FIG. 3.

Quantitative competitive EMSAs demonstrating that the affinity of E. coli RpoN for dsDNA is sequence dependent. Proportions of dsDNA shifted by the binding of E. coli RpoN to the labeled rpoS promoter are shown for the absence and presence of a 125-fold excess of unlabeled competitor dsDNA (n = 3). Competitor dsDNAs consisted of the unlabeled rpoS promoter, a σ⁷⁰-specific flgB promoter, and rpoS promoters with the base pair substitutions and deletions noted. EMSAs were performed with a 63-bp digoxigenin (DIG)-labeled target of the rpoS promoter mixed with a lysate from a strain of E. coli that overexpresses E. coli RpoN.