MOLECULAR MODELING 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 cyclisatio n studies have shown that only the former of these two sequences is si gnificantly curved. By developing novel superhelical symmetry constrai nts we were able to study the energetic and structural aspects of poly meric DNA having a controlled curvature. The results obtained (which d o not take into account specific hydration effects) correlate well wit h the experimental data and offer a molecular level explanation of cur vature. Although curvature is found to be initiated by specific dinucl eotide junctions, deformations spread to surrounding dinucleotide step s and, moreover, sequence effects beyond the dinucleotide level are ob served.