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Title: The role of correlation and solvation in ion interactions with B-DNA

Ionic atmosphere around nucleic acids plays important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important insights into the structure and energetics of the ionic atmosphere but are time- and resource-intensive. In this paper, we demonstrate the use of classical density functional theory to model DNA-ion interactions and explore the balance between ion-DNA, ion-water, and ion-ion interactions. In particular, we compute the distribution of RbCl, SrCl2, and CoHexCl3 (cobalt hexammine chlo- ride) around a B-form DNA molecule. The accuracy of the DFT calculations was assessed by comparison between simulated and experimental ASAXS curves. As expected, these calculations revealed significant differences between the monovalent, divalent, and trivalent cations. About half of the DNA-bound Rb+ ions penetrate into the minor groove of the DNA and half adsorb on the DNA strands. The fraction of cations in the minor groove decreases for the larger Sr2+ ions and becomes zero for CoHex3+ ions, which all adsorb on the DNA strands. The distribution of CoHex3+ ions is mainly determined by Coulomb interactions, while ion-correlation forces play a central role in the monovalent Rb+ distribution and a combination of ion-correlation and hydration forcesmore » affect the Sr2+ distribution around DNA.« less
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Publication Date:
OSTI Identifier:
Report Number(s):
Journal ID: ISSN 0006-3495; WN0219080
DOE Contract Number:
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biophysical Journal; Journal Volume: 110; Journal Issue: 2
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org:
Country of Publication:
United States