The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3′ poly(U) tail

Hfq binding of SgrS variants in vitro. (A) Analysis of interaction between SgrS RNA and Hfq. The ³²P-labeled SgrS RNA (0.2 pmol) was incubated with increasing amounts of purified Hfq-His₆ in 5 μL of binding buffer for 15 min at 37°C. Samples were analyzed by a gel mobility shift assay after the addition of 5 μL of RNA loading buffer. (B) Effects of SgrS variants on SgrS–Hfq interaction. The ³²P-labeled SgrS RNA (0.2 pmol) along with indicated amounts of each of unlabeled SgrS variants were incubated with 0.4 pmol of purified Hfq-His₆ in 5 μL of binding buffer for 15 min at 37°C. Samples were analyzed by a gel mobility shift assay after the addition of 5 μL of RNA loading buffer.