Molecular dynamics simulations of the d(T center dot A center dot T) triple helix

Molecular dynamics (MD) simulations have been used to study the dynamical and time-averaged characteristics of the DNA triple helix d(T)(10).d(A)(10).d(T)(10). The structures sampled during the trajectory resemble closely the B-type model for the DNA tripler proposed on the basis of NMR data, although there are some subtle differences. Alternative P-and A-type conformations for the tripler, suggested from X-ray experiments, are not predicted to contribute significantly to the structure of the DNA tripler in solution. Comparison with the best available experimental data supports the correctnes of the MD-generated structures. The analysis of the collected data gives a detailed picture of the characteristics of triple-helix DNA. A new and interesting pattern of hydration, specific for tripler DNA, an important observation. The results suggest that molecular dynamics can be useful for the study of novel nucleic acid structures.