ArticleThe journal of physical chemistry. B2011
Ion and solvent density distributions around canonical B-DNA from integral equations.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Effects of Probe-Related Correlations on Local Electrostatic Potentials Around DNA.Journal of computational chemistry · 2025Article
- 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
- Measuring Local Electrostatic Potentials Around Nucleic Acids by Paramagnetic NMR Spectroscopy.The journal of physical chemistry letters · 2022Article
- Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations.Biophysical journal · 2022Article
- An Expeditious Approach towards the Synthesis and Application of Water-Soluble and Photostable Fluorogenic Chromones for DNA Detection.Molecules (Basel, Switzerland) · 2022Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Integral equation models for solvent in macromolecular crystals.The Journal of chemical physics · 2022Article
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- Quantifying MgPolymers · 2018Article
- Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
- Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?Journal of the American Chemical Society · 2016Article
- Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.Journal of the American Chemical Society · 2015Article
- Physicochemical Properties of Ion Pairs of Biological Macromolecules.Biomolecules · 2015Review
- Competitive interaction of monovalent cations with DNA from 3D-RISM.Nucleic acids research · 2015Article
- Solvation and cavity occupation in biomolecules.Biochimica et biophysica acta · 2015Article
- Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics.Nucleic acids research · 2015Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Ionic strength independence of charge distributions in solvation of biomolecules.The Journal of chemical physics · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We calculate the water and ion spatial distributions around charged oligonucleotides using a renormalized three-dimensional reference interaction site theory coupled with the HNC closure. Our goal is to understand the balance between inter-DNA strand forces and solvation forces as a function of oligonucleotide length in the short strand limit. The DNA is considered in aqueous electrolyte solutions of 1 M KCl, 0.1 M KCl, or 0.1 M NaCl. The current theoretical results are compared to molecular dynamics (MD) simulations and experiments. It is found that the integral equation (IE) theory replicates the MD and the experimental results for the base-specific hydration patterns in both the major and the minor grooves. We are also able to discern characteristic structural pattern differences between Na(+) and K(+) ions. When compared to Poisson-Boltzmann methods, the IE theory, like simulation, predicts a richly structured ion environment, which is better described as multilayer rather than double layer.
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