ArticleMethods in enzymology2009
Predicting electrostatic forces in RNA folding.
Article in Methods in enzymology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- Ionic liquid-caged nucleic acids enable active folding-based molecular recognition with hydrolysis resistance.Nucleic acids research · 2024Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- IsRNA1:Journal of chemical theory and computation · 2021Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements.Biophysical journal · 2015Article
- DNA under Force: Mechanics, Electrostatics, and Hydration.Nanomaterials (Basel, Switzerland) · 2015Review
- Ion-mediated RNA structural collapse: effect of spatial confinement.Biophysical journal · 2012Article
- Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods.Nucleic acids research · 2012Article
- Electrostatics of nucleic acid folding under conformational constraint.Journal of the American Chemical Society · 2012Article
- RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations.Biophysical journal · 2012Article
- Salt contribution to RNA tertiary structure folding stability.Biophysical journal · 2011Article
- Importance of diffuse metal ion binding to RNA.Metal ions in life sciences · 2011Review
- Predicting ion binding properties for RNA tertiary structures.Biophysical journal · 2010Article
- RNA-ligand molecular docking: advances and challenges.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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2 authors.
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Abstract
Metal ion-mediated electrostatic interactions are critical to RNA folding. Although considerable progress has been made in mechanistic studies, the problem of accurate predictions for the ion effects in RNA folding remains unsolved, mainly due to the complexity of several potentially important issues such as ion correlation and dehydration effects. In this chapter, after giving a brief overview of the experimental findings and theoretical approaches, we focus on a recently developed new model, the tightly bound ion (TBI) model, for ion electrostatics in RNA folding. The model is unique because it can treat ion correlation and fluctuation effects for realistic RNA 3D structures. For monovalent ion (such as Na(+)) solutions, where ion correlation is weak, TBI and the Poisson-Boltzmann (PB) theory give the same results and the results agree with the experimental data. For multivalent ion (such as Mg(2+)) solutions, where ion correlation can be strong, however, TBI gives much improved predictions than the PB. Moreover, the model suggests an ion correlation-induced mechanism for the unusual efficiency of Mg(2+) ions in the stabilization of RNA tertiary folds. In this chapter, after introducing the theoretical framework of the TBI model, we will describe how to apply the model to predict ion-binding properties and ion-dependent folding stabilities.
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