Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure

DsrA binding to Hfq is competed with by poly(U), but not poly(A). 5′-end-labeled DsrA was incubated with increasing concentrations of (A) long polydisperse (200–400 nt) poly(U) (0.5–500 ng, lanes 3–6); (B) long polydisperse poly(A) (0.5–500 ng, lanes 3–7, 8–13); and (C) poly(A)₂₇ (lanes 3–6) at 25°C for 5 min, followed by the addition of 3 μM Hfq (+) or binding buffer (−) and a second incubation at 25°C for 5 min. To control for RNA, RNA interaction DsrA was incubated (A) with (+, lane 8) or without (−, lane 7) 3.6 μg of polydisperse poly(U); or (B) with (0.5–500 ng, lanes 8–13) or without (lane 1) polydisperse poly(A). The top complexes in B are trapped in the well.