Unzipping Double-Stranded DNA by Helicase
This Demonstration carries out simulations related to the unwinding of double-stranded DNA (or dsRNA) by a helicase motor protein. In certain limits, this model is also applicable to force generation via actin polymerization. The location of the helicase is represented as the orange trace. The location of the junction between double-stranded DNA and single-stranded DNA (ssDNA) is represented by the green trace. Specifically, this Demonstration simulates two one-dimensional biased random walks that cannot cross each other. The effect of varying the rate constants for helicase stepping, DNA zipping and unzipping, and so on can be investigated using the sliders. A force that tends to unzip dsDNA may also be varied with a slider. Also presented are three theoretical curves for the mean velocity at which helicase unzips dsDNA. First is the velocity according to a Brownian ratchet model for helicase activity, shown in magenta. Second is the velocity according to a version of the theory, presented by Betterton and Julicher , that incorporates a repulsive interaction between the helicase and the dsDNA-ssDNA junction. This curve is colored blue. Third is Betterton and Julicher's optimum velocity, which is obtained by a particular choice of the interaction strength, and which is shown in red.
 M. D. Betterton and F. Julicher, "A Motor That Makes Its Own Track: Helicase Unwinding of DNA," Physical Review Letters 91, 2003, 2581030-1.