Figure 2. In vitro cleavage assay of minimal versions of hammerhead sequences.

(A) Schematic representation of the consensus sequence of the catalytic core of the hammerhead sequences. The core nucleotides, identified by the boxes, are flanked by the helical stems I-III. The numbering is according to Hertel et al. [33]. (B) Left side: the cleavage assay for the parental and the mutated hammerhead found in reads of 4 occurrences was monitored during 60 min transcription reactions at 22^oC, and was analyzed on a 15% denaturing gel. The non-cleaved full-length transcripts are indicated by the letters NC, while the cleaved products are identified by the letter P. Right side: schematic representation of the tested hammerhead motif found in a read of 4 occurrences in the P7 library. The mutations relative to the parental sequence are identified by arrows where the red arrows denoted insertions.