ArticleThe journal of physical chemistry. B2010
Computational exploration of mobile ion distributions around RNA duplex.
Article in The journal of physical chemistry. B, 2010. 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.
- Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.The journal of physical chemistry. B · 2023Article
- Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.Journal of chemical information and modeling · 2023Article
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation.Biophysical journal · 2021Article
- The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface.Chemical communications (Cambridge, England) · 2021Review
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.Biophysical journal · 2019Article
- Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations.Biophysical journal · 2019Article
- A Kirkwood-Buff derived force field for alkaline earth halide salts.The Journal of chemical physics · 2018Article
- Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Competitive Binding of MgBiophysical journal · 2018Article
- MCTBI: a web server for predicting metal ion effects in RNA structures.RNA (New York, N.Y.) · 2017Article
- Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.Journal of the American Chemical Society · 2015Article
- Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.Journal of chemical theory and computation · 2015Article
- Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition.The journal of physical chemistry. B · 2015Article
- Membrane permeation of a peptide: it is better to be positive.The journal of physical chemistry. B · 2015Article
- Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study.Nucleic acids research · 2014Article
- Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments.The Journal of chemical physics · 2014Article
- Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach.Biopolymers · 2014Article
Corrections and comments
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2 authors.
Funding
Abstract
Atomically detailed distributions of ions around an A-form RNA are computed. Different mixtures of monovalent and divalent ions are considered explicitly. Studies of tightly bound and of diffusive (but bound) ions around 25 base pairs RNA are conducted in explicit solvent. Replica exchange simulations provide detailed equilibrium distributions with moderate computing resources (20 ns of simulation using 64 replicas). The simulations show distinct behavior of single and double charged cations. Binding of Mg(2+) ion includes tight binding to specific sites while Na(+) binds only diffusively. The tight binding of Mg(2+) is with a solvation shell while Na(+) can bind directly to RNA. Negative mobile ions can be found near the RNA but must be assisted by proximate and mobile cations. At distances larger than 16 A from the RNA center, a model of RNA as charged rod in a continuum of ionic solution provides quantitative description of the ion density (the same as in atomically detailed simulation). At shorter distances, the structure of RNA (and ions) has a significant impact on the pair correlation functions. Predicted binding sites of Mg(2+) at the RNA surface are in accord with structures from crystallography. Electric field relaxation is investigated. The relaxation due to solution rearrangements is completed in tens of picoseconds, while the contribution of RNA tumbling continues to a few nanoseconds.
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