Y. Ikawa

发表

RNA Tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology

Junya Ishikawa, H. Furuta, Y. Ikawa, 2013, Wiley interdisciplinary reviews. RNA.

Colorimetric/fluorogenic detection of thiols by N-fused porphyrin in water.

H. Furuta, Y. Ikawa, Satoshi Touden, 2013, Bioorganic & medicinal chemistry.

Trans-activation of the Tetrahymena ribozyme by its P2-2.1 domains.

T. Inoue, Y. Ikawa, H. Shiraishi, 1998, Journal of biochemistry.

N-confused porphyrin possessing glucamine-appendants: aggregation and acid/base properties in aqueous media.

H. Furuta, Y. Ikawa, H. Ogawa, 2008, Bioorganic & medicinal chemistry letters.

Acid-base properties and DNA-binding of water soluble N-confused porphyrins with cationic side-arms.

H. Furuta, Y. Ikawa, H. Harada, 2008, Organic & biomolecular chemistry.

Synthesis of Benzochlorin Monomer, Dimer, and Porphyrin-Benzochlorin Heterodimer from 5-Aryl- and 5,15-Diaryl-octaethylporphyrins

A. Osuka, Y. Ikawa, K. Maruyama, 1992 .

Deprotonation-induced aromaticity enhancement and new conjugated networks in meso-Hexakis(pentafluorophenyl)[26]hexaphyrin.

Byung Sun Lee, Jong Min Lim, Y. Sung, 2012, Chemistry.

Design and analysis of a structural RNA that acts as a template for peptide ligation.

H. Furuta, Y. Ikawa, Norimasa Kashiwagi, 2007, Nucleic acids symposium series.

Artificial RNA Motifs Expand the Programmable Assembly between RNA Modules of a Bimolecular Ribozyme Leading to Application to RNA Nanostructure Design

Y. Ikawa, Md. Motiar Rahman, Shigeyoshi Matsumura, 2017, Biology.

Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures.

H. Sugiyama, Masayuki Endo, Kumi Hidaka, 2020, Journal of bioscience and bioengineering.

TectoRNP: self‐assembling RNAs with peptide recognition motifs as templates for chemical peptide ligation

H. Furuta, Y. Ikawa, K. Yamashita, 2012, Journal of peptide science : an official publication of the European Peptide Society.

Rational Engineering of a Modular Group I Ribozyme to Control Its Activity by Self-Dimerization.

Y. Ikawa, Shigeyoshi Matsumura, Takahiro Tanaka, 2017, Methods in molecular biology.

Water-soluble doubly N-confused hexaphyrin: a near-IR fluorescent Zn(II) ion sensor in water.

Masaaki Suzuki, A. Osuka, H. Furuta, 2010, Chemical communications.

Synthesis and Electrochemical Properties of Dinuclear Manganese(II) Complexes with Octadentate Schiff-base Macrocycles. Fine Tuning of the Redox Behavior

Y. Ikawa, K. Maruyama, T. Nagata, 1993 .

Effect of the ligating anion on the catalase activity of dinuclear manganese(II) complexes of Schiff-base macrocycles

Y. Ikawa, K. Maruyama, T. Nagata, 1994 .

Sulfur-assisted interconversion between N-confused porphyrin and N-fused porphyrin

Ryuichi Sakashita, H. Furuta, Y. Ikawa, 2012 .

Spectrometric Detection of DNA by the Bis-Zn(II) Complex of a Water-soluble Doubly N-Confused Hexaphyrin

Ryuichi Sakashita, H. Furuta, Y. Ikawa, 2014 .

N-fused porphyrin with pyridinium side-arms: a new class of aromatic ligand with DNA-binding ability.

H. Furuta, Y. Ikawa, Satoshi Touden, 2011, Organic & biomolecular chemistry.

Facile syntheses of BODIPY derivatives for fluorescent labeling of the 3' and 5' ends of RNAs.

H. Furuta, Y. Ikawa, Shoji Moriyama, 2008, Analytical biochemistry.

Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis.

T. Ishikawa, M. Masuda, K. Nishimura, 2016, International journal of systematic and evolutionary microbiology.

Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers.

