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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