Research output per year
Research output per year
- 1 - 50 out of 118 results
Search results
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2024
Catalytic cleave of an RNA substrate that bypasses the reorganization of its secondary structure during substrate recognition by a trans-acting VS ribozyme
Miyzaki, Y., Nakane, R., Tanishi, S., Matsumura, S. & Ikawa, Y., 2024, (Accepted/In press) In: Nucleosides, Nucleotides and Nucleic Acids.Research output: Contribution to journal › Article › peer-review
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2023
Pairwise Engineering of Tandemly Aligned Self-Splicing Group I Introns for Analysis and Control of Their Alternative Splicing
Ueda, T., Nishimura, K. I., Nishiyama, Y., Tominaga, Y., Miyazaki, K., Furuta, H., Matsumura, S. & Ikawa, Y., 2023/04, In: Biomolecules. 13, 4, 654.Research output: Contribution to journal › Article › peer-review
Open Access -
Structural Expansion of Catalytic RNA Nanostructures through Oligomerization of a Cyclic Trimer of Engineered Ribozymes
Siddika, M. A., Oi, H., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2023/09, In: Molecules. 28, 18, 6465.Research output: Contribution to journal › Article › peer-review
Open Access -
2022
A Hexameric Ribozyme Nanostructure Formed by Double-Decker Assembly of a Pair of Triangular Ribozyme Trimers
Yu, K., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2022/03/18, In: ChemBioChem. 23, 6, e202100573.Research output: Contribution to journal › Article › peer-review
3 Scopus citations -
Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers
Islam, M. D., Hidaka, K., Suzuki, Y., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2022/09, In: Journal of Bioscience and Bioengineering. 134, 3, p. 195-202 8 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes
Siddika, M. A., Yamada, T., Aoyama, R., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2022/12, In: Molecules. 27, 23, 8298.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
2021
An rna triangle with six ribozyme units can promote a trans-splicing reaction through trimerization of unit ribozyme dimers
Akagi, J., Yamada, T., Hidaka, K., Fujita, Y., Saito, H., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2021/03/02, In: Applied Sciences (Switzerland). 11, 6, 2583.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module
Dobirul Islam, M., Motiar Rahman, M., Matsumura, S. & Ikawa, Y., 2021, In: Nucleosides, Nucleotides and Nucleic Acids. 40, 9, p. 867-883 17 p.Research output: Contribution to journal › Article › peer-review
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Flexible Assembly of Engineered Tetrahymena Ribozymes Forming Polygonal RNA Nanostructures with Catalytic Ability
Mori, Y., Oi, H., Suzuki, Y., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2021/06/15, In: ChemBioChem. 22, 12, p. 2168-2176 9 p.Research output: Contribution to journal › Article › peer-review
5 Scopus citations -
2020
Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures
Kiyooka, R., Akagi, J., Hidaka, K., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2020/09, In: Journal of Bioscience and Bioengineering. 130, 3, p. 253-259 7 p.Research output: Contribution to journal › Article › peer-review
1 Scopus citations -
Effects of external molecular factors on adaptation of bacterial RNase P ribozymes to thermophilic conditions
Rahman, M. S., Matsumura, S. & Ikawa, Y., 2020/03/05, In: Biochemical and Biophysical Research Communications. 523, 2, p. 342-347 6 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes
Rahman, M. S., Gulshan, M. A., Matsumura, S. & Ikawa, Y., 2020/05/03, In: Nucleosides, Nucleotides and Nucleic Acids. 39, 5, p. 715-729 15 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
2019
Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA–RNA interface between two structural modules
Tsuruga, R., Uehara, N., Suzuki, Y., Furuta, H., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2019/10, In: Journal of Bioscience and Bioengineering. 128, 4, p. 410-415 6 p.Research output: Contribution to journal › Article › peer-review
9 Scopus citations -
Rational design of an orthogonal pair of bimolecular rnase p ribozymes through heterologous assembly of their modular domains
Nozawa, Y., Hagihara, M., Rahman, M. S., Matsumura, S. & Ikawa, Y., 2019/09, In: Biology. 8, 3, 65.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
2018
Biogenic triamine and tetraamine activate core catalytic ability of Tetrahymena group I ribozyme in the absence of its large activator module
Gulshan, M. A., Rahman, M. M., Matsumura, S., Higuchi, T., Umezawa, N. & Ikawa, Y., 2018/02/05, In: Biochemical and Biophysical Research Communications. 496, 2, p. 594-600 7 p.Research output: Contribution to journal › Article › peer-review
8 Scopus citations -
Comparative study of polyethylene polyamines as activator molecules for a structurally unstable group I ribozyme
Gulshan, A., Matsumura, S., Higuchi, T., Umezawa, N. & Ikawa, Y., 2018, In: Bioscience, biotechnology, and biochemistry. 82, 8, p. 1404-1407 4 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Distinct modulation of group I ribozyme activity among stereoisomers of a synthetic pentamine with structural constraints
Gulshan, M. A., Tsuji, K., Matsumura, S., Higuchi, T., Umezawa, N. & Ikawa, Y., 2018/10/12, In: Biochemical and Biophysical Research Communications. 504, 4, p. 698-703 6 p.Research output: Contribution to journal › Article › peer-review
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Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers
Rahman, M. M., Matsumura, S. & Ikawa, Y., 2018/12/09, In: Biochemical and Biophysical Research Communications. 507, 1-4, p. 136-141 6 p.Research output: Contribution to journal › Article › peer-review
6 Scopus citations -
Engineered group i ribozymes as RNA-based modular tools to control gene expression
Ikawa, Y. & Matsumura, S., 2018/04/10, Applied RNA Bioscience. Springer Singapore, p. 203-220 18 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review
3 Scopus citations -
Modular architecture of bacterial RNase P ribozymes as a structural platform for RNA nanostructure design
Nozawa, Y., Hagihara, M., Matsumura, S. & Ikawa, Y., 2018, In: Chimia. 72, 12, p. 882-887 6 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site
Rahman, M. M., Matsumura, S. & Ikawa, Y., 2018/08/01, In: Journal of Molecular Evolution. 86, 7, p. 431-442 12 p.Research output: Contribution to journal › Article › peer-review
8 Scopus citations -
Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain
Inuzuka, S., Kakizawa, H., Nishimura, K. I., Naito, T., Miyazaki, K., Furuta, H., Matsumura, S. & Ikawa, Y., 2018/06, In: Genes to Cells. 23, 6, p. 435-447 13 p.Research output: Contribution to journal › Article › peer-review
Open Access12 Scopus citations -
2017
Artificial rna motifs expand the programmable assembly between RNA modules of a bimolecular ribozyme leading to application to RNA nanostructure design
Rahman, M. M., Matsumura, S. & Ikawa, Y., 2017/12, In: Biology. 6, 4, 37.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Heterodimerization of Group I Ribozymes Enabling Exon Recombination through Pairs of Cooperative trans-Splicing Reactions
Tanaka, T., Hirata, Y., Tominaga, Y., Furuta, H., Matsumura, S. & Ikawa, Y., 2017/08/17, In: ChemBioChem. 18, 16, p. 1659-1667 9 p.Research output: Contribution to journal › Article › peer-review
9 Scopus citations -
Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes
Oi, H., Fujita, D., Suzuki, Y., Sugiyama, H., Endo, M., Matsumura, S. & Ikawa, Y., 2017/05/01, In: Journal of Biochemistry. 161, 5, p. 451-462 12 p.Research output: Contribution to journal › Article › peer-review
20 Scopus citations -
Rational engineering of a modular group I ribozyme to control its activity by self-dimerization
Tanaka, T., Ikawa, Y. & Matsumura, S., 2017, In: Methods in Molecular Biology. p. 325-340 16 p.Research output: Contribution to journal › Article › peer-review
4 Scopus citations -
2016
Characterization of an RNA receptor motif that recognizes a gcga tetraloop
Furukawa, A., Maejima, T., Matsumura, S. & Ikawa, Y., 2016, In: Bioscience, biotechnology, and biochemistry. 80, 7, p. 1386-1389 4 p.Research output: Contribution to journal › Article › peer-review
6 Scopus citations -
Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism
Inuzuka, S., Nishimura, K. I., Kakizawa, H., Fujita, Y., Furuta, H., Matsumura, S. & Ikawa, Y., 2016/09/01, In: Journal of Biochemistry. 160, 3, p. 153-162 10 p.Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules
Inuzuka, S., Matsumura, S. & Ikawa, Y., 2016/08/01, In: Journal of Bioscience and Bioengineering. 122, 2, p. 183-187 5 p.Research output: Contribution to journal › Article › peer-review
5 Scopus citations -
Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis
Masuda, M., Hirose, N., Ishikawa, T., Ikawa, Y. & Nishimura, K., 2016/03, In: International Journal of Systematic and Evolutionary Microbiology. 66, 3, p. 1510-1520 11 p.Research output: Contribution to journal › Article › peer-review
Open Access47 Scopus citations -
Tecto-GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self-Dimerization
Tanaka, T., Matsumura, S., Furuta, H. & Ikawa, Y., 2016/08/03, In: ChemBioChem. p. 1448-1455 8 p.Research output: Contribution to journal › Article › peer-review
15 Scopus citations -
Use of a fluorescent aptamer RNA as an exonic sequence to analyze self-splicing ability of a group i intron from structured RNAs
Furukawa, A., Tanaka, T., Furuta, H., Matsumura, S. & Ikawa, Y., 2016/12/01, In: Biology. 5, 4, 43.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Water-soluble porphyrinoids as G-quadruplex binders and telomerase inhibitors
Ikawa, Y., Katsumata, S., Sakashita, R., Sato, S., Takenaka, S. & Furuta, H., 2016/08/01, In: Journal of Porphyrins and Phthalocyanines. 20, 8-11, p. 1041-1048 8 p.Research output: Contribution to journal › Article › peer-review
4 Scopus citations -
2015
Artificial ligase ribozymes isolated by a “design and selection” strategy
Matsumura, S. & Ikawa, Y., 2015/05/16, In: Methods in molecular biology (Clifton, N.J.). 1316, p. 113-125 13 p.Research output: Contribution to journal › Article › peer-review
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Modulation of group I ribozyme activity by cationic porphyrins
Matsumura, S., Ito, T., Tanaka, T., Furuta, H. & Ikawa, Y., 2015/03/24, In: Biology. 4, 2, p. 251-263 13 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
2014
Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme
Tanaka, T., Furuta, H. & Ikawa, Y., 2014/04, In: Journal of Bioscience and Bioengineering. 117, 4, p. 407-412 6 p.Research output: Contribution to journal › Article › peer-review
12 Scopus citations -
Multiple genome modifications by the CRISPR/Cas9 system in zebrafish
Ota, S., Hisano, Y., Ikawa, Y. & Kawahara, A., 2014/07, In: Genes to Cells. 19, 7, p. 555-564 10 p.Research output: Contribution to journal › Article › peer-review
Open Access99 Scopus citations -
Spectrometric detection of DNA by the Bis-Zn(II) complex of a water-soluble doubly N-confused hexaphyrin
Ikawa, Y., Katsumata, S., Sakashita, R. & Furuta, H., 2014, In: Chemistry Letters. 43, 12, p. 1929-1931 3 p.Research output: Contribution to journal › Article › peer-review
