Structural Flexibility of the d(CCAGTACTGG)₂B-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 flexibility 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 at 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 simulations and the X-ray results. The structural differences between the solid state 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 simulations provide a dynamical picture of DNA and give information in addition to the X-ray results.