Hammerhead ribozyme mechanism: a ribonucleotide 5' to the substrate cleavage site is not essential

Three hammerhead ribozymes with triplet specificities for cleavage 3' of CUC, GUC, and GUA have been evaluated for their sensitivity to the substitution of thymidine or 2'-deoxyuridine at central nucleotide position 16.1 in the substrate triplet. All three ribozymes cleaved their respective substrates, containing uridine or the modifications, with comparable rates. This indicates that the 2'-hydroxy group at position 16.1 is not essential for activity even though X-ray structure analysis shows it participates in H-bonding interactions. These H-bonds were considered to be of functional significance because an earlier report had provided data that thymidine at position 16.1 is deleterious for catalytic activity [Yang, J.-H., Perreault, J.-P., Labuda, D., Usman, N., and Cedergren, R. (1990) Biochemistry 29, 11156-11160].