General random walk model of ATP-driven helicase translocation along DNA

A general random walk model is presented which can be used to statistically describe ATP-driven movement of a helicase (DNA unwinding enzyme) along a DNA chain with a nonuniform distribution of obstacles on the chain. These obstacles are representative of DNA-bound proteins, drugs, counterions, and DNA packing environment. We carried out a calculation on a DNA chain with an obstacle distribution that mimics DNA in chromatin (folded DNA-protein material in cells becomes chromosome in partially unfolded form). Our calculated helicase movement speed shows significant reduction with increasing obstacle strength. At the strong strength limit, the calculated speed is found to be consistent with the observed helicase unwinding rate for chromatin DNA. Therefore the model presented in this work is of potential application in the analysis of the effect of random obstacles on biomolecular translocation along DNA. The behavior of the helicase translocation under different obstacle strengths and along different lengths of DNA is discussed.