D. Sprous et Sc. Harvey, ACTION AT A DISTANCE IN SUPERCOILED DNA - EFFECTS OF SEQUENCE ON SLITHER, BRANCHING, AND INTRAMOLECULAR CONCENTRATION, Biophysical journal, 70(4), 1996, pp. 1893-1908
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.