ArticleBiophysical journal2007
Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Modeling riboswitches: The impact of concentration of MgBiophysical journal · 2025Article
- Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations.Scientific reports · 2024Article
- Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking.Journal of the American Chemical Society · 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
- Functional DNA-Polymer Conjugates.Chemical reviews · 2021Review
- Experimental approaches for investigating ion atmospheres around nucleic acids and proteins.Computational and structural biotechnology journal · 2021Review
- Modeling Microtubule Counterion Distributions and Conductivity Using the Poisson-Boltzmann Equation.Frontiers in molecular biosciences · 2021Article
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.Biophysical journal · 2019Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
- Explicit ions/implicit water generalized Born model for nucleic acids.The Journal of chemical physics · 2018Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
- Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS.Biophysical reviews · 2016Article
- The Role of Correlation and Solvation in Ion Interactions with B-DNA.Biophysical journal · 2016Article
- Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.Journal of the American Chemical Society · 2015Article
- Competitive interaction of monovalent cations with DNA from 3D-RISM.Nucleic acids research · 2015Article
- Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.Physical review letters · 2015Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Poisson-Boltzmann (PB) theory is among the most widely applied electrostatic theories in biological and chemical science. Despite its reasonable success in explaining a wide variety of phenomena, it fails to incorporate two basic physical effects, ion size and ion-ion correlations, into its theoretical treatment. Recent experimental work has shown significant deviations from PB theory in competitive monovalent and divalent ion binding to a DNA duplex. The experimental data for monovalent binding are consistent with a hypothesis that attributes these deviations to counterion size. To model the observed differences, we have generalized an existing size-modified Poisson-Boltzmann (SMPB) theory and developed a new numerical implementation that solves the generalized theory around complex, atomistic representations of biological molecules. The results of our analysis show that good agreement to data at monovalent ion concentrations up to approximately 150 mM can be attained by adjusting the ion-size parameters in the new size-modified theory. SMPB calculations employing calibrated ion-size parameters predict experimental observations for other nucleic acid structures and salt conditions, demonstrating that the theory is predictive. We are, however, unable to model the observed deviations in the divalent competition data with a theory that only accounts for size but neglects ion-ion correlations, highlighting the need for theoretical descriptions that further incorporate ion-ion correlations. The accompanying numerical solver has been released publicly, providing the general scientific community the ability to compute SMPB solutions around a variety of different biological structures with only modest computational resources.
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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.