ArticleBiochemistry2013
Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions.
Article in Biochemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 47 citations in OpenAlex.
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly.ACS central science · 2023Article
- Review
- Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA.Current biology : CB · 2022Article
- Functional Roles of Chelated Magnesium Ions in RNA Folding and Function.Biochemistry · 2021Article
- NMR analysis of nucleotide π-stacking in prebiotically relevant crowded environment.Communications chemistry · 2020Article
- Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
- Optimal molecular crowding accelerates group II intron folding and maximizes catalysis.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Lipid vesicles chaperone an encapsulated RNA aptamer.Nature communications · 2018Article
- Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis.Nature communications · 2018Article
- Article
- Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.Biochemistry · 2017Article
- Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics.Methods (San Diego, Calif.) · 2017Article
- Prebiotic Factors Influencing the Activity of a Ligase Ribozyme.Life (Basel, Switzerland) · 2017Article
- Entropic stabilization of folded RNA in crowded solutions measured by SAXS.Nucleic acids research · 2016Article
- Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.RNA (New York, N.Y.) · 2016Article
- The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents.Biophysical reviews · 2016Review
- Bridging the gap between in vitro and in vivo RNA folding.Quarterly reviews of biophysics · 2016Article
- Challenge of mimicking the influences of the cellular environment on RNA structure by PEG-induced macromolecular crowding.Biochemistry · 2015Article
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4 authors at 2 institutions in 1 country.
Funding
Abstract
In an effort to relate RNA folding to function under cellular-like conditions, we monitored the self-cleavage reaction of the human hepatitis delta virus-like CPEB3 ribozyme in the background of physiological ionic concentrations and various crowding and cosolute agents. We found that at physiological free Mg(2+) concentrations (∼0.1-0.5 mM), both crowders and cosolutes stimulate the rate of self-cleavage, up to ∼6-fold, but that in 10 mM Mg(2+) (conditions widely used for in vitro ribozyme studies) these same additives have virtually no effect on the self-cleavage rate. We further observe a dependence of the self-cleavage rate on crowder size, wherein the level of rate stimulation is diminished for crowders larger than the size of the unfolded RNA. Monitoring effects of crowding and cosolute agents on rates in biological amounts of urea revealed additive-promoted increases at both low and high Mg(2+) concentrations, with a maximal stimulation of more than 10-fold and a rescue of the rate to its urea-free values. Small-angle X-ray scattering experiments reveal a structural basis for this stimulation in that higher-molecular weight crowding agents favor a more compact form of the ribozyme in 0.5 mM Mg(2+) that is essentially equivalent to the form under standard ribozyme conditions of 10 mM Mg(2+) without a crowder. This finding suggests that at least a portion of the rate enhancement arises from favoring the native RNA tertiary structure. We conclude that cellular-like crowding supports ribozyme reactivity by favoring a compact form of the ribozyme, but only under physiological ionic and cosolute conditions.
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