Theoretical analysis of disruptions in DNA minicircles.

Under sufficient bending stress, which appears in DNA minicircles and small DNA loops, the double helix experiences local disruptions of its regular structure. We developed a statistical-mechanical treatment of the disruptions in DNA minicircles, studied experimentally by Du et al. The model of disruptions used in our Monte Carlo simulation of minicircle conformations specifies these conformations by three parameters: DNA bend angle at the disruption, theta(d); local DNA unwinding caused by the disruption; and the free energy associated with the disruption in the unstressed double helix, G(d). The model is applicable to any structural type of disruption, kinks or opening of single basepairs. The simulation shows that accounting for both torsional and bending deformation associated with the disruptions is very important for proper analysis. We obtained a relationship between values of G(d) and theta(d) under which the simulation results are compatible with the experimental data. The relationship suggests that the free energy of basepair opening, which includes flipping out both bases, is significantly higher than the generally accepted value. The model is also applied to the analysis of j-factors of very short DNA fragments.