Structural probing confirms predicted secondary structure. A: RNase V1 (V1), RNase A (A), no reaction (NR), hydroxyl cleavage (-OH), denaturing RNAse T1 (T1), and two independent replicates of in-line probing reactions (IL) where the cleavage products have been separated by denaturing 10% PAGE. Cleaved cytosine and uridine residues in the RNase A reaction and cleaved guanosines in the denaturing T1 reaction were used to map cleavage to the RNA structure, and regions of strong in-line cleavage are labeled. B: Mapping of prominent cleavage sites to the structure of Rra-RNA6; bases in black are resolved on the gel. TSS indicates predicted transcription start site. Cleavage sites largely confirm structure anticipated from comparative genomics.