FIG. 3.

Supercoiling sensitivity transcription assay. For each T3S promoter cloned on a transcription plasmid, a series of plasmid topoisomers was generated over a range of superhelical densities (σ) from 0 (completely relaxed DNA) to >−0.08 (highly negatively supercoiled). Each topoisomer was transcribed by σ⁶⁶ RNA polymerase in an in vitro transcription reaction to measure the promoter activity at different superhelical densities. The greatest difference in promoter activity over this range of superhelical densities was calculated as fold change and is reported as the average of three independent experiments. For each promoter, the temporal expression class (early, mid, or late) is listed.