Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: Influence of the crystal environment

Molecular dynamics (MD) simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure. Two cry stal simulations were carried out; one consisted of one unit cell containin g two duplexes, and the other of two unit cells containing four duplexes. T wo solution simulations were also carried out, one starting from canonical B-DNA and the other starting from the crystal structure, For many helicoida l parameters, the results from the crystal and solution simulations were es sentially identical. However, for other parameters, in particular, alpha, g amma, delta, (epsilon - zeta), phase, and helical twist, differences betwee n crystal and solution simulations were apparent. Notably, during crystal s imulations, values of helical twist remained comparable to those in the cry stal structure, to include the sequence-dependent differences among base st eps, in which values ranged from 20 degrees to 50 degrees per base step, Ho wever, in the solution simulations, not only did the average values of heli cal twist decrease to similar to 30 degrees per base step, but every base s tep was similar to 30 degrees, suggesting that the sequence-dependent infor mation may be lost. This study reveals that MD simulations of the crystal e nvironment complement solution simulations in validating the applicability of MD to the analysis of DNA structure.