Simulations of extension distributions for DNA confined in nanochannels near the persistence length

DNA has been used extensively as a model system to study confined polymers. A particularly important application of strongly confined DNA is genome mapping, where DNA molecules labeled at sequence-specific sites along their backbone are stretched by confinement in nanochannels with widths close to the DNA persistence length. The distributions of the fractional extension obtained in genome mapping experiments are skewed-left from a Gaussian distribution. Mehlig and coworkers proposed an explanation for these skewed distributions by obtaining the asymptotic solution for a weakly correlated telegraph model of a channel-confined polymer in the limit of small channels and long chains. We have tested the predictions of this theory using pruned-enriched Rosenbluth method (PERM) simulations. The simulated distributions are in reasonable agreement with theory in the relevant asymptotic limits. However, deviations are observed as we move away from the strict inequalities in the limits of the theory, corresponding to situations that are more representative of experimental systems.