Competitive interaction of monovalent cations with DNA from 3D-RISM

• Published in: Nucleic acids research 2015-09, Vol.43 (17), p.8405-8415
• Main Authors: Giambaşu, George M, Gebala, Magdalena K, Panteva, Maria T, Luchko, Tyler, Case, David A, York, Darrin M
• Format: Article
• Language: English
• Subjects: Cations, Monovalent - chemistry; DNA - chemistry; Models, Molecular; Molecular Biology; Molecular Dynamics Simulation; Nucleic Acid Conformation; RNA - chemistry; Thermodynamics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkv830

The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition.