Yoshiy Ikawa Publications

Yoshiya Ikawa Publications

2025
(139) 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]
(138) 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]

2024
(137) Ikawa, Y.
リボザイムとその応用
RNAの科学：時代を拓く生体分子（金井昭夫編、朝倉書店）, p214-p227 (2024) [Link]

2023
(136) 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]
(135) 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
(134) 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]
(133) 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]
(132) 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
(131) Ikawa, Y.
        構造モジュールの集積と再構成によるRNA触媒の人工ナノ集積
        CSJカレントレビュー vol.41, 進化を続ける核酸化学 , 93-99 (2021) [Link]
(130) 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]
(129) 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]
(128) 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
(127) Ikawa, Y.
        機能性RNA (第2部-13)
        核酸科学ハンドブック（杉本直己編、講談社サイエンティフィク）, p421-425 (2020) [Link]
(126) 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]
(125) 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]
(124) 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
(123) 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]
(122) 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
(121) 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]
(120) 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]
(119) 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]
(118) 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]
(117) 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]
(116) 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]
(115) 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]
(114) 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
(113) 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]
(112) 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]
(111) 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]
(110) 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]
(109) 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
(108) Ikawa,Y., Katsumata, S., Sakashita, R., Sato, S., Takenaka, S., & Furuta, H.
        Water-soluble porphyrinoids as G-quadruplex binders and telomerase inhibitors.
        J. Porphyrins Phthalocyanines, 20, 1041-1048 (2016) [Link]
(107) 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]
(106) 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]
(105) Ikawa, Y.
        分子デザインと進化工学によるRNA構造エンジニアリング
        生物工学会誌, 94, 477-480 (2016) [Link]
(104) 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]
(103) 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]
(102) 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]
(101) Masuda, M., Hirose, N., Ishikawa, T., Ikawa,Y., & Nishimura, K.
        Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis.
        Int. J. Syst. Evol. Microbiol., 66, 1510-1520 (2016) [PubMed]

2015
(100) 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]
(99) 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]
(98) Ikawa, Y.
        集積ナノ構造と生体分子デバイス構築に向けたモジュール型RNAの人工改変
        ファルマシア (日本薬学会会誌), 51, 42-46 (2015) [Link]

2014
(97) Ikawa,Y., Katsumata, S., Sakashita, R., & Furuta, H.
        Spectrometric detection of DNA by bis-Zn(II) complex of a water-soluble doubly N-confused hexaphyrin.
        Chem. Lett., 43, 1929-1931 (2014) [Link]
(96) Ota, S., Hisano, Y., Ikawa, Y., & Kawahara, A.
        Multiple genome modifications by the CRISPR/Cas9 system in zebrafish.
        Genes to Cells, 19, 555-564 (2014) [PubMed]
(95) Tanaka, T., Furuta, H., & Ikawa, Y.
        Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme.
        J. Biosci. Bioeng., 117, 407-412 (2014) [PubMed]

2013
(94) Ikawa,Y., Touden, S., Katsumata, S., & Furuta, H.
        Colorimetric/fluorogenic detection of thiols by N-fused porphyrin in water.
        Bioorg. Med. Chem., 21, 6501-6505 (2013) [PubMed]
(93) Ishikawa, J., Furuta, H., & Ikawa, Y.
        RNA Tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology.
        WIREs RNA, 4, 651-664 (2013) [PubMed]
(92) Ikawa, Y.
        in vitro進化分子工学による人工RNA触媒の創製およびその機能解析と応用利用
        進化分子工学 (NTS出版) , 355-367 (2013) [Link]
(91) Tanaka, T., Furuta, H., & Ikawa, Y.
        Natural selection and structural polymorphism of RNA 3D structures involving GNRA loops and their receptor motifs.
        in RNA Nanotechnology and Therapeutics (ed. Guo, P., CRC press), 109-120 (2013) [Link]
(90) Ikawa, Y.
        グループIイントロン研究の新たな潮流
        実験医学増刊, 生命分子を統合するRNA , 75-82 (2013) [Link]
(89) Ishikawa, J., Furuta, H., & Ikawa, Y.
        An in vitro-selected RNA receptor for the GAAC loop: modular receptor for non-GNRA-type tetraloop.
        Nucleic Acids Res., 41, 3748-3759 (2013) [PubMed]
(88) Isomoto, N., Maeda, Y., Tanaka, T., Furuta, H., & Ikawa, Y.
        Fixation and accumulation of thermotolerant catalytic competence of a pair of ligase ribozymes through complex formation and cross ligation.
        J. Mol. Evol., 76, 48-58 (2013) [PubMed]

