The appearance of molecular replicators (molecules that can be copied) was probably a critical step in the origin life. However, parasitic would take over and have prevented life from taking off unless were compartmentalized reproducing protocells. Paradoxically, control protocell reproduction seem to require evolved replicators. We show here simpler population structure, based on cycles transient compartmentalization (TC) mixing RNA replicators, is sufficient prevent takeover by mutants. TC...

RNA, which acts as a medium for transmitting genetic information, plays variety of roles in cell. As with proteins, elucidation the three- dimensional (3D) structures RNAs is important understanding their various roles. Determination atomic crystallized ribosome has enabled identification previously unknown RNA structural motifs. The kink-turn (K-turn or GA) motif, causes sharp bend an double helix, was identified one these To biochemically characterize K-turn, motif inserted into hinge...

Arbitrary manipulation of molecular recognition at the atomic level has many applications. However, systematic design and de novo synthesis an artificial enzyme based on such been a long-standing challenge in field chemistry biotechnology. In this report, we developed RNA ligase by implementing synthetic strategy that fuses series 3D modelings naturally occurring RNA–RNA motifs with small-scale combinatorial modular catalytic unit. The resulting produces 3′–5′ linkage template-directed...

The 17-3 RNA aptamer recognizes DMHBI and induces its fluorescence. We showed that the predominantly induced emission of phenolate form DMHBI. also demonstrated active structure minimal possessed three stem elements two large loop elements, which we named Karashi sequence-optimized variant, Jigarashi, respectively. Chemical modification experiments suggested regions formed tertiary interactions and/or non-Watson–Crick base pairs, no remarkable structural alterations occurred upon binding....

RNA is a biopolymer that attractive for constructing nano-scale objects with complex structures. Three-dimensional (3D) structures of naturally occurring RNAs often have modular architectures. The 3D structure group I (GI) ribozyme from Tetrahymena has typical architecture, which can be separated into two structural modules (ΔP5 and P5abc). fully active reconstructed by assembling the separately prepared through highly specific strong assembly between ΔP5 P5abc RNA. Such non-covalent allows...

RNA is a promising biomaterial for self-assembly of nano-sized structures with wide range applications in nanotechnology and synthetic biology. Several RNA-based nanostructures have been reported, but most are unrelated to intracellular RNA, which possesses modular that sufficiently large complex serve as catalysts promote sophisticated chemical reactions. In this study, we designed dimeric based on the Tetrahymena group I ribozyme. The resulting RNAs (tecto ribozyme; tecto-GIRz) exhibit...

The Vc2 riboswitch possesses an aptamer domain belonging to the class-I c-di-GMP family. This has been analysed and molecular mechanism by which it recognizes ligand elucidated. On other hand, regulatory of full-length control its downstream open reading frame (ORF) remains largely unknown. In this study, we performed in vivo reporter assays vitro biochemical analyses domain. We evaluated results elucidate riboswitch. present suggest that recognition downregulates expression ORF primarily at...

We previously developed a synthetic cis ‐acting RNA ligase ribozyme with 3′–5′ joining activity termed “DSL” (designed and selected ligase). DSL was easily transformed into trans form because of its highly modular architecture. In this study, we investigated the properties turnover capabilities DSL, t DSL‐1/GUAA. DSL‐1/GUAA exhibited remarkably high compared parental it attained number. Taken together, results indicate that loop–receptor interaction plays significant role in determining...

The riboswitch is a class of RNA ‐based gene regulatory machinery that dependent on recognition its target ligand by tertiary structures. Ligand achieved the aptamer domain, and ligand‐dependent structural changes expression platform then usually mediate termination transcription or translational initiation. Ligand‐dependent domain have been reported for several riboswitches with short (<40 nucleotides) platforms. In this study, we characterized Vc2 c‐di‐ GMP represses translation...

A bimolecular ribozyme consisting of a core (ΔP5 RNA) and an activator module (P5abc has been used as platform to design assembled RNA nanostructures. The tight specific assembly between the P5abc ΔP5 modules depends on two sets intermodule interactions. interface must be controlled when designing To expand repertoire molecular recognition in P5abc/ΔP5 interface, we modified by replacing parent tertiary interactions with artificial engineered interfaces were characterized biochemically...

Abstract Group I (GI) self‐splicing ribozymes are attractive tools for biotechnology and synthetic biology. Several trans ‐splicing related reactions based on GI have been developed the purpose of recombining their target mRNA sequences. By combining systems with rational modular engineering it was possible to achieve more complex editing RNA In this study we a cooperative system through use dimeric derived from Tetrahymena group intron ribozyme. The resulting pairs exhibited catalytic...

Tertiary interactions between a new RNA motif and tetraloops were analyzed to determine whether this shows preference for GCGA tetraloop. In the structural context of ligase ribozyme, discriminated loop from 3 other tetraloops. The affinity its receptor is strong enough carry out ribozyme activity.

Group I self-splicing intron constitutes an important class of functional RNA molecules that can promote chemical transformation. Although the fundamental mechanism auto-excision from its precursor has been established, convenient assay systems for splicing activity are still useful a further understanding detailed and application. Because some host sequences, to which group introns inserted form stable three-dimensional (3D) structures, effects 3D structures exonic elements on efficiency...

The modular structural domains of multidomain RNA enzymes can often be dissected into separate domain RNAs and their noncovalent assembly reconstitute active enzymes. These properties are important to understand basic characteristics useful for application RNA-based nanostructures. Bimolecular forms bacterial RNase P ribozymes consisting S-domain C-domain attractive as platforms catalytic nanostructures, but S-domain/C-domain was not optimized this purpose. Through analysis engineering...

The modular structure of bacterial ribonuclease P (RNase P) ribozymes, which recognize tertiary structures precursor tRNAs (pre-tRNAs) to cleave their 5′ leader sequence, can be dissected physically into the two structured domain RNAs (S-domain and C-domain). Separately prepared S-domain RNA C-domain assemble form bimolecular forms RNase ribozymes. We analyzed effects polyethylene glycols (PEGs) on pre-tRNA cleavage catalyzed by ribozymes examine molecular crowding reaction. PEG crowders...

Ribozymes with modular architecture constitute an attractive class of structural platforms for design and construction nucleic acid nanostructures biological functions. Through engineering the Tetrahymena ribozyme, we have designed unit RNAs (L-RNAs), assembly which formed ribozyme-based closed trimers tetramers. Their catalytic activity was dependent on oligomer formation. In this study, variety L-RNA oligomers extended by tuning their elements, yielding pentamers hexamers. properties were...

Ribonuclease P (RNase P) is a class of enzymes involved in the processing precursor tRNAs to remove their 5'-leader sequences. are classified into two completely distinct classes, i.e. an RNA-based enzyme and protein-only enzyme. The functions as ribozyme which catalytic machinery supported by its RNA component consisting single molecule. Bacterial RNase RNAs classical ribozymes structures mechanisms have been studied extensively. bacterial has modular tertiary structure large domains, each...