Structural flexibility of the d(CCAGTACTGG)(2) B-DNA decamer and its complex with two polyamides

Molecular dynamics simulations of the d(CCAGTACTGG)(2) B-DNA decamer alone and complexed with two polyamide-ligands exhibit a distinct structural flex ibility of the DNA. In contrast to the X-ray-determined structures, the DNA double helices are curved in the simulation. The bending is mainly due to a large positive roll of the three Y-R steps. These two T-G/C-A steps one a t each end and the T-A step in the middle of the DNA sequence have already been observed to introduce bending into DNA and deviate most from the X-ray structure. Crystal effects tend to disturb the local conformation of such highly flexible sites, which explains the differences between our simulatio ns and the X-ray results. The structural differences between the solid stat e and the solution structure of the simulation can also be made responsible for a different B-I/B-II conformational substate pattern in solution. The different ionic environments in the simulation and in the X-ray crystal are assumed to be the reason for the structural differences. So our simulation s provide a dynamical picture of DNA and give information in addition to th e X-ray results.