RNase P recognition of IRES substrates containing an altered RNA structure in the central domain. (A) A uniformly labeled transcript carrying a single nucleotide substitution of GUAA to GUAG in the GNRA tetraloop (Fernandez-Miragall and Martinez-Salas 2003) was incubated with RZ 6803, parallel to wt RNA. A long arrow depicts three new digestion products of 185, 140, and 120 nt. The transcript 3 carrying a substitution of AAAAG to CGCCC in the RAAA motif was processed in the same way. A substitution mutant in the C-rich motif, C235–238 of this domain, was used as a control of a nonreorganized RNA structure. (B) Ribozyme 6803 digestion of 3′-pCp-labeled transcripts, processed as in A.
