A Hexameric Ribozyme Nanostructure Formed by Double‐Decker Assembly of a Pair of Triangular Ribozyme Trimers
Sign Up to like & getrecommendations! Published in 2022 at "ChemBioChem"
DOI: 10.1002/cbic.202100573
Abstract: The modular architecture of naturally occurring ribozymes makes them a promising class of structural platform for the design and assembly of three‐dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can… read more here.
Keywords: hexameric ribozyme; ribozyme nanostructure; ribozyme trimers; double decker ... See more keywords
Mapping the Conformational Landscape of the Neutral Network of RNA Sequences That Connect Two Functional Distinctly Different Ribozymes
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DOI: 10.1002/cbic.202200022
Abstract: During evolution of an RNA world, the development of enzymatic function was essential. Such enzymatic function was linked to RNA sequences capable of adopting specific RNA folds that possess catalytic pockets to promote catalysis. Within… read more here.
Keywords: rna sequences; neutral network; ribozyme; rna ... See more keywords
Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Molecular Evolution"
DOI: 10.1007/s00239-018-9862-8
Abstract: The emergence of cellular compartmentalization was a crucial step in the hypothetical RNA world and its evolution because it would not only prevent the extinction of RNA self-replication systems due to dispersion/diffusion of their components… read more here.
Keywords: bimolecular ribozyme; ribozyme; assembly form; oligomerization bimolecular ... See more keywords
Development of Quenching-qPCR (Q-Q) assay for measuring absolute intracellular cleavage efficiency of ribozyme.
Sign Up to like & getrecommendations! Published in 2018 at "Analytical biochemistry"
DOI: 10.1016/j.ab.2018.04.007
Abstract: Ribozyme (Rz) is a very attractive RNA molecule in metabolic engineering and synthetic biology fields where RNA processing is required as a control unit or ON/OFF signal for its cleavage reaction. In order to use… read more here.
Keywords: cleavage efficiency; cleavage; ribozyme; intracellular cleavage ... See more keywords
Dynamic nuclear polarization on a hybridized hammerhead ribozyme: An explorative study of RNA folding and direct DNP with a paramagnetic metal ion cofactor.
Sign Up to like & getrecommendations! Published in 2019 at "Solid state nuclear magnetic resonance"
DOI: 10.1016/j.ssnmr.2019.04.005
Abstract: While uniform isotope labeling of ribonucleic acids (RNA) can simply and efficiently be achieved by in-vitro transcription, the specific introduction of nucleotides in larger constructs is non-trivial and often ineffective. Here, we demonstrate how a… read more here.
Keywords: hammerhead ribozyme; dnp; ribozyme; nuclear polarization ... See more keywords
RNA Polymerase Ribozyme That Recognizes the Template-Primer Complex through Tertiary Interactions.
Sign Up to like & getrecommendations! Published in 2023 at "Biochemistry"
DOI: 10.1021/acs.biochem.3c00091
Abstract: RNA enzymes (ribozymes) often rely on specific base-pairing interactions to engage RNA substrates, which limits the substrate sequence generality of these enzymes. An RNA polymerase ribozyme that was previously optimized by directed evolution to operate… read more here.
Keywords: polymerase ribozyme; polymerase; template primer; ribozyme ... See more keywords
Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.
Sign Up to like & getrecommendations! Published in 2018 at "Biochemistry"
DOI: 10.1021/acs.biochem.8b00031
Abstract: Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme,… read more here.
Keywords: deprotonation exceeds; bond formation; hdv ribozyme; ribozyme ... See more keywords
Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA
Sign Up to like & getrecommendations! Published in 2019 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.8b13298
Abstract: Molecular evolution can be conceptualized as a walk over a “fitness landscape”, or the function of fitness (e.g., catalytic activity) over the space of all possible sequences. Understanding evolution requires knowing the structure of the… read more here.
Keywords: self aminoacylating; ribozyme; landscape; fitness landscape ... See more keywords
Site-specific RNA methylation by a methyltransferase ribozyme
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DOI: 10.1038/s41586-020-2854-z
Abstract: Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification, including RNA methylation. Methylated nucleotides are among the evolutionarily most-conserved features of transfer (t)RNA and ribosomal (r)RNA 1 , 2 . Many contemporary methyltransferases use… read more here.
Keywords: methylation; site specific; ribozyme; rna ... See more keywords
Hovlinc is a recently evolved class of ribozyme found in human lncRNA
Sign Up to like & getrecommendations! Published in 2021 at "Nature Chemical Biology"
DOI: 10.1038/s41589-021-00763-0
Abstract: Although naturally occurring catalytic RNA molecules—ribozymes—have attracted a great deal of research interest, very few have been identified in humans. Here, we developed a genome-wide approach to discovering self-cleaving ribozymes and identified a naturally occurring… read more here.
Keywords: hovlinc; class; ribozyme; rna ... See more keywords
Corroboration of Zn( ii )–Mg( ii )-tertiary structure interplays essential for the optimal catalysis of a phosphorothiolate thiolesterase ribozyme
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DOI: 10.1039/c8ra05083j
Abstract: The TW17 ribozyme, a catalytic RNA selected from a pool of artificial RNA, is specific for the Zn2+-dependent hydrolysis of a phosphorothiolate thiolester bond. Here, we describe the organic synthesis of both guanosine α-thio-monophosphate and… read more here.
Keywords: ribozyme catalysis; ribozyme; catalysis; phosphorothiolate ... See more keywords