MOLECULAR-DYNAMICS SIMULATION OF THE HYDRATED D(CGCGAATTCGCG)2 DODECAMER

A 150-ps MD simulation of the DNA dodecamer d(CGCGAATTCGCG)2 surrounded by 22 sodium counterions and 1431 water molecules was performed with the AMBER force field. The trajectory of the simulation shows that the DNA structure was stable in the first 60 ps, it changed continuously in the interval 60-100 ps, and it stabilized again in the interval 100-150 ps. The structure was analyzed in the two time periods of simulation, 20-60 and 100-150 ps, in which the structure fluctuated around a stable average. The averaged DNA structure in the 100-150 ps of the simulation is highly distorted. Kinks are observed near the C3,G4 and C9,G10 residues. The helix is significantly unwound in the central AATT region. The base pairing and stacking interactions are also disturbed. The analysis of the trajectories of the counterions shows that they are quite mobile. They distribute equally between two types of configurations: in one the Na+ reside in a direct coordination with the phosphate group, in the other the coordination to the phosphate is through a hydration sphere. The water molecules distribute in two solvation domains. The first solvation domain is very stable during the dynamics, while the rest undergoes a small expansion. The main hydration site in DNA is the phosphate group. The average number of water molecules hydrating a G-C base pair is 21.38, while the A-T pair is solvated by an average of 20.45 water molecules. The results raise the question whether a longer MD simulation would result in a ''unique'' stable structure of DNA.