The Role of Correlation and Solvation in Ion Interactions with B-DNA

Biophysical Journal
Maria L SushkoNathan A Baker

Abstract

The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle x-ray scattering can provide important insights into the structure and energetics of such atmospheres but are time- and resource intensive. In this article, we use classical density functional theory to explore the balance among ion-DNA, ion-water, and ion-ion interactions in ionic atmospheres of RbCl, SrCl2, and CoHexCl3 (cobalt hexamine chloride) around a B-form DNA molecule. The accuracy of the classical density functional theory calculations was assessed by comparison between simulated and experimental anomalous small-angle x-ray scattering curves, demonstrating that an accurate model should take into account ion-ion correlation and ion hydration forces, DNA topology, and the discrete distribution of charges on the DNA backbone. As expected, these calculations revealed significant differences among monovalent, divalent, and trivalent cation distributions around DNA. Approximately half of the DNA-bound Rb(+) ions penetrate into the minor groove of the DNA and half adsorb on the DNA backbone. The fraction of cations in the minor groove dec...Continue Reading

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Citations

Apr 15, 2016·The Journal of Physical Chemistry. B·Frédéric PoitevinHenri Orland
Mar 17, 2017·Annual Review of Biophysics·Li-Zhen SunShi-Jie Chen
Apr 19, 2018·Metallomics : Integrated Biometal Science·Stefan K KolevGeorgi N Vayssilov
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Mar 20, 2018·Physical Review. E·Aykut ErbaşJohn F Marko
Oct 12, 2018·The Journal of Chemical Physics·Igor S TolokhAlexey V Onufriev
Dec 31, 2016·Nucleic Acids Research·David R Jacobson, Omar A Saleh
Apr 2, 2021·Biophysical Journal·Alexa M Salsbury, Justin A Lemkul
Dec 22, 2017·Journal of Chemical Theory and Computation·Ahmad ElbahnsiChristophe Oguey
Oct 9, 2021·Physical Chemistry Chemical Physics : PCCP·Chun Yu MaMartina Havenith
Oct 12, 2021·Journal of Chemical Theory and Computation·Egor S KolesnikovAlexey V Onufriev

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