Dynamics of Site Juxtaposition in Supercoiled DNA

Brownian dynamics simulations are used to study the kinetics of juxtaposition between specific sites in supercoiled DNA at physiological ionic conditions. At this environment, supercoiled DNA adopts interwound conformations and the probability of spatial site juxtaposition is much higher in comparison to such relations in relaxed DNA. We find, however, that supercoiling does not correspondingly increase the rate of juxtaposition at these high salt conditions. Analysis of the juxtaposition dynamics helps understand this unexpected result. Namely, although a particular site i1 in supercoiled DNA nearly always juxtaposes with another site of the molecule i2, the change of i2 occurs very slowly. Since highly supercoiled DNA fluctuates about interwound conformations at physiological ionic conditions, internal slithering of opposite segments of the superhelix is the only way of changing the contact sites i2. During slithering, i2 changes slowly and nearly continuously, and this produces long correlations between successive values of i2 . Such correlation trends increase the average time of juxtaposition between specific sites of the molecule. Therefore, the juxtaposition kinetics uncovered here is profoundly different from the nearly independent random collisions of sites in relaxed DNA as well as the dynamics of supercoiled DNA at low salt concentrations.

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