Dda helicase unwinds a DNA–PNA chimeric substrate: Evidence for an inchworm mechanism

Helicases are ubiquitous enzymes involved in all aspects of DNA metabolism including replication, repair, recombination, and transcription. The mechanism of the bacteriophage T4 Dda helicase was investigated by preparing a DNA–PNA chimeric substrate. Surprisingly, Dda was able to unwind a substrate containing 12 PNA moieties in the loading strand of the enzyme. We suggest a mechanism whereby the Dda helicase contains two distinct DNA binding domains which allow an inchworm mechanism for translocation. A single step of the enzyme is sufficient to unwind the DNA–PNA chimera because several base pairs melt spontaneously due to thermal fraying. Hence, Dda helicase can unwind the substrate without actually translocating along the PNA.