Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus.

The two ribozymes found in hepatitis delta virus RNA form related but non-identical secondary structures and display similar cleavage properties in vitro. Three of the non-duplex elements hypothesized to contribute nucleotides to the catalytic core vary slightly in length between the two ribozymes and the differences are conserved in clinical isolates. Possible functional relationships of the core sequence elements were tested by systematically exchanging sequences between the two ribozymes. It was found that switching two of the elements (L3 and J4/2) from one ribozyme to the other reduced cleavage activity in both. On the other hand, exchanging the third region (J1/4) resulted in enhanced activity for one ribozyme and a smaller increase in activity for the other. Combining exchanges did not reveal any compensatory interactions involving these particular elements nor did a pattern emerge that would suggest an optimal combination of core sequences for a generalized HDV ribozyme. Non-compensatory behavior reinforces the idea that the non-duplex sequences may form sequence-specific contacts with duplex portions of the ribozyme, but, in addition, these data suggest that there may be selective pressures on the ribozyme sequences in the virus that are not reflected in the in vitro self-cleavage assays.