FIG. 2.

RNA structures predicted for the 5′ ends of wild-type and mutated lcrV mRNAs. RNA structures were predicted using the program Mfold at http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/rna-form1.cgi. The first and the last codons of the 42-bp region mutated in the Scramble mutant (Fig. 1A) are indicated with an asterisk and an arrowhead, respectively. Shown here are upstream and downstream flanking regions of 50 bp, but regions of 20, 40, 60, 80, and 100 bp were also used in the analysis (for details, see Materials and Methods). The two stem-loops predicted to span this region in wild-type LcrV (left) were conserved in all but one of the potential structures obtained (data not shown) but were clearly altered in the Scramble mutant (right).