2012
(87) Ikawa, Y., Harada, H., Katsumata, S., & Furuta, H.
        Facile conjugation of porphyrin and N-confused porphyrin with nona-arginine peptide by click reaction.
        Report of the Center of Advanced Instrumental Analysis Kyushu University, 30, 1-9 (2012) [Link]
(86) Cha, T.,Lim, J., Yoon, M., Sung, Y., Lee, B., Katsumata, S., Suzuki, M., Mori, H., Ikawa, Y., Furuta, H., Osuka, A., & Kim, D.
        Deprotonation-induced aromaticity enhancement and new conjugated networks in meso-hexakis(pentafluorophenyl) [26]hexaphyrin.
        Chem. Eur. J. 18, 15838-15844 (2012) [Link]
(85) Touden, S., Ikawa, Y., Sakashita, R., Toganoh, M., Mori, S., & Furuta, H.
        Sulfur-assisted interconversion between N-confused porphyrin and N-fused porphyrin.
        Tetrahedron Lett., 53, 6071-6074 (2012) [Link]
(84) Tanaka, T., Furuta, H., & Ikawa, Y.
        A two-piece derivative of a group I intron RNA as a platform for designing self-assembling RNA templates to promote peptide ligation.
        J. Nucleic Acids, vol. 2012, Article ID 305867, 10 pages, doi:10.1155/2012/305867 (2012) [PubMed]
(83) Yamashita, K., Tanaka, T., Furuta, H., & Ikawa, Y.
        TectoRNP: self-assembling RNAs with peptide-recognition motifs as templates for chemical peptide ligation.
        J. Pep. Sci., 18, 635-642 (2012) [PubMed]
(82) Tanaka, T., Furuta, H., & Ikawa, Y.
        RNA立体構造のボトムアップ構築とリボザイム・リボスイッチの人工改変.
        Antisense, 16, 13-23 (2012) [Link]
(81) Ikawa, Y., Touden, S., Katsumata, S., & Furuta, H.
        Water soluble N-confused porphyrinoids for bio-related chemistry.
        Kyushu University Global COE program, Science for Future Molecular Systems Journal, 5, 6-8 (2012) [Link]
(80) Fujita, Y., Tanaka, T., Furuta, H., & Ikawa, Y.
        Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch.
        J. Biosci. Bioeng., 113, 141-145 (2012) [PubMed]
(79) 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,T.
        Site-specific isotope labeling of long RNA for structural and mechanistic studies.
        Nucleic Acids Res., 40, e7 (2012) [PubMed]

2011
(78) Ohmori, R., Saito, H., Ikawa. Y., Fujita, Y., & Inoue, T.
        Self-amplification reactions dependent on tertiary interaction motifs in self-assembling ribozymes.
        J. Mol. Evol., 73, 221-229 (2011) [PubMed]
(77) Ikawa,Y., Touden, S., & Furuta, H.
        N-fused porphyrin with cationic side-arms: A new class of aromatic ligand with DNA-binding ability.
        Org. Biomol. Chem., 9, 8068-8078 (2011) [PubMed]
(76) Yamashita, K., Kashiwagi, N., Furuta, H., & Ikawa, Y.
        Turnover ability of an RNA template for chemical peptide ligation.
        Biosci. Biotech. Biochem., 75, 2021-2024 (2011) [PubMed]
(75) Ikawa, Y.
        モジュール工学と進化工学による人工RNA触媒の創製
        CSJカレントレビュー vol.6, 核酸化学のニュートレンド , p93-100 (2011) [Link]
(74) Maeda, Y., Furuta, H., & Ikawa, Y.
        Trans-acting RNAs as molecular probes for monitoring time-dependent structural change of an RNA complex adapting two structures.
        J. Biosci. Bioeng., 111, 370-376 (2011) [PubMed]
(73) Ishikawa, J., Fujita, Y., Maeda, Y.,Furuta, H., & Ikawa, Y.
        GNRA/receptor interacting modules: versatile modular units for natural and artificial RNA architectures.
        Methods, 54, 226-238 (2011) [PubMed]

