Backfolding of DNA Confined in Nanotubes: Flory Theory versus the Two-State Cooperativity Model

Abstract

We compare two theories for backfolding of semiflexible polymers, such as DNA, confined in circular tubes of diameter of the order of the persistence length of the macromolecule. The first theory was proposed by Odijk on the basis of a one-dimensional analogue of Flory theory, and the second theory is a cooperativity model of deflection segments and S-loops suggested by Dai et al. By performing Monte Carlo chain growth simulations of long chains, we find that Odijk’s scaling theory not only captures the contour length dependence of extension of the confined chain but also correctly predicts its asymptotic value. In contrast, the cooperativity model appears to quantify the extension only for the contour lengths that were used to parametrize the model and systematically deviates from the simulation data as the contour length increases.