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. 2009 Feb 10;37(6):1973–1983. doi: 10.1093/nar/gkp027

Figure 6.

Figure 6.

PerpAB DNA is naturally bent, and binding of EbfC alters DNA conformation. (A) A 250 bp segment of the erpAB locus, spanning the two high-affinity EbfC-binding sequences and the transcriptional promoter, is illustrated in the center of the panel. Above the DNA sequence is the G + C content and predicted naturally occurring bending pattern of this DNA. Note that an extended bend of 8°–10° per 10.5 bp helical turn is predicted to occur over a 50 bp region that overlaps the −35 and −10 promoter sequences (40°−50° total curvature). Sequences of five overlapping 150 bp DNA probes are indicated underneath. (B) DNA probes 1–5 after polyacrylamide gel electrophoresis, stained with ethidium bromide. The number of each DNA is indicated above the lanes. DNA size markers (bp) were separated in the first lane. (C) DNA probes 1–5 in randomized order, subjected to polyacrylamide gel electrophoresis and ethidium bromide staining. The number of each DNA probe is indicated above the lanes. DNA size markers (bp) were separated in the last lane. (D) EMSA of probes 1–5 with EbfC. The number of each DNA probe is indicated above the lanes.