Dynamics of small loops in DNA molecules

The kinetics and thermodynamics of loop formation by short segments of doub le-stranded DNA was studied by computer simulation. The DNA molecule was mo deled as a discrete wormlike chain. Brownian dynamics was used to simulate the dynamic properties of the chain. Since the average time of loop formati on, tau(a), grows sharply when the loop size drops below DNA persistence le ngth, we were unable to simulate the process directly for such small loops. Instead, we used the relationship between the equilibrium probability of l oop formation, P, tau(a), and the average time of loop decay, tau(d). The v alues of P and za were simulated directly. A new Monte Carlo algorithm was developed allowing efficient calculation of P for small DNA loops. The algo rithm is also applicable to more complex models of a polymer chain, particu larly to DNA models with intrinsic curvature. We also considered loop forma tion by a segment of a DNA molecule and found that the values of tau(d) and tau(a), are weakly affected by the total chain size. Our results showed th at the formation of small loops is a very slow process: for loops less than 50 nn in size tau(a) can be comparable to the lifetime of the cell.