INTERNAL MOTION OF SUPERCOILED DNA - BROWNIAN DYNAMICS SIMULATIONS OFSITE JUXTAPOSITION

Thermal motions in supercoiled DNA are studied by Brownian dynamics (B D) simulations with a focus on the site juxtaposition process. It had been shown in the last decade that the ED approach is capable of descr ibing actual times of large-scale DNA motion, The bead model of DNA us ed here accounts for bending and torsional elasticity as well as the e lectrostatic repulsion among DNA segments. The hydrodynamic interactio n among the beads of the model chain and the aqueous solution is incor porated through the Rotne-Prager tensor. All simulations were performe d for the sodium ion concentration of 0.01 M. We first showed, to test our ED procedure, that the same distributions of equilibrium conforma tional properties are obtained as by Monte Carlo simulations for the c orresponding DNA model. The ED simulations also predict with accuracy published experimental values of the diffusion coefficients of superco iled DNA. To describe the rate of conformational changes, we also calc ulated the autocorrelation functions for the writhe and radius of gyra tion for the supercoiled molecules. The rate of site juxtaposition was then studied for DNA molecules up to 3000 bp in length. We find that site juxtaposition is a very slow process: although accelerated by a f actor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two ord ers of magnitude higher than the relaxation times of writhe and the ra dius of gyration for the same molecules. By inspecting successive simu lated conformations of supercoiled DNA, we conclude that slithering of opposing segments of the interwound superhelix is not an efficient me chanism to accomplish site juxtaposition, at least for conditions of l ow salt concentration. Instead, transient distortions of the interwoun d superhelix, followed by continuous reshaping of the molecule, contri bute more significantly to site juxtaposition kinetics. (C) 1998 Acade mic Press.