Fig. 2

HDV ribozyme consensus models and the characteristics of a newly found HDV ribozyme representative from fungi. a General consensus for HDV self-cleaving ribozymes as reported previously [49]. N designates any nucleotide, H designates adenosine, cytidine or uridine, and parentheses identify optional nucleotides. Solid lines indicate zero-length connectors with the exception of a variable-length connector labeled var. The arrowhead identifies the site of cleavage (Clv). b Consensus sequence and secondary structure model for HDV ribozyme variants identified in fungi. Yellow boxes encompass nucleotides and structures that are different from the general consensus depicted in a, including a “loop E” motif. Other annotations are as described for Fig. 1. c Sequence and predicted secondary structure of a bimolecular ribozyme construct derived from an HDV ribozyme from the fungus P. chrysogenum. An 18-nucleotide “substrate” strand was separated from a larger “ribozyme” strand by disconnecting the two sub-domains at the junction between P1 and P2. Nucleotides depicted in red match the highly-conserved positions in the fungal HDV ribozyme consensus in Fig. 2b. d PAGE separation of 5ˊ ³²P-labeled substrate RNA after partial digestion with RNase T1 (T1), partial digestion with alkali (^–OH), or incubation with 100 nM of the ribozyme strand (R) of the P. chrysogenum bimolecular construct under permissive reaction conditions (See Methods). NR designates no reaction. Bands corresponding to the substrate (S), 5ˊ cleavage product (5ˊ Clv) and various products generated by RNase T1 cleavage after G residues are also identified