Molecular dynamics studies of ion distributions around DNA duplexes and duplex dimers: Salt effects and the connection to cooperative DNA melting

We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius R counter which is on the order of 25 A from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated R counter , we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 A leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 A. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates.