ArticleThe journal of physical chemistry letters2015
Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties.
Article in The journal of physical chemistry letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
28 citing papers in PubMed, 59 citations in OpenAlex.
- Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes.The journal of physical chemistry. B · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Similarities and Differences between NaJournal of chemical theory and computation · 2021Article
- Cation enrichment in the ion atmosphere is promoted by local hydration of DNA.Physical chemistry chemical physics : PCCP · 2021Article
- Assessment of the DNA partial specific volume and hydration layer properties from CHARMM Drude polarizable and additive MD simulations.Physical chemistry chemical physics : PCCP · 2021Article
- In situ Surface Charge Density Visualization of Self-assembled DNA Nanostructures after Ion Exchange.Chemphyschem : a European journal of chemical physics and physical chemistry · 2020Article
- Polarizable Molecular Dynamics Simulations of TwoJournal of chemical theory and computation · 2020Article
- Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment.Frontiers in physics · 2019Article
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.Biophysical journal · 2019Article
- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
- Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.Chemical reviews · 2019Review
- Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.Annual review of biophysics · 2019Review
- Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization.Journal of chemical theory and computation · 2019Article
- Polarizable force field for RNA based on the classical drude oscillator.Journal of computational chemistry · 2018Article
- AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.Journal of chemical theory and computation · 2018Article
- Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.Carbohydrate research · 2018Article
- Mapping the Drude polarizable force field onto a multipole and induced dipole model.The Journal of chemical physics · 2017Article
- Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein.Journal of molecular modeling · 2017Article
- Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.Journal of chemical theory and computation · 2017Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
The present report demonstrates that the conformational properties of DNA in solution are sensitive to the type of monovalent ion. Results are based on the ability of a polarizable force field using the classical Drude oscillator to reproduce experimental solution X-ray scattering data more accurately than two nonpolarizable DNA models, AMBER Parmbsc0 and CHARMM36. The polarizable model is then used to calculate scattering profiles of DNA in the presence of four different monovalent salts, LiCl, NaCl, KCl, and RbCl, showing the conformational properties of DNA to vary as a function of ion type, with that effect being sequence-dependent. The primary conformational mode associated with the variations is contraction of the DNA minor groove width with decreasing cation size. These results indicate that the Drude polarizable model provides a more realistic representation of ion-DNA interactions than additive models that may lead to a new level of understanding of the physical mechanisms driving salt-mediated biological processes involving nucleic acids.
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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.