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. Author manuscript; available in PMC: 2015 Apr 28.
Published in final edited form as: Nat Commun. 2014 Oct 28;5:5270. doi: 10.1038/ncomms6270

Figure 5. UV laser DDFA of the pagC promoter region.

Figure 5

Plasmid DNA containing the pagC region was incubated in the presence of 600 nM H-NS, 100 nM SlyA, and 500 nM PhoP-P as indicated and exposed to a single pulse of 266 nm radiation. Crosslinking was quantified by fluorescent primer extension. The relative distance to the TSS is indicated in base pairs on the horizontal axis. Results are presented as DDFA plots, representing the difference in fluorescent peak height (RFU) between the protein-free control and the experimental sample (a). DDFA plots are also shown for the H-NS + SlyA, H-NS + PhoP-P, and H-NS + SlyA + PhoP-P reactions representing the difference between the H-NS control and the experimental sample (b). Peaks represent a protein-induced change in DNA structure, typically due to increased intramolecular contacts or DNA-protein crosslinks. Valleys also represent a change in DNA structure, due to decreased intramolecular contacts. Approximate sizes of peaks of note are indicated. Data represent the mean ± SD; n = 3. See Supplementary Fig. 6 for representative raw chromatograms.