23S RIBOSOMAL-RNA SIMILARITY FROM SELECTION FOR PEPTIDYL TRANSFERASE MIMICRY

RNAs from a randomized pool were selected by affinity elution for bind ing to the molecule CCdApPuro, a high-affinity ligand of ribosomal pep tidyl transferase designed as a transition-state analogue of peptide f ormation. The selected RNAs show affinity for CCdApPuro comparable to that of the peptidyl transferase center itself (K-d approximate to 10 nM). Chemical modification/protection experiments implicate bases comp letely conserved among the selected RNAs in CCdApPuro interaction, whi ch appears to involve both CCdA and puromycin moieties, that is, both A- and P-site homologues, The apparent selected binding site shows up to 17 nucleotides with similarity to conserved nucleotides of the pept idyl transferase loop domain of 23S rRNA and is conserved when reselec ted under mutagenesis. Thus, these nucleotides of 23S rRNA likely prov ide elements of the peptidyl transferase active center that bind the r eactants near the site of peptide bond formation. Binding of CCdApPuro by a peptidyl transferase-like motif in the absence of protein streng thens the hypothesis that peptidyl transfer originated in an RNA world .