‘Hairpin’ catalytic RNA model: evidence for helices and sequence requirement for substrate RNA

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Abstract
We have identified the catalytic domain within the sequence of the negative strand of the satellite RNA of tobacco ringspot virus. Minimum energy RNA folding calculations predict a two dimensional model with four major helical regions which are supported by mutagenesis experiments. This model for the catalytic complex consists of a 50 base catalytic RNA and a 14 base substrate RNA folded together in a type of hairpin two dimensional structure. Part of the recognition region between the catalyst and substrate is two helices of 6 bases and 4 bases respectively. Catalytic activity remains when the bases in these helices are changed but base pairing is maintained. Thus an appropriately engineered ''hairpin'' catalyst is capable of cleaving heterologous RNA.