  Helicase opening of double-stranded nucleic acids may be "active" (the
helicase directly destabilizes the dsNA to promote opening) or "passive" (the
helicase binds ssNA available due to a thermal fluctuation which opens part of
the dsNA). We describe helicase opening of dsNA, based on helicases which bind
single NA strands and move towards the double-stranded region, using a discrete
``hopping'' model. The interaction between the helicase and the junction where
the double strand opens is characterized by an interaction potential. The form
of the potential determines whether the opening is active or passive. We
calculate the rate of passive opening for the helicase PcrA, and show that the
rate increases when the opening is active. Finally, we examine how to choose
the interaction potential to optimize the rate of strand separation. One
important result is our finding that active opening can increase the unwinding
rate by 7 fold compared to passive opening.
