Monte Carlo Simulation on Stretching of Single DNA Molecules in Confined Environments

Stretching and relaxation of a single DNA molecule tethered in a specially designed thin slit were studied using Monte Carlo simulation combined with bondfluctuation method. It was found that the extension and relaxation of the single DNA molecule are greatly affected by the confined environment. If the extent of the confined environment is increased by decreasing the distance between the two planar surfaces of the slit, the extension of the single DNA molecule increases, due to the screening of the hydrodynamic interaction of DNA segments by the planar surfaces of the slit. The relaxation of the single DNA molecule in different confined environments verifies this assumption completely. The correlation between the end-to-end separation and flow velocity obtained by Monte Carlo simulation is in good agreement with either the experimental results or theoretical consideration reported previously.