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. Author manuscript; available in PMC: 2014 Oct 23.
Published in final edited form as: J Mol Biol. 2013 May 28;425(20):3824–3838. doi: 10.1016/j.jmb.2013.05.016

Figure 2. Dbp2 exhibits a preference for strand annealing with single stranded overhang RNA substrates at low ATP concentration.

Figure 2

(A–C) Graphical representation of unwinding and annealing assays with 0.1 mM ATP using (A) the blunt end RNA duplex, (B) the RNA duplex with 3’ single strand overhang or (C) the blunt end RNA-DNA hybrid. Unwinding and annealing assays were conducted as above but with 0.1 mM ATP and 2 mM MgCl2. Data from the unwinding and annealing assays were fitted as above. Representative non-denaturing gels are shown in Fig S3. (D) Kinetic parameters for Dbp2 unwinding at 0.1 mM ATP. Since there is little or no observable unwinding, the unwinding data cannot be fitted with the steady state equation as mentioned above and are listed as ND (not determined). Therefore, we assumed the kobs(ann) is the same as kanneal and converted the reported kobs(ann) to the first-order rate constant as described26. This reveals that Dbp2 exhibits higher annealing on RNA duplexes with single stranded overhangs at low ATP.