ArticleJournal of the American Chemical Society2013
Crowders perturb the entropy of RNA energy landscapes to favor folding.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- Simulating Crowding In Vitro: Not an Elusive Goal Any Longer.Sub-cellular biochemistry · 2025Review
- Protocell Effects on RNA Folding, Function, and Evolution.Accounts of chemical research · 2024Article
- Ionic liquid-caged nucleic acids enable active folding-based molecular recognition with hydrolysis resistance.Nucleic acids research · 2024Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.Biochemistry · 2022Article
- Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA.Current biology : CB · 2022Article
- Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- Understanding DNA interactions in crowded environments with a coarse-grained model.Nucleic acids research · 2020Article
- NMR analysis of nucleotide π-stacking in prebiotically relevant crowded environment.Communications chemistry · 2020Article
- 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
- Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms.Biochemistry · 2018Article
- Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.Journal of molecular biology · 2018Article
- Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.Biochemistry · 2017Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- The 2D Structure of theJournal of nucleic acids · 2017Article
- Entropic stabilization of folded RNA in crowded solutions measured by SAXS.Nucleic acids research · 2016Article
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Authors and funding
5 authors.
Funding
Abstract
Biological macromolecules have evolved to fold and operate in the crowded environment of the cell. We have shown previously that molecular crowding stabilizes folded RNA structures. Here we report SAXS measurements on a 64 kDa bacterial group I ribozyme in the presence of mono- and divalent ions and PEG crowders of different molecular weight. These experiments show that crowders always stabilize the folded RNA, but this stabilization is weaker in NaCl solutions than MgCl2 solutions. Additionally, we find that RNAs with the same global structure, parametrized by Rg, have different scattering functions depending upon the ratio of electrostatic and entropic stabilization by ions and crowders, respectively. We quantify this difference using the scattering length per scattering volume and find that this ratio is larger for RNAs that fold in lower ionic strength solutions due to the higher crowder content. We conclude that lower RNA flexibility, or reduced configurational entropy, widens the free energy gap between the unfolded and folded RNA in crowded MgCl2 solutions.
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