Stretching DNA in hard-wall potential channels

Abstract: A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The macroscopic helical parameters are computed performing statistical averages over the ensemble of microscopic base pair fluctuations. The average molecule elongation, measured by the end-to-end distance, is derived as a function of the channel potential parameters both for a homogeneous and a heterogeneous chain. The overall results suggest that the mesoscopic model, with the channel potential term, yields consistent quantitative estimates for the stretching and twisting of short chains.