Figure 2.

Different scenarios for the interaction potential between the helicase and double strand (ds). (a) Crystal structure of T7 helicase (Protein Data Bank (PDB): 1E0J) and a cartoon of dsDNA are shown. The helicase encircles one strand and excludes the other, suggesting that the interaction with the junction must happen from a distance, presumably because of electrostatic forces. (b) Shown is the crystal structure of the PcrA helicase bound to dsDNA (PDB: 3PJR), showing the overlap of the helicase domains with bases beyond the junction. Shown below both the figures are the corresponding interaction potentials U(j). Identical expressions for the unwinding velocity and run-length result for both the potentials. To see this figure in color, go online.