FIG. 2.

DNase I footprinting assays of oxidized OxyR binding to the top and bottom strands of the dsbG promoter in the absence of RNA polymerase (A) and to the top strand in the presence of RNA polymerase (B). The regions protected by OxyR are indicated by the brackets in panel A. All samples were run in parallel with Maxam-Gilbert G/A sequencing ladders. (A) For OxyR binding to the top strand relative to the dsbG promoter, the 230-bp EcoRI-BamHI fragment of pGSO123 was labeled with ³²P at the EcoRI site. For OxyR binding to the bottom strand relative to the dsbG promoter, the ³²P-labeled primer 710 and unlabeled primer 709 were used to PCR amplify a 430-bp fragment containing both the ahpC and dsbG promoter sequences. (B) For OxyR and RNA polymerase binding to the top strand relative to the dsbG promoter, a 250-bp fragment was PCR amplified from pGSO124 using primers 710 and 726. The amplified fragment was digested with EcoRI, labeled with ³²P, and then digested with SmaI.