Telegraph model of DNA confinement in a nanochannel

The classical models of a wormlike chain in channel confinement correspond to either (i) a chain of Odijk deflection segments (when the channel size is much smaller than the persistence length) or (ii) a chain of de Gennes blobs (when the channel size exceeds the thermal blob size). Unfortunately, the vast majority of the experimental data for DNA confinement in a nanochannel, which is a very convenient experimental system, lie between these two limiting cases. We have developed a new model, based on a correlated telegraph model, that describes the regime between Odijk and de Gennes behavior. The model naturally leads to a new scaling parameter alpha that reflects the typical number of overlaps per hairpin turn in the channel, and we have developed scaling laws for both the chain extension and variance in terms of alpha. The extension and variance produced by detailed simulations of confined wormlike chains collapse onto a single master curve in terms of alpha, and that these simulations are in exact agreement with simulations of the telegraph model. We also find that the theory provides good collapse of the experimental data for approximately square nanochannels.