FIG. 2.

Gel mobility shift analysis of the CsrA-hfq RNA interaction. 5′-end-labeled hfq RNA was incubated with the concentration of CsrA shown at the bottom of each lane. Gel shift assays were performed in the absence (A) or presence (B) of various unlabeled competitor RNAs. The concentration of each competitor RNA is shown at the bottom of each lane in panel B. The positions of bound (B) and free (F) hfq RNA are shown at the left of each gel. (A) Determination of the equilibrium binding constant of the CsrA-hfq RNA interaction. The simple binding curve for these data is shown at the right. (B) Competition assay for the CsrA-hfq RNA interaction to establish binding specificity. Lanes corresponding to competition with specific (hfq and SELEX) and nonspecific (trpL) RNAs are indicated.