The interaction between the translational stop signal and the polypeptide chain release factor protein (RF) within complexes of Escherichia coli ribosomes has been investigated by site-directed photochemical cross-linking experiments. Twelve mRNA analogues containing 4-thiouridine residues as part of stop signals were synthesized. Highly efficient cross-linking to RF-2 from 4-thiouridine (sU) residues of sUGAN-containing mRNAs was observed, and cross-linking from those of sUAAN was observed at a lower efficiency. This indicates that RF-2 is in close physical contact with the stop signal on the ribosome. The yield of the RF-2-mRNA cross-link depended on the identity of the fourth base for the sUGAN set of signals, suggesting that the fourth base of the stop signal affects the interaction between RF-2 and the stop codon. A region previously implicated as part of the decoding site of the small ribosomal subunit, 1385-1420 of the 16 S rRNA, was also cross-linked with these mRNAs. No new cross-links were obtained in the presence of the release factor. The data are consistent with models in which the RF has an anticodon-like domain that contacts the stop signal directly at or near the ribosomal site in which sense codons are decoded.