title: Ion and solvent density distributions around canonical B-DNA from integral equations.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Houston, Houston, Texas 77204-5003, USA.
authors.forename: Jesse J
authors.initials: JJ
authors.lastname: Howard
authors.forename: Gillian C
authors.initials: GC
authors.lastname: Lynch
authors.forename: B Montgomery
authors.initials: BM
authors.lastname: Pettitt
mesh_terms: D002712:Chlorides / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D011188:Potassium / Q000737:chemistry; D012965:Sodium Chloride / Q000737:chemistry; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D002712:Chlorides; D007477:Ions; D009841:Oligonucleotides; D012997:Solvents; D012965:Sodium Chloride; D004247:DNA; D011188:Potassium