ArticleBiophysical journal2011
Salt contribution to RNA tertiary structure folding stability.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
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- Solution structure determination and biophysical characterization studies of 7SK RNP and 7SL SRP RNAs.RNA (New York, N.Y.) · 2025Article
- Metal Ion Signaling in Biomedicine.Chemical reviews · 2025Review
- Counterintuitive DNA destabilization by monovalent salt at high concentrations due to overcharging.Nature communications · 2025Article
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- High Recovery Chromatographic Purification of mRNA at Room Temperature and Neutral pH.International journal of molecular sciences · 2023Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophysical journal · 2023Article
- Effect of salinity on ccmfn gene RNA editing of mitochondria in wild barley and uncommon types of RNA editing.Functional & integrative genomics · 2023Article
- Biophysical characterization of the structure of a SARS-CoV-2 self-amplifying RNA (saRNA) vaccine.Biology methods & protocols · 2023Article
- Morphological Phenotypes, Cell Division, and Gene Expression ofMicroorganisms · 2022Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress.Frontiers in plant science · 2022Article
- Established Protocols for cRNA Expression and Voltage-Clamp Characterization of the P2X7 Receptor in Xenopus laevis Oocytes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- A Synthetic Riboswitch to Regulate Haloarchaeal Gene Expression.Frontiers in microbiology · 2021Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
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2 authors.
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Abstract
Accurate quantification of the ionic contribution to RNA folding stability could greatly enhance our ability to understand and predict RNA functions. Recently, motivated by the potential importance of ion correlation and fluctuation in RNA folding, we developed the tightly bound ion (TBI) model. Extensive experimental tests showed that the TBI model can lead to better treatment of multivalent ions than the Poisson-Boltzmann equation. In this study, we use the model to quantify the contribution of salt (Na(+) and Mg(2+)) to the RNA tertiary structure folding free energy. Folding of the RNA tertiary structure often involves intermediates. We focus on the folding transition from an intermediate state to the native state, and compute the electrostatic folding free energy of the RNA. Based on systematic calculations for a variety of RNA molecules, we derive a set of formulas for the electrostatic free energy for tertiary structural folding as a function of the sequence length and compactness of the RNA and the Na(+) and Mg(2+) concentrations. Extensive comparisons with experimental data suggest that our model and the extracted empirical formulas are quite reliable.
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