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 t he 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-de fined counterion density is shown to be present around the minor groove, wh ile density patches are found in the major groove in regions where DNA bend ing is observed. A residence time analysis reveals the dynamic nature of th ese distributions. The resulting picture agrees with previous theoretical a nd experimental studies of A-tract DNA sequences, and is consistent with th e polyelectrolyte, condensation model.