Figure 8

Quantitative comparisons of the protection patterns of the bottom strands of MJcj and MJpc substrates. (A) The top panel shows densitometer tracings of the two footprinted lanes (MJcj, red, and MJpc, green) of the sequencing gel shown in Figure 7b. The similarly color-coded boxed lanes are shown immediately below the panel. Tracings show differences in the intensities of bands from the two substrates. Annotation within the panel is based on the sequence of the bottom strand with numbering as described in Figure 7. Individual peaks in the top panel are identified by red dots for the covalently joined substrate and green dots for the nicked substrate; corresponding red and green vertical lines identify the nature and number of every fifth base. Differences in the protection patterns of the two substrates are indicated by brackets (within which the protected residues are identified) immediately beneath the troughs. Labels (a), (c) and (d) are as described in Figure 7. Brackets labeled with a black asterisk or (b) indicate sequences that are more strongly protected in MJpc than in MJcj. Enhanced residues in the two substrates are shown by sharply rising peaks and are identified by the eight red asterisks for the MJcj substrate and the four green asterisks for the MJpc substrate. (B) Consensus of the protection patterns of the bottom strand of the MJcj and MJpc substrates are derived from the data in Figures 7A, B and Figure 8A. Numbering and annotations are as described in Figure 7. Asterisks identify enhanced residues. MJcj: covalently joined minicircle junction substrate; MJpc: precleaved minicircle junction substrate.