Figure 11

Curvature analyses for the minicircle junction and IS 2 target sites. (A) (i ) Predicted curvature profiles obtained by the bend.it server for a 200-bp region encompassing the MCJ. Colored regions are: IRR (yellow and red), IRL (blue and yellow), protein binding domains (yellow), cleavage domains (red and blue). Numbered base pairs correspond to the four maxima found in these regions, which also match or are located in close vicinity to enhanced residues. The maximum located at position L60 corresponds to the region harboring the indigenous P_IRL promoter. (ii ) Three-dimensional representation of the region encompassing the MCJ where the five curvature maxima appear as highlighted bases. The region shaded green represents the intrinsic curvature of the P_IRL promoter. (B) Predicted curvature profiles of four representative regions reported in the literature to harbor IS2 target sites. Each window represents a 200-bp fragment encompassing the target site(s) (filled circles). Regions R1 to R4 were arbitrarily chosen in order to facilitate the comparison between graphs. Although some disparity exists when comparing the relative intensity of the peaks (which results from comparing different DNA sequences), all four regions appear to be conserved. Coding references or nucleotide sequences given in brackets are in accordance with the nomenclature given in the original publication. Additional predicted curvature profiles are shown in Additional file 3. (C) Three-dimensional representations of the four regions encompassing IS2 target sites (highlighted in green). S-like (and L-like) shaped regions were preferentially obtained and intrinsic curvature was observed to occur next to the insertion site. Additional data on the three-dimensional representation of IS2 target sites can be found as Additional file 4. bp: base pair; IRR/IRL: right and left inverted repeats; MCJ: minicircle junction.