A variant form of a group I ribozyme, optimized by in vitro evolution
for its ability to catalyze magnesium-dependent phosphoester transfer
reactions involving DNA substrates, also catalyzes the cleavage of an
unactivated alkyl amide when that linkage is presented in the context
of an oligodeoxynucleotide analog. Substrates containing an amide bond
that joins either two DNA oligos, or a DNA oligo and a short peptide,
are cleaved in a magnesium-dependent fashion to generate the expected
products. The first-order rate constant, k(cat), is 0.1 x 10(-5) min(
-1) to 1 x 10(-5) min(-1) for the DNA-flanked substrates, which corres
ponds to a rate acceleration of more than 10(3) as compared with the u
ncatalyzed reaction.