ACTION AT A DISTANCE IN SUPERCOILED DNA - EFFECTS OF SEQUENCE ON SLITHER, BRANCHING, AND INTRAMOLECULAR CONCENTRATION

We report a computer modeling study of DNA supercoiling in model plasm ids over the size range of 140-1260 bp. We used a computer model with basepair resolution. Molecular dynamics was used to produce ensembles at 300 K and to investigate intramolecular motions, The plasmid models varied by their sequence. The sequence types employed for comparison included a curve-bearing plasmid, a heterogenous sequence plasmid, and a homogenous sequence. Within the three sequence types tested at the 1260-bp plasmid size, we observed several sequence-dependent phenomena , Writhe, radius of gyration, slither motion, and branching probabilit y were seen to be sequence dependent, Branching probability was the le ast in the homogenous plasmid and the greatest in the curve-bearing pl asmid, The curve imposed a symmetry on the plasmid that was absent in the heterogenous sequence. Significant localizations and enhancements of intramolecular concentration were seen to a persistence length. Mol ecular dynamics allowed us to observe the mechanism of branch formatio n and reabsorption, We observed a size-dependent change in the types o f motion observed in plasmids, Slither motion predominated in plasmids up to 600 bp in size, whereas global rearrangements were more importa nt in the 1260 mer.