2001 - 2010
2010
(72) Fujita, Y., Ishikawa, J., Furuta, H., & Ikawa, Y.
        Generation and development of RNA ligase ribozymes with modular architecture through "design and selection".
        Molecules, 15, 5850-5865 (2010) [PubMed]
(71) Ikawa, Y., Takeda, M., Suzuki, M., Osuka, A., & Furuta, H.
        Water-soluble doublyN-confused hexaphyrin: a near-IR fluorescent Zn(II) ion sensor in water.
        Chem. Comm., 46, 5689-5691 (2010) [PubMed]
(70) Toganoh, M., Harada, H., Ikawa, Y., & Furuta, H.
        Self-assembly of Zn(II) porphyrin-1,2,3-triazole conjugate with alcohol glue.
        Chem. Lett., 39, 252-253 (2010) [Link]
(69) Fujita, Y., Furuta. H., & Ikawa, Y.
        Evolutionary optimization of a modular ligase ribozyme: a small catalytic unit and a hairpin motif masking an element that could form an inactive structure.
        Nucleic Acids Res., 38, 3328-3339 (2010) [PubMed]
(68) Ishikawa, J., Isomoto, N., Fujita, Y., Furuta, H., & Ikawa, Y.
        The trans DSL ligase ribozyme can utilize various forms of modules to clamp its substrate and enzyme units.
        Biosci. Biotech. Biochem., 74, 872-874 (2010) [PubMed]

2009
(67) Kashiwagi, N., Yamashita, K., Furuta, H., & Ikawa, Y.
        Designed RNAs with two peptide binding units as artificial templates for native chemical ligation of RNA binding peptides.
        ChemBioChem, 10, 2745-2752 (2009) [PubMed]
(66) 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]
(65) 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]
(64) Ikawa. Y., Furuta, H., Yamashita, K., & Kashiwagi, N.
        Toward a reciprocal evolution system between RNA and peptides as an artificial model for the early RNP world.
        Nucleic Acids Symp. Ser., 53, 33-34 (2009) [PubMed]
(63) Ikawa. Y., Harada, H., Toganoh, M., & Furuta, H.
        Synthesis and protonation behavior of a water-soluble N-fused porphyrin: Conjugation with oligoarginine by click chemistry.
        Bioorg. Med. Chem. Lett., 19, 2448-2452 (2009) [PubMed]
(62) Ikawa, Y.
        RNAワールドへの逆進化
        遺伝子医学MOOK 15　最新RNAと疾患研究, p198-202 (2009) [Link]
(61) Fujita, Y., Furuta. H., & Ikawa, Y.
        Tailoring RNA modular units on a common scaffold: a modular ribozyme with a catalyticunit for β-nicotinamide mononucleotide-activated RNA ligation.
        RNA, 15, 877-888 (2009) [PubMed]
(60) Kashiwagi, N., Furuta, H., & Ikawa, Y.
        Primitive templated catalysis of a peptide ligation by self-folding RNAs.
        Nucleic Acids Res., 37, 2574-2583 (2009) [PubMed]
(59) Ikawa, Y., Shiohara, T., Ohuchi, S., & Inoue, T.
        Concerted effects of two activator modules on the group I ribozyme reaction.
        J. Biochem. (Tokyo), 139, 429-435 (2009) [PubMed]
(58) Ikawa, Y.
        RNA医薬としてのリボザイムの現状と展望
        核酸医薬の最前線 (CMC出版), p176-186 (2009) [Link]

2008
(57) Ikawa. Y., Ogawa, H., Harada, H., & Furuta, H.
        N-confused porphyrin possessing glucamine-appendants: aggregation and acid/base properties in aquaous media.
        Bioorg. Med. Chem. Lett., 18, 6394-6397 (2008) [PubMed]
(56) Ikawa. Y., Moriyama, S., Harada, H., & Furuta, H.
        Acid-base properties and DNA-binding of water soluble N-confused porphyrins with cationic side-arms.
        Org. Biomol. Chem., 6, 4157-4166 (2008) [PubMed]
(55) Ishikawa, J., Furuta. H., & Ikawa, Y.
        Mutation analysis of the base-pair connecting two functional modules in the DSL ribozyme.
        Nucleic Acids Symp. Ser., 52, 523-524 (2008) [PubMed]
(54) Ikawa. Y., Moriyama S., & Furuta, H.
        Facile syntheses of BODIPY derivatives for fluorescent labeling of the 5' and 3' ends of RNAs.
        Anal. Biochem., 378, 166-170 (2008) [PubMed]
(53) Ohuchi, SP., Ikawa, Y., & Nakamura Y.
        Selection of a novel class of RNA-RNA interaction motifs based on the ligase ribozyme with defined modular architecture.
        Nucleic Acids Res, 36, 3600-3607 (2008) [PubMed]

