Yoshiya Ikawa

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

The self-splicing intron ribozymes have been regarded as primitive forms of the splicing machinery for eukaryotic pre-mRNAs. The splicing activity of group I self-splicing introns is dependent on an absolutely conserved and exceptionally densely packed core region composed of two helical domains, P3-P7 and P4-P6, that are connected rigidly via base triples. Here we show that a mutant group I intron ribozyme lacking both the P4-P6 domain and the base triples can perform the phosphoester transfer reactions required for splicing at both the 5′ and 3′ splice sites, demonstrating that the elements required for splicing are concentrated in the stacked helical P3-P7 domain. This finding establishes that the conserved core of the intron consists of two physically and functionally separable components, and we present a model showing the architecture of a prototype of this class of intron and the course of its molecular evolution.

Multiple genome modifications by the CRISPR/Cas9 system in zebrafish.

The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated (Cas) system, which is an adaptive immune system of bacteria, has become a powerful tool for genome editing in various model organisms. Here, we demonstrate multiple genome modifications mediated by CRISPR/Cas9 in zebrafish (Danio rerio). Multiple genes including golden/gol and tyrosinase/tyr, which are involved in pigment formation, and s1pr2 and spns2, which are involved in cardiac development, were disrupted with insertion and/or deletion (indel) mutations introduced by the co‐injection of multiple guide RNAs (gRNAs) and the nuclease Cas9 mRNA. We simultaneously observed two distinct phenotypes, such as, the two hearts phenotype and the hypopigmentation of skin melanophores and the retinal pigment epithelium, in the injected F0 embryos. Additionally, we detected the targeted deletion and inversion genes as a 7.1‐kb fragment between the two distinct spns2 targeted sites together with indel mutations. Conversely, chromosomal translocations among five target loci were not detected. Therefore, we confirmed that the CRISPR/Cas9‐induced indel mutations and a locus‐specific deletion were heritable in F1 embryos. To screen founders, we improved heteroduplex mobility assay (HMA) for simultaneously detecting indel mutations in different target loci. The results suggest that the multi‐locus HMA is a powerful tool for identification of multiple genome modifications mediated by the CRISPR/Cas9 system.

Design and development of a catalytic ribonucleoprotein

Ribonucleoproteins (RNPs) consisting of derivatives of a ribozyme and an RNA‐binding protein were designed and constructed based upon high‐resolution structures of the corresponding prototype molecules, the Tetrahymena group I self‐splicing intron RNA and two proteins (bacteriophage λN and HIV Rev proteins) containing RNA‐binding motifs. The splicing reaction proceeds efficiently only when the designed RNA associates with the designed protein either in vivo or in vitro. In vivo mutagenic protein selection was effective for improving the capability of the protein. Kinetic analyses indicate that the protein promotes RNA folding to establish an active conformation. The fact that the conversion of a ribozyme to an RNP can be accomplished by simple molecular design supports the RNA world hypothesis and suggests that a natural active RNP might have evolved readily from a ribozyme.

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

A water-soluble doubly N-confused hexaphyrin (N(2)CH) having two octa-arginine peptide arms displays an enhanced near-infrared (NIR) emission around 1050 nm in the presence of Zn(2+) in aqueous solution.

Design, Construction, and Analysis of a Novel Class of Self-Folding RNA

RNA can play multiple biological roles through use of its three-dimensional (3-D) structures. Recent advances in RNA structural biology have revealed that complex RNA 3D structures are assemblages of double-stranded helices with a variety of tertiary structural motifs. By employing RNA tertiary structural motifs together with the helices, we designed a novel class of self-folding RNA. In RNA composed of three helices (P1, P2, and P3), P1 interacts with P3 via a tetraloop-receptor interaction and P2 forms consecutive base-triples. Two designed RNAs of this class were prepared and their folding properties indicate that they form defined tertiary structures as designed. These RNAs may be used as modular units for constructing artificial ribozymes or nanometer-scale materials.

