Studies on the hammerhead RNA self-cleaving domain

Nine different hammerhead RNA self-cleaving domains consistent with the consensus secondary structure proposed by Keese and Symons (1987) were prepared and tested for cleavage. Each hammerhead was constructed from two oligoribonucleotides in two different configurations. Although cleavage was observed in all nine cases, the rates of cleavage varied by more than a thousand fold. The presence of RNA secondary structure incompatible with hammerhead formation in the individual oligos may be responsible for the large rate differences. We have also examined the degree of participation of a proposed dimer hammerhead intermediate in one case and conclude that, while such a four-stranded structure can form, it is not the preferred reaction intermediate.