ArticleBiophysical journal2014
Ion counting from explicit-solvent simulations and 3D-RISM.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed, 108 citations in OpenAlex.
- Ion NMR for Biomolecular Systems.Journal of molecular biology · 2025Review
- Effects of Probe-Related Correlations on Local Electrostatic Potentials Around DNA.Journal of computational chemistry · 2025Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- Review
- 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 DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- Computational Study of the pH-Dependent Ionic Environment around β-Lactoglobulin.The journal of physical chemistry. B · 2022Article
- RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations.The journal of physical chemistry. B · 2022Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking.Journal of the American Chemical Society · 2022Article
- Integral equation models for solvent in macromolecular crystals.The Journal of chemical physics · 2022Article
- Cation enrichment in the ion atmosphere is promoted by local hydration of DNA.Physical chemistry chemical physics : PCCP · 2021Article
- Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor.Biochemistry · 2021Article
- Experimental approaches for investigating ion atmospheres around nucleic acids and proteins.Computational and structural biotechnology journal · 2021Review
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.Biophysical journal · 2019Article
- Behavior of α, β tubulin in DMSO-containing electrolytes.Nanoscale advances · 2019Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The ionic atmosphere around nucleic acids remains only partially understood at atomic-level detail. Ion counting (IC) experiments provide a quantitative measure of the ionic atmosphere around nucleic acids and, as such, are a natural route for testing quantitative theoretical approaches. In this article, we replicate IC experiments involving duplex DNA in NaCl(aq) using molecular dynamics (MD) simulation, the three-dimensional reference interaction site model (3D-RISM), and nonlinear Poisson-Boltzmann (NLPB) calculations and test against recent buffer-equilibration atomic emission spectroscopy measurements. Further, we outline the statistical mechanical basis for interpreting IC experiments and clarify the use of specific concentration scales. Near physiological concentrations, MD simulation and 3D-RISM estimates are close to experimental results, but at higher concentrations (>0.7 M), both methods underestimate the number of condensed cations and overestimate the number of excluded anions. The effect of DNA charge on ion and water atmosphere extends 20-25 Å from its surface, yielding layered density profiles. Overall, ion distributions from 3D-RISMs are relatively close to those from corresponding MD simulations, but with less Na(+) binding in grooves and tighter binding to phosphates. NLPB calculations, on the other hand, systematically underestimate the number of condensed cations at almost all concentrations and yield nearly structureless ion distributions that are qualitatively distinct from those generated by both MD simulation and 3D-RISM. These results suggest that MD simulation and 3D-RISM may be further developed to provide quantitative insight into the characterization of the ion atmosphere around nucleic acids and their effect on structure and stability.
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