ArticleNucleic acids research2015
Competitive interaction of monovalent cations with DNA from 3D-RISM.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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Who cites it
30 citing papers in PubMed, 53 citations in OpenAlex.
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Effects of Probe-Related Correlations on Local Electrostatic Potentials Around DNA.Journal of computational chemistry · 2025Article
- The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.The Journal of chemical physics · 2024Article
- The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle.bioRxiv : the preprint server for biology · 2024Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- 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
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.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
- 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
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.Nucleic acids research · 2019Article
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.Biophysical journal · 2019Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
- Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4.Nucleic acids research · 2019Article
- Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory.Journal of the American Chemical Society · 2019Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.