Y. Ikawa, Md. Motiar Rahman, Shigeyoshi Matsumura, 2018, Biochemical and biophysical research communications.

Site-specific isotope labeling of long RNA for structural and mechanistic studies

C. Kojima, Yoshiyuki Tanaka, Junya Ishikawa, 2011, Nucleic acids research.

Multiple genome modifications by the CRISPR/Cas9 system in zebrafish

Satoshi Ota, Y. Ikawa, A. Kawahara, 2014, Genes to cells : devoted to molecular & cellular mechanisms.

Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes

H. Sugiyama, Masayuki Endo, Kumi Hidaka, 2022, Molecules.

Coordinated control of a designed trans‐acting ligase ribozyme by a loop–receptor interaction

Hirohide Saito, Tan Inoue, Hirohide Saito, 2009, FEBS letters.

Redesign of an Artificial Ligase Ribozyme Based on the Analysis of Its Structural Elements

Tan Inoue, Y. Ikawa, S. Horie, 2005, RNA biology.

Modular engineering of a Group I intron ribozyme.

Tan Inoue, Y. Ikawa, Hideaki Shiraishi, 2002, Nucleic acids research.

Primitive templated catalysis of a peptide ligation by self-folding RNAs

H. Furuta, Y. Ikawa, Norimasa Kashiwagi, 2009, Nucleic acids research.

Fixation and Accumulation of Thermotolerant Catalytic Competence of a Pair of Ligase Ribozymes Through Complex Formation and Cross Ligation

H. Furuta, Y. Ikawa, Y. Maeda, 2013, Journal of Molecular Evolution.

Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism.

H. Furuta, Y. Ikawa, Yuki Fujita, 2016, Journal of biochemistry.

Genes to Cells

H. Furuta, Y. Ikawa, Katsushi Miyazaki, 2018 .

Design and development of a catalytic ribonucleoprotein

S. Atsumi, Tan Inoue, Y. Ikawa, 2001, The EMBO journal.

A conserved motif in group IC3 introns is a new class of GNRA receptor.

T. Inoue, Y. Ikawa, N. Aono, 1999, Nucleic acids research.

Distinct modulation of group I ribozyme activity among stereoisomers of a synthetic pentamine with structural constraints.

Y. Ikawa, T. Higuchi, N. Umezawa, 2018, Biochemical and biophysical research communications.

Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP.

S. Atsumi, Tan Inoue, Y. Ikawa, 2003, Nucleic acids research.

Selections for constituting new RNA-protein interactions in catalytic RNP.

S. Atsumi, Tan Inoue, Y. Ikawa, 2003, Nucleic acids research.

Concerted effects of two activator modules on the group I ribozyme reaction.

Tan Inoue, Y. Ikawa, S. Ohuchi, 2009, Journal of biochemistry.

Mispaired P3 region in the hierarchical folding pathway of the Tetrahymena ribozyme

Tan Inoue, Y. Ikawa, Hideaki Shiraishi, 2002, Genes to cells : devoted to molecular & cellular mechanisms.

Design, construction, and analysis of a novel class of self-folding RNA.

Tan Inoue, Y. Ikawa, Shin-ichi Watanabe, 2002, Structure.

Relationship between the self-splicing activity and the solidity of the master domain of the Tetrahymena group I ribozyme.

Tan Inoue, Y. Ikawa, Hideaki Shiraishi, 2002, Biochemical and biophysical research communications.

Conserved base-pairings between C266-A268 and U307-G309 in the P7 of the Tetrahymena ribozyme is nonessential for the in vitro self-splicing reaction.

