Similar cleavage efficiencies of an oligoribonucleotide substrate and an mdr1 mRNA segment by a hammerhead ribozyme

Hammerhead ribozymes (Rz) can specifically recognize and cleave target RNAs in trans. This makes them attractive in antisense RNA approaches for specific gene inactivation in vivo. A severe limitation is the poor cleavage efficiency of large RNA substrates, in contrast to the high activities observed with small oligoribonucleotides (oligos) as model substrates. It was suggested that the low efficiency is caused by poor accessibility of the target sequence in the structure of the long RNA substrates. This means it should be possible to overcome this limitation by judicious choice of the target sequence, although experimental proof was lacking. We observed similar cleavage efficiencies of small and large RNA substrates with a hammerhead Rz directed against multidrug resistance-encoding mdr1 mRNA. Accordingly, large RNAs can also be good substrates, if an optimal target sequence is selected.