Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).
Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, [d(CGAGGTTTAAACCTCG)](2), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.
Savelyev
Alexey
A
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.
Papoian
Garegin A
GA
D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011188:Potassium / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry*; D055672:Static Electricity; D014867:Water / Q000737:chemistry*
D014867:Water; D004247:DNA; D012964:Sodium; D011188:Potassium