Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage

The secondary structures proposed for the cis-acting hepatitis delta virus (HDV) ribozymes contain four duplex regions, three sequences joining the duplexes and two hairpin loops. The core and active site of the ribozyme could be formed by portions of the joining sequences, J1/4 and J4/2, together with one of the hairpin loops, L3. To establish the core region and define essential bases within this putative active site 28 single base changes at 15 positions were made and tested for effects on ribozyme cleavage. At 14 of the 15 positions all of the changes resulted in detectable decreased rates of cleavage. At seven of the positions one or more of the changes resulted in a 500-fold or greater decrease in the observed rate constant for cleavage. Mutations that resulted in 10(3)-fold effects were found in all three regions hypothesized to form the core. At the cleavage site substitutions of the cytosine 5' of the site of cleavage did not provide strong support for a sequence-specific interaction involving this nucleotide. In contrast, an A-C combination was the most effective substitution for a potential G-U pair 3' of the cleavage site, suggesting a requirement for a wobble pair at that position.