期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 115, 期 3, 页码 547-556出版社
AMER CHEMICAL SOC
DOI: 10.1021/jp107383s
关键词
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资金
- National Institutes of Health [GM066813]
- Robert A. Welch Foundation [E-1028]
- Keck Center for Computational and Structural Biology of the Gulf Coast Consortia [5T15LM07093]
We calculate the water and ion spatial distributions around charged oligonucleotides using a renormalized three-dimensional reference interaction site theory coupled with the HNC closure. Our goal is to understand the balance between inter-DNA strand forces and solvation forces as a function of oligonucleotide length in the short strand limit. The DNA is considered in aqueous electrolyte solutions of 1 M KCl, 0.1 M KCl, or 0.1 M NaCl. The current theoretical results are compared to molecular dynamics (MD) simulations and experiments. It is found that the integral equation (IE) theory replicates the MD and the experimental results for the base-specific hydration patterns in both the major and the minor grooves. We are also able to discern characteristic structural pattern differences between Na+ and K+ ions. When compared to Poisson-Boltzmann methods, the IE theory, like simulation, predicts a richly structured ion environment, which is better described as multilayer rather than double layer.
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