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   Articles with "ribozyme" as a keyword



A Hexameric Ribozyme Nanostructure Formed by Double‐Decker Assembly of a Pair of Triangular Ribozyme Trimers

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recommendations! 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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recommendations! Published in 2022 at "ChemBioChem"

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

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recommendations! 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.

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recommendations! 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.

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recommendations! 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.

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recommendations! 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.

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recommendations! 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

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recommendations! 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

Emergent ribozyme behaviors in oxychlorine brines indicate a unique niche for molecular evolution on Mars

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recommendations! Published in 2024 at "Nature Communications"

DOI: 10.1038/s41467-024-48037-2

Abstract: Mars is a particularly attractive candidate among known astronomical objects to potentially host life. Results from space exploration missions have provided insights into Martian geochemistry that indicate oxychlorine species, particularly perchlorate, are ubiquitous features of… read more here.

Keywords: ribozyme; oxychlorine brines; unique niche; evolution mars ... See more keywords

Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy

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recommendations! Published in 2025 at "Nature Communications"

DOI: 10.1038/s41467-025-65502-8

Abstract: Many RNAs rely on their 3D structures for function. While acquiring functional 3D structures, certain RNAs form misfolded, non-functional states (‘kinetic traps’). Instead, other RNAs sequentially assemble into their functional conformations over pre-folded scaffolds. Elucidating… read more here.

Keywords: dynamic assembly; multidomain; ribozyme; non functional ... See more keywords
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Site-specific RNA methylation by a methyltransferase ribozyme

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recommendations! Published in 2020 at "Nature"

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