A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions:: diffusion and averaged binding of water and cations

Four different molecular dynamics (MD) simulations have been performed for ordered DNA decamers, d(5'-ATGCAGTCAG).d(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine(3+) (Spd(3+)) and putrescine(2+) (Put(2+)), the synthetic polyamine diaminopropane(2+) (DAP(2+)) and Na+. The simulation set-up corresponds to an infinite array of parallel DNA mimicking the state in oriented DNA fibers or crystals. This work describes general properties of polyamine and Na+ binding to DNA. Simulated diffusion coefficients show satisfactory agreement with experimental NMR diffusion data of comparable systems. The interaction of the polyamines with DNA is dynamic in character and the cations mostly form short-lived contacts with the electronegative binding sites of DNA. Polyamines, Na+ and water interact most frequently with the charged phosphate atoms with preference for association from the minor groove side with O1P over O2P. There is a strong anti-correlation in the cation binding to the electronegative groups of DNA, i.e. the presence of a cation near one of the DNA sites repels other cations from binding to this and to the other sites separated by <7.5 Angstrom from each other. In contrast to the other polyamines, DAP(2+) is able to form 'bridges' connecting neighboring phosphate groups along the DNA strand. A small fraction of DAP(2+) and Put(2+) can be found in the major grooves, while Spd(3+) is absent there. The results of the MD simulations reveal principal differences in the polyamine-DNA interactions between the natural (Spd(3+), Put(2+) and spermine(4+)) and synthetic (DAP(2+)) polyamines.