Fig. 5

Electrophoretic mobility shift assays with AcrC protein and the intergenic region of acbE and acbD. a EMSAs with the 342 bp fragment of the intergenic region of acbE/acbD, the 217 bp intergenic region malE/acrC as well as the 203 bp region dapE/ACSP50_6389. 0.05 pmol Cy3 labeled PCR fragments were incubated with 80 pmol purified AcrC protein, 0.05 μg herring sperm DNA for blocking of unspecific binding, and 100 mg BSA. 12.5 pmol unlabeled double-stranded oligonucleotides (ds oligo) covering the acrC site plus 5 bp up- and downstream were added as indicated. Separation was carried out with 10% native polyacrylamide (TBE) gels and visualized by fluorescence imaging. b Intergenic region of acbE and acbD used for the EMSAs with the promoter motives described in [14] and the acrC binding sites. c Intergenic region of malE and acrC used for the EMSA with promoter motives