As an example, the effect of DNA cyclization rates upon protein binding has been observed for the catabolite activator protein (CAP) (Kahn and Crothers, 1992). The CAP binding site was phased against an intrinsically bend stretch of adenine tract (Atract) DNA. Monte Carlo simulations of DNA cyclization kinetics were then used, in conjunction with these experimental results, to determine the actual degree of bending of CAP (Kahn and Crothers, 1998).

This program performs these Monte Carlo calculations using the procedures published previously (Levene and Crothers, 1986a, 1986b; Kahn and Crothers, 1998) and introduces the concept of performing "independent calculations" within a single simulation. Additionally, a simple method has been developed to allow the user to adjust the parameters that define the DNA chain under study.