2007
(52) Kashiwagi, N., Furuta. H., & Ikawa, Y.
        Design and analysis of a structural RNA that acts as a template for peptide ligation.
        Nucleic Acids Symp. Ser., 51, 387-388 (2007) [PubMed] [cited in]
(51) Moriyama, S., Ikawa. Y., & Furuta, H.
        Synthesis of a water soluble N-confused porphyrin and its interaction with nucleic acids.
        Nucleic Acids Symp. Ser., 51, 207-208 (2007) [PubMed]

2006
(50) Ikawa, Y.
        人工RNA触媒創製の新手法：de novoデザインと進化分子工学の融合.
       蛋白質核酸酵素, 51, 950-957 (2006)
(49) Fujita, Y., Furuta. H., & Ikawa, Y.
        Construction of an artificial ribozyme which ligates an RNA fragment activated by nicotinamide mononucleotide.
        Nucleic Acids Symp. Ser., 50, 349-350 (2006) [PubMed] [cited in]
(48) Inoue, T., & Ikawa, Y.
        Protein switched ribozymes.
        in Nucleic Acid Switches and Sensors. (ed. Silverman, SK., Landes Bioscience), p37-47 (2006) [Link]
(47) Horie, S., Ikawa, Y., & Inoue,T.
        Structural and biochemical characterization of DSL ribozyme.
        Biochem. Biophys. Res.Comm., 339, 115-121 (2006) [PubMed]

2005
(46) Ikawa, Y.
        RNAアーキテクチャ（RNA建築学）と人工リボザイム創製への応用
       RNA工学の最前線 (CMC出版) 198-204 (2005) [Link]
(45) Ikawa, Y.
       人工リボザイム
       RNA工学の最前線 (CMC出版) 185-189 (2005) [Link]
(44) Kuramitsu, S., Ikawa, Y.,& Inoue, T.
        Rational installation of an allosteric effector on a designed ribozyme.
        Nucleic Acids Symp. Ser., 49, 349-350 (2005) [PubMed] [cited in]
(43) Ikawa, Y., Matsumoto, J., Horie, S,& Inoue, T.
        Redesign of an artificial ligase ribozyme based on its structural elements.
        RNA Biology, 2, 137-142 (2005) [PubMed]
(42) Ikawa, Y.
        RNA立体構造情報を活用したリボザイムの効率的な創製と改変
        FBC Newsletter, no.17, 13-17 (2005) [pdf]

2004
(41) Ikawa, Y., & Inoue, T.
       リボザイムの分子設計法--RNA構造情報の分子デザインへの還元. 実験医学増刊 , 22, no.17, 51(2401)-57(2407) (2004) [pdf]
(40) Yoshioka, W. Ikawa, Y., Jaeger, L. Shiraishi. H.,& Inoue, T.
        Generation of a catalytic module on a self-folding RNA.
        RNA, 10, 1900-1906 (2004) [PubMed]
(39) Yoshioka, Y., Ikawa, Y., Jaeger, L.,& Inoue, T.
        A ligase ribozyme obtained from a structural pool.
        Nucleic Acids Symp. Ser., 48,, 209-210 (2004) [PubMed]
(38) 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]
(37) Ohuchi, SJ, Ikawa, Y. , Shiraishi, H. & Inoue, T.
       Artificial modules for enhancing rate constants of a group I intron ribozyme without a P4-P6 core element.
        J. Biol. Chem., 279, 540-546 (2004) [PubMed]

2003
(36) Matsumura, S, Ikawa, Y., & Inoue, T.
        Biochemical characterization of the kink-turn RNA motif.
        Nucleic Acids Res., 31, 5544-5571 (2003) [PubMed]
(35) Ikawa, Y., Sasaki, K., Tominaga, H. & Inoue, T.
        The P5 activator of a group IC ribozyme can replace the P7.1/7.2 activator of a group IA ribozyme.
        J. Biochem. (Tokyo), 133, 665-670 (2003) [PubMed]
(34) 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]
(33) Ikawa, Y. & Inoue, T.
        Designed structural rearrangement of an active group I ribozyme.
        J. Biochem. (Tokyo), 133, 189-195 (2003) [PubMed]
(32) Atsumi, S., Ikawa, Y., Shiraishi, H. & Inoue, T.
        Selections for constituting new RNA-protein interactions in catalytic RNP.
        Nucleic Acids Res., 31, 661-669 (2003) [PubMed]

