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
.