FIG. 9.

Heelprinting of hairpin phase variants. mRNAs from AvaII-digested pPS1b, pPS7b, pPS1c, and pPS7c were subjected to heelprint analysis as detailed in Materials and Methods. Heelprints of each RNA are shown alongside a sequencing ladder (TCGA) prepared from two of the plasmids. Each reaction mixture contained 20 ng of the relevant single-stranded DNA template, 0.4 ng of primer, and 3 μl of RPFs. The position of the start of the +2 and zero-phase pseudoknots and hairpins and the site of the corresponding ribosomal pauses are indicated by arrows. The primary sequences of the mRNA upstream of the various structures are shown at the bottom, and the position of the pseudoknot- or hairpin-dependent heelprints are indicated with arrowheads (the first four pseudoknot and hairpin residues are shown in bold type in each case).