2002
(31) Ikawa, Y., Yoshimura, T., Hara, H., Shiraishi, H. & Inoue, T.
        Two conserved structural components, A-rich bulge and P4 X J6/7 base-triples, in activating the group I ribozymes.
        Genes to Cells, 7, 1205-1216 (2002) [PubMed]
(30) 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]
(29) Ohki, Y., Ikawa, Y., Shiraishi, H. & Inoue, T.
        Role of a conserved J8/7 XP4 base-triple in the Tetrahymena ribozyme.
        J. Biochem. (Tokyo), 132, 713-718 (2002) [PubMed]
(28) Ohuchi, SJ., Ikawa, Y., Shiraishi, H. & Inoue, T.
        Modular engineering of a group I intron ribozyme.
        Nucleic Acids Res., 30, 3473-3480 (2002) [PubMed]
(27) Ohki, Y.,Ikawa, Y., Shiraishi, H. & Inoue, T.
        Mispaired P3 region in the hierarchical folding pathway of the Tetrahymena ribozyme.
        Genes to Cells, 7, 851-860 (2002) [PubMed]
(26) Oe, Y.,Ikawa, Y., Shiraishi, H. & Inoue, T.
        The relationship between the self-splicing activity and the solidity of the master domain of the Tetrahymena group I ribozyme.
        Biochem. Biophys. Res. Commun., 291, 1225-1231 (2002) [PubMed]
(25) Ikawa, Y., Fukada, K., Watanabe, S., Shiraishi H. & Inoue T.
        Design, construction and analysis of a novel class of self-folding RNA.
        Structure, 10, 527-534 (2002) [PubMed]

2001
(24) Ohuchi, SJ., Ikawa, Y., Shiraishi, H. & Inoue, T.
        A simulated molecular evolution from minimal catalytic domain of a group I ribozyme.
        Nucleic Acids Res.,Supplment, 1, 125-126 (2001) [PubMed]
(23) Atsumi, S., Ikawa, Y., Shiraishi, H. & Inoue, T.
        Design and development of a catalytic ribonucleoprotein.
        EMBO J., 20. 5453-5460 (2001) [PubMed]
(22) Ikawa, Y., Nohmi, K., Atsumi, S., Shiraishi, H. & Inoue, T.
       A comparative study on two GNRA-tetraloop receptors: 11-nt and IC3 motif.
        J. Biochem. (Tokyo), 130, 251-255 (2001) [PubMed]
(21) Oe, Y.,Ikawa, Y., Shiraishi, H. & Inoue, T.
       Conserved base-pairing between C266-A268 and U307-G309 in the P7 of the Tetrahymena ribozyme is nonessential for the in vitro self-splicing reaction.
       Biochem. Biophys. Res. Commun., 284, 948-954 (2001) [PubMed]
(20) Ikawa, Y. & Inoue, T.
        究極のグループイントロン--セルフスプライシングRNAのコアを求めて
        蛋白質核酸酵素, 46, 644-651(2001) [pdf]
(19) Ohki, Y.,Ikawa, Y., Shiraishi, H. & Inoue, T.
        A deteriorated triple-helical scaffold accelerates formation of the Tetrahymena ribozyme active-structure.
        FEBS Lett.,493, 95-100 (2001) PubMed]
(18) Ikawa, Y., Yoshioka, W., Ohki, Y., Shiraishi, H. & Inoue, T.
        Self-splicing of the Tetrahymena group I ribozyme without conserved base-triples.
        Genes to Cells, 6, 411-420 (2001) [PubMed]

