Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation

The localisation and dynamics of sodium counterions around the DNA duplex d(AGCGTACTAG-TACGCT)(2) corresponding to the trp operator fragment used in the crystal structure of the half site complex has been studied by a 1.4 ns molecular dynamics simulation in explicit solvent. A continuous and well-defined counterion density is shown to be present around the minor groove, while density patches are found in the major groove in regions where DNA bending is observed. A residence time analysis reveals the dynamic nature of these distributions. The resulting picture agrees with previous theoretical and experimental studies of A-tract DNA sequences, and is consistent with the polyelectrolyte, condensation model.