MODULATION OF INTRAMOLECULAR INTERACTIONS IN SUPERHELICAL DNA BY CURVED SEQUENCES - A MONTE-CARLO SIMULATION STUDY

A Monte Carlo model for the generation of superhelical DNA structures at thermodynamic equilibrium (Klenin et al., 1991; Vologodskii et al., 1992) was modified to account for the presence of local curvature. Eq uilibrium ensembles of a 2700-bp DNA chain at linking number differenc e Delta Lk = -15 were generated, with one or two permanent bends up to 120 degrees inserted at different positions. The computed structures were then analyzed with respect to the number and positions of the end loops of the interwound superhelix, and the intramolecular interactio n probability of different segments of the DNA. We find that the super helix structure is strongly organized by permanent bends. A DNA segmen t with a 30 degrees bend already has a significantly higher probabilit y of being at the apex of a superhelix than the control, and for a 120 degrees bend the majority of DNAs have one end loop at the position o f the bend. The entropy change due to the localization of a 120 degree s permanent bend in the end loop is estimated to be -17 kJ mol(-1) K-1 . When two bends are inserted, the conformation of the superhelix is f ound to be strongly dependent on their relative positions: the straigh t interwound form dominates when the two bends are separated by 50% of the total DNA length, whereas the majority of the superhelices are in a branched conformation when the bends are separated by 33%. DNA segm ents in the vicinity of the permanent bend are strongly oriented with respect to each other.