Escherichia coli DbpA Is a 3′ → 5′ RNA helicase

Previous work has demonstrated that Escherichia coli DbpA is a nonprocessive RNA helicase that can disrupt short RNA helices on either the 5′ side or 3′ side of hairpin 92 of 23S rRNA. Here the directionality of the helicase activity of DbpA was determined by using substrates containing a short reporter helix in the presence of a second adjacent helix of varying stability placed either 5′ or 3′ of the reporter helix. When the second helix was on the 5′ side of the reporter helix, it had no effect on the dissociation rate of the reporter helix. However, when the second helix was on the 3′ side of the reporter helix, its dissociation rate determined the dissociation rate of the reporter helix. This defines DbpA as a 3′ → 5′ helicase. Like other helicases, DbpA requires a single-stranded RNA loading site on the 3′ side of the duplex for disruption to be observed. Since the loading site could be on either strand of the helix that was disrupted, hairpin 92 does not influence the directionality of the helicase but only aids in targeting RNA substrates.