Molecular modelling of (A(4)T(4)NN)(n) and (T(4)A(4)NN)(n): Sequence elements responsible for curvature

The molecular modelling program JUMNA has been used to investigate the origins of the strikingly different curvature of the two sequences, (A(4)T(4)NN)(n) and (T(4)A(4)NN)(n). Gel electrophoresis and cyclisation studies have shown that only the former of these two sequences is significantly curved. By developing novel superhelical symmetry constraints we were able to study the energetic and structural aspects of polymeric DNA having a controlled curvature. The results obtained (which do not take into account specific hydration effects) correlate well with the experimental data and offer a molecular level explanation of curvature. Although curvature is found to be initiated by specific dinucleotide junctions, deformations spread to surrounding dinucleotide steps and, moreover, sequence effects beyond the dinucleotide level are observed.