Figure 6
Summary of footprinting patterns of the double-stranded right and left ends of IS 2. (I) Double-stranded sequences of IRR and IRL are shown within the large brackets, numbered from the outside ends to inside ends as described in Figure 4. Protected nucleotides, strong (black) and weak (grey), (as described in Figure 4) are indicated by filled horizontal bars. Enhanced nucleotides are indicated by asterisks. Conserved and non-conserved elements are as described in Figure 1. (II) Three-dimensional representations of the protection patterns shown in part I. For IRR, the red helix represents the lower strand (IRRB- 5'TGGATT... TTAA3') and the gray helix, the upper strand (IRRA- 5'TTAA... AATCCA3'). For IRL the red helix represents the upper strand (IRLA - 5'TAG... TTAA3') and the grey helix the lower strand (IRLB- 5'TTAA... CTA3'). Strong and weak protections are shown as filled blue and yellow circles, respectively. Vertical purple shaded bars highlight the difference between the selective binding of the cleavage domain of IRL, illustrated by intermittent binding of three of the eleven nucleotides and the extensive protection of the cleavage domain of IRR with a single gap at its inner end (see text). Annotation is as described in part I. In both parts, numbering is as described in Figure 4. The inside terminus of IRL shows protection of the sequence numbered 39 to 48 that includes the proposed binding sequence for the repressor function of the OrfA protein [20]. The 5'TGAT3' sequence of base pairs 48 to 51 represents the first four bases of the weak indigenous extended-10 promoter (PIRL, see Figure 1) located adjacent to the inner end of IRL. IRR/IRL: right and left inverted repeats.