ArticleJournal of the American Chemical Society2014
Molecular crowding accelerates ribozyme docking and catalysis.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 49 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
49 citing papers in PubMed, 92 citations in OpenAlex.
- A passive protein environment offsets RNA folding energetics in cells.bioRxiv : the preprint server for biology · 2026Article
- Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced sampling.Physical chemistry chemical physics : PCCP · 2026Article
- Aggregation of Phosphates Enhances Enzyme Activity in Aqueous Solution.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Allosteric regulation of enzymatic catalysis by molecular crowding.Communications chemistry · 2026Article
- Reticular Chemistry: A Versatile Platform for Engineering Heterogenous Biocatalysts.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Compartmentalization and Aggregation of Biomolecular Condensates in Crowded Hydrogels for Enhanced Nucleic Acid Diagnosis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Engineering of Small Ribozymes Acting on RNA: What is Needed to Make a New Function Work with an Existing Catalyst?Chembiochem : a European journal of chemical biology · 2025Review
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Protocell Effects on RNA Folding, Function, and Evolution.Accounts of chemical research · 2024Article
- Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding.Nature communications · 2023Article
- Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly.ACS central science · 2023Article
- When Phased without Water: Biophysics of Cellular Desiccation, from Biomolecules to Condensates.Chemical reviews · 2023Review
- Excluded Volume and Weak Interactions in Crowded Solutions Modulate Conformations and RNA Binding of an Intrinsically Disordered Tail.The journal of physical chemistry. B · 2023Article
- Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations.Nature communications · 2023Article
- Dynamic RNA Fitness Landscapes of a Group I Ribozyme during Changes to the Experimental Environment.Molecular biology and evolution · 2022Article
- RNA self-splicing by engineered hairpin ribozyme variants.Nucleic acids research · 2022Article
- Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA.Current biology : CB · 2022Article
- Stability and Activity of the 10-23 DNAzyme Under Molecular Crowding Conditions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi.Nucleic acids research · 2021Article
- Biochemical analysis of cleavage and ligation activities of the pistol ribozyme fromRNA biology · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
All biological processes take place in highly crowded cellular environments. However, the effect that molecular crowding agents have on the folding and catalytic properties of RNA molecules remains largely unknown. Here, we have combined single-molecule fluorescence resonance energy transfer (smFRET) and bulk cleavage assays to determine the effect of a molecular crowding agents on the folding and catalysis of a model RNA enzyme, the hairpin ribozyme. Our single-molecule data reveal that PEG favors the formation of the docked (active) structure by increasing the docking rate constant with increasing PEG concentrations. Furthermore, Mg(2+) ion-induced folding in the presence of PEG occurs at concentrations ∼7-fold lower than in the absence of PEG, near the physiological range (∼1 mM). Lastly, bulk cleavage assays in the presence of the crowding agent show that the ribozyme's activity increases while the heterogeneity decreases. Our data is consistent with the idea that molecular crowding plays an important role in the stabilization of ribozyme active conformations in vivo.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.