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

Modified Domain II (DsrA_MDII) competed with full-length DsrA for binding to Hfq. 5′-end-labeled DsrA was incubated with increasing concentrations of DsrA_MDII or DsrA_DII at 25°C for 5 min, followed by the addition of Hfq and an incubation at 25°C for 5 min. The four modified nucleotides are marked by triangles on the structure of DsrA_MDII. Samples were incubated without (−) or with (+) 3 μM Hfq. The gels were quantitated with a phosphorimager, and the K_c was calculated for MDII (180 nM) and DII (100 nM).