8 Scopus citations -
2013
An in vitro-selected RNA receptor for the GAAC loop: Modular receptor for non-GNRA-type tetraloop
Ishikawa, J., Furuta, H. & Ikawa, Y., 2013/04, In: Nucleic Acids Research. 41, 6, p. 3748-3759 12 p.Research output: Contribution to journal › Article › peer-review
Open Access10 Scopus citations -
Colorimetric/fluorogenic detection of thiols by N-fused porphyrin in water
Ikawa, Y., Touden, S., Katsumata, S. & Furuta, H., 2013/11/01, In: Bioorganic and Medicinal Chemistry. 21, 21, p. 6501-6505 5 p.Research output: Contribution to journal › Article › peer-review
13 Scopus citations -
Fixation and accumulation of thermotolerant catalytic competence of a pair of ligase ribozymes through complex formation and cross ligation
Isomoto, N., Maeda, Y., Tanaka, T., Furuta, H. & Ikawa, Y., 2013/02, In: Journal of Molecular Evolution. 76, 1-2, p. 48-58 11 p.Research output: Contribution to journal › Article › peer-review
3 Scopus citations -
Natural selection and structural polymorphism of RNA 3D structures involving GNRA loops and their receptor motifs
Tanaka, T., Furuta, H. & Ikawa, Y., 2013/01/01, RNA Nanotechnology and Therapeutics. CRC Press, p. 109-120 12 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review
2 Scopus citations -
RNA Tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology
Ishikawa, J., Furuta, H. & Ikawa, Y., 2013/11, In: Wiley Interdisciplinary Reviews: RNA. 4, 6, p. 651-664 14 p.Research output: Contribution to journal › Review article › peer-review
45 Scopus citations -
2012
A two-piece derivative of a group i intron RNA as a platform for designing self-assembling RNA templates to promote peptide ligation
Tanaka, T., Furuta, H. & Ikawa, Y., 2012, In: Journal of Nucleic Acids. 2012, 305867.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Deprotonation-induced aromaticity enhancement and new conjugated networks in meso-hexakis(pentafluorophenyl)[26]hexaphyrin
Cha, W. Y., Lim, J. M., Yoon, M. C., Sung, Y. M., Lee, B. S., Katsumata, S., Suzuki, M., Mori, H., Ikawa, Y., Furuta, H., Osuka, A. & Kim, D., 2012/12/03, In: Chemistry - A European Journal. 18, 49, p. 15838-15844 7 p.Research output: Contribution to journal › Article › peer-review
28 Scopus citations -
Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch
Fujita, Y., Tanaka, T., Furuta, H. & Ikawa, Y., 2012/02, In: Journal of Bioscience and Bioengineering. 113, 2, p. 141-145 5 p.Research output: Contribution to journal › Article › peer-review
17 Scopus citations -
Site-specific isotope labeling of long RNA for structural and mechanistic studies
Kawahara, I., Haruta, K., Ashihara, Y., Yamanaka, D., Kuriyama, M., Toki, N., Kondo, Y., Teruya, K., Ishikawa, J., Furuta, H., Ikawa, Y., Kojima, C. & Tanaka, Y., 2012/01, In: Nucleic Acids Research. 40, 1, p. e7Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Sulfur-assisted interconversion between N-confused porphyrin and N-fused porphyrin
Touden, S., Ikawa, Y., Sakashita, R., Toganoh, M., Mori, S. & Furuta, H., 2012/11/07, In: Tetrahedron Letters. 53, 45, p. 6071-6074 4 p.Research output: Contribution to journal › Article › peer-review
14 Scopus citations -
TectoRNP: Self-assembling RNAs with peptide recognition motifs as templates for chemical peptide ligation
Yamashita, K., Tanaka, T., Furuta, H. & Ikawa, Y., 2012/10, In: Journal of Peptide Science. 18, 10, p. 635-642 8 p.Research output: Contribution to journal › Article › peer-review
2 Scopus citations -
2011
GNRA/receptor interacting modules: Versatile modular units for natural and artificial RNA architectures
Ishikawa, J., Fujita, Y., Maeda, Y., Furuta, H. & Ikawa, Y., 2011/06, In: Methods. 54, 2, p. 226-238 13 p.Research output: Contribution to journal › Review article › peer-review
27 Scopus citations