Backbone tracking by the SF2 helicase NPH-II

Members of the DExH/D family of proteins, a subset of helicase superfamily 2 (SF2), are involved in virtually all aspects of RNA metabolism. NPH-II, a prototypical member of this protein family, exhibits robust RNA helicase activity in vitro. Using a series of modified substrates to explore the unwinding mechanism of NPH-II, we observed that the helicase tracks exclusively on the loading strand, where it requires covalent continuity and specifically recognizes the ribose-phosphate backbone. NPH-II unwinding was unaffected by lesions and nicks on the top strand, which has a minimal role in substrate recognition. NPH-II required physical continuity of phosphodiester linkages on the loading strand, although abasic regions were tolerated. These findings suggest that SF2 helicases are mechanistically distinct from other helicase families that can tolerate breaks in the loading strand and for which bases are the primary recognition determinant.