Branch migration enzyme as a Brownian ratchet.

ABSTRACT

In recent years, it has been shown that helicases are able to perform functions beyond their traditional role in unwinding of double-stranded nucleic acids; yet the mechanistic aspects of these different activities are not clear. Our kinetic studies of Holliday junction branch migration catalysed by a ring-shaped helicase, T7 gp4, show that heterology of as little as a single base stalls catalysed branch migration. Using single-molecule analysis, one can locate the stall position to within a few base pairs of the heterology. Our data indicate that the presence of helicase alone promotes junction unfolding, which accelerates spontaneous branch migration, and individual time traces reveal complex trajectories consistent with random excursions of the branch point. Our results suggest that instead of actively unwinding base pairs as previously thought, the helicase exploits the spontaneous random walk of the junction and acts as a Brownian ratchet, which walks along duplex DNA while facilitating and biasing branch migration in a specific direction.