T. Inoue, Y. Ikawa, Hideaki Shiraishi, 2001, Biochemical and biophysical research communications.

A deteriorated triple‐helical scaffold accelerates formation of the Tetrahymena ribozyme active structure

T. Inoue, Y. Ikawa, Hideaki Shiraishi, 2001, FEBS letters.

Modulation of Group I Ribozyme Activity by Cationic Porphyrins

H. Furuta, Y. Ikawa, Shigeyoshi Matsumura, 2015, Biology.

Self-assembly of Zn(II) Porphyrin-1,2,3-Triazole Conjugate with Alcohol Glue

H. Furuta, Y. Ikawa, M. Toganoh, 2010 .

Designed RNAs with Two Peptide‐Binding Units as Artificial Templates for Native Chemical Ligation of RNA‐Binding Peptides

H. Furuta, Y. Ikawa, Norimasa Kashiwagi, 2009, Chembiochem : a European journal of chemical biology.

Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch.

H. Furuta, Y. Ikawa, Yuki Fujita, 2012, Journal of bioscience and bioengineering.

A small structural element, Pc-J5/5a, plays dual roles in a group IC1 intron RNA.

T. Inoue, Y. Ikawa, H. Shiraishi, 2000, Biochemical and biophysical research communications.

An in vitro-selected RNA receptor for the GAAC loop: modular receptor for non–GNRA-type tetraloop

Junya Ishikawa, H. Furuta, Y. Ikawa, 2013, Nucleic acids research.

Evolutionary optimization of a modular ligase ribozyme: a small catalytic unit and a hairpin motif masking an element that could form an inactive structure

H. Furuta, Y. Ikawa, Yuki Fujita, 2010, Nucleic acids research.

Long-range interaction between the P2.1 and P9.1 peripheral domains of the Tetrahymena ribozyme.

T. Inoue, Y. Ikawa, Hideaki Shiraishi, 1997, Nucleic acids research.

Characterization of the newly constructed domains that replace P5abc within the Tetrahymena ribozyme

T. Inoue, Y. Ikawa, Hideaki Shiraishi, 1996, FEBS letters.

Minimal catalytic domain of a group I self-splicing intron RNA

Tan Inoue, Y. Ikawa, Hideaki Shiraishi, 2000, Nature Structural Biology.

GNRA/receptor interacting modules: versatile modular units for natural and artificial RNA architectures.

Junya Ishikawa, H. Furuta, Y. Ikawa, 2011, Methods.

Comparative study of polyethylene polyamines as activator molecules for a structurally unstable group I ribozyme

Y. Ikawa, T. Higuchi, N. Umezawa, 2018, Bioscience, biotechnology, and biochemistry.

A Two-Piece Derivative of a Group I Intron RNA as a Platform for Designing Self-Assembling RNA Templates to Promote Peptide Ligation

H. Furuta, Y. Ikawa, Takahiro Tanaka, 2012, Journal of nucleic acids.

Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes

Y. Ikawa, M. Rahman, Shigeyoshi Matsumura, 2020, Nucleosides, nucleotides & nucleic acids.

Effects of external molecular factors on adaptation of bacterial RNase P ribozymes to thermophilic conditions.

Y. Ikawa, M. Rahman, Shigeyoshi Matsumura, 2019, Biochemical and biophysical research communications.

Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module

Y. Ikawa, Shigeyoshi Matsumura, Md Dobirul Islam, 2021, Nucleosides, nucleotides & nucleic acids.

Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA-RNA interface between two structural modules.

H. Sugiyama, Masayuki Endo, Yuki Suzuki, 2019, Journal of bioscience and bioengineering.

Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site

Y. Ikawa, Md. Motiar Rahman, Shigeyoshi Matsumura, 2018, Journal of Molecular Evolution.

Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes

H. Sugiyama, D. Fujita, Masayuki Endo, 2017, Journal of biochemistry.

Tecto‐GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self‐Dimerization

H. Furuta, Y. Ikawa, Shigeyoshi Matsumura, 2016, Chembiochem : a European journal of chemical biology.

Characterization of an RNA receptor motif that recognizes a GCGA tetraloop

Y. Ikawa, Shigeyoshi Matsumura, A. Furukawa, 2016, Bioscience, biotechnology, and biochemistry.

Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme.

H. Furuta, Y. Ikawa, Takahiro Tanaka, 2014, Journal of bioscience and bioengineering.

Generation and Development of RNA Ligase Ribozymes with Modular Architecture Through “Design and Selection”

Junya Ishikawa, H. Furuta, Y. Ikawa, 2010, Molecules.