1992 - 2000
2000
(17) Oe, Y., Ikawa, Y., Shiraishi, H. & Inoue, T.
        Analysis of the P7 region within the catalytic core of the Tetrahymena ribozyme by employing in vitro selection.
        Nucleic Acids Symp. Ser., 44, 197-198 (2000) [PubMed]
(16) Ikawa, Y., Shiraishi, H. & Inoue, T.
        Minimal catalytic domain of a group I self-splicing intron RNA.
        Nat. Struct. Biol., 7, 1032-1035 (2000) [PubMed]
(15) Ikawa, Y., Naito, D., Shiraishi, H. & Inoue, T.
        Structure-function relationships of two closely related group IC3 intron ribozymes from Azoarcus and Synechococcus pre-tRNA.
        Nucleic Acids Res., 28, 3269-3277 (2000) [PubMed]
(14) Inoue, T & Ikawa, Y.
        Activation of the group I intronribozymes with their peripheral domains.
        in Ribozyme biochemistry and biotechnology. (eds. Krupp, G. & Gaur, K.,Biotechiques Books, Eaton press), p27-42 (Section II), (2000) [Abstract] [Link]
(13) Ikawa, Y., Shiraishi, H. & Inoue, T.
        A small structural element, Pc-J5/5a, plays dual roles in a group IC1 intron RNA.
        Biochem. Biophys. Res. Commun., 274, 259-265 (2000) [PubMed]
(12) Ikawa, Y., Shiraishi, H. & Inoue, T.
        Characterization of P8 and J8/7 elements in the conserved core of the Tetrahymena group I intron ribozyme.
        Biochem. Biophys. Res. Commun., 267, 85-90 (2000) [PubMed]

1999
(11) Ikawa, Y., Naito, D., Aono, N., Shiraishi, H. & Inoue, T.
        A conserved motif in group IC3 introns is a new class of GNRA receptor.
        Nucleic Acids Res., 27, 1859-1865 (1999) [PubMed]
(10) Ikawa, Y., Shiraishi, H. & Inoue, T.
        Trans-activation of the Tetrahymena group I intron ribozyme via a non-native RNA-RNA interaction.
        Nucleic AcidsRes., 27, 1650-1655 (1999) [PubMed]

1998
(9) Ikawa, Y., Shiraishi,H. & Inoue, T.
Trans-activationof the Tetrahymena ribozyme by its P2-2.1 domains.
J. Biochem. (Tokyo), 123, 528-533 (1998) [PubMed]

1997
(8) Ikawa, Y., Okada, A., Imahori, H., Shiraishi, H. & Inoue, T.
        Identification of the nucleotides in the A-rich bulge of the Tetrahymenaribozyme responsible for an efficient self-splicing reaction.
        J. Biochem. (Tokyo), 122, 878-882 (1997) [PubMed]
(7) Ikawa, Y., Ohta, H., Shiraishi, H. & Inoue, T.
        Long-range interaction between the P2.1 and P9.1 peripheral domains of the Tetrahymena ribozyme.
        Nucleic Acids Res., 25, 1761-1765 (1997) [PubMed]

1996
(6) Ikawa, Y., Shiraishi, H. & Inoue, T.
        Characterization of the newly constructed domains that replace P5abc within the Tetrahymena ribozyme.
        FEBS Lett., 394, 5-8 (1996) [PubMed]
(5) Ikawa, Y., Naito, Y., Shiraishi, H. & Inoue, T.
        Structure, function and molecular evolution of Group I intron ribozyme.
        Nucleic Acids Symp. Ser., 35, 195-196(1996) [pdf]

1995
(4) Ikawa, Y., Shiraishi, H. & Inoue, T.
The Tetrahymena ribozyme tolerates diverse activator domains that replace P5abc.
in Tracing Biological Evolution in Protein and Gene Structures (eds. M. Go & P. Schimmel, Elsevier), p115-123 (1995) [Link]

1994
(3) Nagata, T., Ikawa, Y. & Maruyama, K.
Effect of the ligating anion on the catalase activity of dinuclear manganase (II) complex of schiff-base macrocycles. J.,
Chem. Soc. Chem. Comm., 471-472 (1994) [Link]

1993
(2) Ikawa, Y., Nagata, T. & Maruyama, K.
Synthesis and electrochemical properties of dinuclear manganase(II) complex with octadentate schiff-base macrocycles.
Chem. Lett., 1049-1052 (1993) [Link]

1992
(1) Osuka, A., Ikawa, Y. & Maruyama, K.
Synthesis of benzochlorin monomer, dimer, and porphyrin-benzochlorin heterodimer from 5-aryl- and 5,15-diaryl-octaethylporphyrins.
Bull. Chem. Soc. Japan, 65,3322-3330 (1992) [Link]