A motor that makes its own track: helicase unwinding of DNA

We study the unwinding of DNA by helicase proteins as a representative system in which a motor protein interacts with a mobile obstacle. In our discrete model, the interaction between the helicase and the DNA fork is characterized by an interaction potential. For the case of a hard-wall potential, the helicase opens the DNA by rectifying thermal fluctuations which spontaneously open base pairs. A potential with nonzero range describes the destabilization of the double strand by the enzymatic action of the helicase. We derive solutions for the opening speed as a function of the potential shape and relate our results to experiments on helicase motion.