Selection of a novel class of RNA–RNA interaction motifs based on the ligase ribozyme with defined modular architecture

To develop molecular tools for the detection and control of RNA molecules whose functions rely on their 3D structures, we have devised a selection system to isolate novel RNA motifs that interact with a target RNA structure within a given structural context. In this system, a GAAA tetraloop and its specific receptor motif (11-ntR) from an artificial RNA ligase ribozyme with modular architecture (the DSL ribozyme) were replaced with a target structure and random sequence, respectively. Motifs recognizing the target structure can be identified by in vitro selection based on ribozyme activity. A model selection targeting GAAA-loop successfully identified motifs previously known as GAAA-loop receptors. In addition, a new selection targeting a C-loop motif also generated novel motifs that interact with this structure. Biochemical analysis of one of the C-loop receptor motifs revealed that it could also function as an independent structural unit.

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

Interactions between GNRA tetraloops and their receptors are found frequently as modular units in various types of naturally occurring structured RNAs. Due to their functional importance, GNRA/receptor interactions have been studied extensively with regard to their 3D structures and biochemical and biophysical properties. Artificial non-natural GNRA/receptor modules have also been generated not only to obtain a better understanding of this class of motifs in natural RNA structures but also for application of these modular units to the design and construction of artificial RNA structures that can be used as platforms to generate functional RNAs applicable for nanobiotechnology. In this review, we present a survey of structures, functions, and analyses as well as artificial generation and application of GNRA/receptor interacting modules.

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

meso-Hexakis(pentafluorophenyl)-substituted neutral hexaphyrin with a 26π-electronic circuit can be regarded as a real homolog of porphyrin with an 18π-electronic circuit with respect to a quite flat molecular structure and strong aromaticity. We have investigated additional aromaticity enhancement of meso-hexakis(pentafluorophenyl)[26]hexaphyrin(1.1.1.1.1.1) by deprotonation of the inner N-H groups in the macrocyclic molecular cavity to try to induce further structural planarization. Deprotonated mono- and dianions of [26]hexaphyrin display sharp B-like bands, remarkably strong fluorescence, and long-lived singlet and triplet excited-states, which indicate enhanced aromaticity. Structural, spectroscopic, and computational studies have revealed that deprotonation induces structural deformations, which lead to a change in the main conjugated π-electronic circuit and cause enhanced aromaticity.

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

Water soluble N-confused porphyrins, 5,10,15,20-tetrakis(alpha-pyridinio-p-tolyl)-2-aza-21-carbaporphyrin (pPyNCP) and its N-methyl derivative, 2-N-methyl-5,10,15,20-tetrakis(alpha-pyridinio-p-tolyl)-2-aza-21-carbaporphyrin (NMe-pPyNCP), have been synthesized by introducing cationic side-arms at the meso-positions of N-confused porphyrin. Their acid-base properties (pK(1-4)) and DNA-binding ability in aqueous solutions were elucidated in comparison with the corresponding porphyrin derivative. Photophysical behaviors of pPyNCP were largely influenced by buffer compositions and DNA structures, whereas NMe-pPyNCP is considerably robust against these factors. In addition, significant enhancement of the fluorescence was observed with NMe-pPyNCP by the addition of DNA. The unique properties of pPyNCP and NMe-pPyNCP stem from the confused pyrrole rings in the macrocycle.

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

RNA molecules are versatile biomaterials that act not only as DNA‐like genetic materials but also have diverse functions in regulation of cellular biosystems. RNA is capable of regulating gene expression by sequence‐specific hybridization. This feature allows the design of RNA‐based artificial gene regulators (riboregulators). RNA can also build complex two‐dimensional (2D) and 3D nanostructures, which afford protein‐like functions and make RNA an attractive material for nanobiotechnology. RNA tectonics is a methodology in RNA nanobiotechnology for the design and construction of RNA nanostructures/nanoobjects through controlled self‐assembly of modular RNA units (tectoRNAs). RNA nanostructures designed according to the concept of RNA tectonics are also attractive as tools in synthetic biology, but in vivo RNA tectonics is still in the early stages. This review presents a summary of the achievements of RNA tectonics and its related researches in vitro, and also introduces recent developments that facilitated the use of RNA nanostructures in bacterial cells. WIREs RNA 2013, 4:651–664. doi: 10.1002/wrna.1185