A variant of the Tetrahymena ribozyme that efficiently cleaves single stranded DNA under simulated physiological conditions [Tsang, J. & Joyce, G.F. (1994) Biochemistry 33, 5966-5973] was evaluated as a potential therapeutic agent on the basis of its ability to cleave synthetic oligonucleotide substrates corresponding to conserved target sites within HIV-1 cDNA. In order to increase the sequence selectivity of the ribozyme, its substrate recognition domain was extended from 6 to 12 nucleotides, allowing base pairing with substrate nucleotides that lie both upstream and downstream of the cleavage site. The sequence of the extended recognition domain could be changed to allow cleavage of a variety of different DNA targets. The ribozyme exhibited a high degree of sequence specificity, discriminating by a factor of 10² to more than 10⁴ against substrates that form a single-base mismatch with the ribozyme's recognition domain. Mismatches that ocurred close to the cleavage site led to a greater decrease in activity compared to those that occurred farther away.