [PubMed]
(12) Tanaka, T., Matsumura, S., Furuta, H., & Ikawa, Y.
        Tecto-GIRz: engineered group I ribozymes the catalytic ability of which can be controlled by self-dimerization.
        ChemBioChem, 17, 1448-1455 (2016) [PubMed]
(11) Inuzuka, S., Matsumura, S., & Ikawa, Y.
        Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules.
        J. Biosci. Bioeng., 122, 183-187 (2016) [PubMed]
(10) Furukawa, A., Maejima, T., Matsumura, S., & Ikawa, Y.
        Characterization of an RNA receptor motif that recognizes a GCGA tetraloop.
        Biosci. Biotech. Biochem., 80, 1386-1389 (2016) [PubMed]

2015
(9) Matsumura, S., & Ikawa, Y.
        Artificial ligase ribozymes isolated by a “design and selection” strategy.
        Methods in Molecular Biology (RNA scaffolds), 1316, 113-125 (2015) [PubMed]
(8) Matsumura, S., Ito, T., Tanaka, T., Furuta, H., & Ikawa, Y.
        Modulation of group I ribozyme activity by cationic porphyrins.
        Biology, 4, 251-263 (2015) [PubMed]

2012
(7) Matsumura, S., Coldren, F.M., Marin, A., Fallah-Araghi, A., Griffiths, A.D., & Ryckelynck, M.
Why is the minimum unit of life a cell? : Building an “RNA world” model protocell using droplet-based microfluidics.
Proceedings of MicroTAS, 16, 166-168 (2012)

2009
(6) Ishikawa, J. Matsumura, S., Jaeger, L., Inoue, T., Furuta, H., & Ikawa. Y.
        Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules.
        Arch. Biochem. Biophys., 490, 163-170 (2009) [PubMed]
(5) Matsumura, S., Ohmori, R., Saito, H.,Ikawa. Y., & Inoue, T.
        trans-acting ligase ribozyme by a loop-receptor interaction.
        FEBS Lett., 583, 2819-2826 (2009) [PubMed]

2004
(4) Ikawa, Y., Tsuda, K., Matsumura, S.,& Inoue, T.
De novo synthesis and development of an RNA enzyme.
Proc. Natl. Acad. Sci. USA., 88, 13750-13755 (2004) [PubMed]

2003
(3) Matsumura, S.,Ikawa, Y., & Inoue, T.
        Biochemical characterization of the kink-turn RNA motif.
        Nucleic Acids Res., 31, 5544-5571 (2003) [PubMed]
(2) Ikawa, Y., Tsuda, K., Matsumura, S., Atsumi, S. & Inoue,T.
        Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP.
        Nucleic Acids Res., 31, 1488-1496 (2003) [PubMed]

2002
(1) Ikawa, Y., Tsuda, K., Matsumura, S., Atsumi, S. & Inoue, T.
Modelling of a possible evolutional process from a ribozyme to a catalytic RNP.
Nucleic Acids Res.,Supplment, 2, 119-120 (2002) [PubMed]