Two conserved structural components, A‐rich bulge and P4 XJ6/7 base‐triples, in activating the group I ribozymes

Tan Inoue, Y. Ikawa, Hideaki Shiraishi, 2002, Genes to cells : devoted to molecular & cellular mechanisms.

Self‐splicing of the Tetrahymena group I ribozyme without conserved base‐triples

Tan Inoue, Y. Ikawa, Hideaki Shiraishi, 2001, Genes to cells : devoted to molecular & cellular mechanisms.

Trans-acting RNAs as molecular probes for monitoring time-dependent structural change of an RNA complex adapting two structures.

H. Furuta, Y. Ikawa, Y. Maeda, 2011, Journal of bioscience and bioengineering.

Synthesis and protonation behavior of a water-soluble N-fused porphyrin: conjugation with an oligoarginine by click chemistry.

H. Furuta, Y. Ikawa, M. Toganoh, 2009, Bioorganic & medicinal chemistry letters.

Rational Design of an Orthogonal Pair of Bimolecular RNase P Ribozymes through Heterologous Assembly of Their Modular Domains

Y. Ikawa, M. Rahman, Shigeyoshi Matsumura, 2019, Biology.

Heterodimerization of Group I Ribozymes Enabling Exon Recombination through Pairs of Cooperative trans‐Splicing Reactions

H. Furuta, Y. Ikawa, Y. Hirata, 2017, Chembiochem : a European journal of chemical biology.

De novo synthesis and development of an RNA enzyme.

Tan Inoue, Y. Ikawa, Tan Inoue, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Structural Expansion of Catalytic RNA Nanostructures through Oligomerization of a Cyclic Trimer of Engineered Ribozymes

Masayuki Endo, Kumi Hidaka, Y. Ikawa, 2023, Molecules.

Biochemical characterization of the kink-turn RNA motif.

Tan Inoue, Y. Ikawa, Tan Inoue, 2003, Nucleic acids research.

Fixation and Accumulation of Thermotolerant Catalytic Competence of a Pair of Ligase Ribozymes Through Complex Formation and Cross Ligation

H. Furuta, Y. Ikawa, Y. Maeda, 2013, Journal of Molecular Evolution.

Self-Replication Reactions Dependent on Tertiary Interaction Motifs in an RNA Ligase Ribozyme

Y. Fujita, Tan Inoue, Hirohide Saito, 2011, Journal of Molecular Evolution.

An RNA Triangle with Six Ribozyme Units Can Promote a Trans-Splicing Reaction through Trimerization of Unit Ribozyme Dimers

Y. Fujita, H. Sugiyama, Masayuki Endo, 2021 .

Water-soluble doubly N-confused hexaphyrin: a near-IR fluorescent Zn(II) ion sensor in water.

A. Osuka, Y. Ikawa, Mari Takeda, 2010, Chemical communications.

Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules.

Y. Ikawa, Yoshiya Ikawa, Shigeyoshi Matsumura, 2016, Journal of bioscience and bioengineering.

Engineered Group I Ribozymes as RNA-Based Modular Tools to Control Gene Expression

Y. Ikawa, Shigeyoshi Matsumura, 2018 .

Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site

Y. Ikawa, Md. Motiar Rahman, Shigeyoshi Matsumura, 2018, Journal of Molecular Evolution.

The transDSL Ligase Ribozyme Can Utilize Various Forms of Modules to Clamp Its Substrate and Enzyme Units

Junya Ishikawa, H. Furuta, Y. Ikawa, 2010, Bioscience, biotechnology, and biochemistry.

Tailoring RNA modular units on a common scaffold: a modular ribozyme with a catalytic unit for beta-nicotinamide mononucleotide-activated RNA ligation.

H. Furuta, Y. Ikawa, Yuki Fujita, 2009, RNA.

Use of a Fluorescent Aptamer RNA as an Exonic Sequence to Analyze Self-Splicing Ability of a Group I Intron from Structured RNAs

Hiroyuki Furuta, H. Furuta, Y. Ikawa, 2016, Biology.