Dynamics of site juxtaposition in supercoiled DNA

Juxtaposition kinetics between specific sites in supercoiled DNA is investi gated at close to physiological ionic conditions by Brownian dynamics simul ations. At such conditions, supercoiled DNA is interwound, and the probabil ity of spatial site juxtaposition is much higher than in relaxed DNA. We fi nd, however, that supercoiling does not correspondingly increase the rate o f juxtaposition at these physiological conditions. An explanation to this u nexpected finding emerges on analysis of the juxtaposition dynamics. We not e that although a particular site ii in supercoiled DNA is often in close p roximity (juxtaposed) to another site ir, the change of it occurs very slow ly and depends largely on internal slithering of opposite segments of the D NA superhelix. Such slithering results in long correlations between success ive values of it; these correlations increase the average time of juxtaposi tion between two DNA sites. Random collisions between sites located on diff erent superhelix branches-although increasing in importance with DNA size-c ontribute less substantially to site juxtaposition at high sa It than slith ering for DNA up to 6 kb in length.