Effects of tetracycline and spectinomycin on the tertiary structure of ribosomal RNA in the Escherichia coli 30 S ribosomal subunit

Structural analysis of the 16 S rRNA in the 30 S subunit and 70 S ribosome in the presence of ribosome-specific antibiotics was performed to determine whether they produced rRNA structural changes that might provide further i nsight to their action. An UV cross-linking procedure that determines the p attern and frequency of intramolecular 16 S RNA cross-links was used to det ect differences reflecting structural changes. Tetracycline and spectinomyc in have specific effects detected by this assay. The presence of tetracycli ne inhibits the cross-link C967 x C1400 completely, increases the frequency of cross-link C1402 x 1501 twofold, and decreases the cross-link G894 x U2 44 by one-half without affecting other cross-links. Spectinomycin reduces t he frequency of the cross-link C934 x U1345 by 60% without affecting cross- linking at other sites. The structural changes occur at concentrations at w hich the antibiotics exert their inhibitory effects. For spectinomycin, the apparent binding site and the affected crosslinking site are distant in th e secondary structure but are close in tertiary structure in several recent models, indicating a localized effect. For tetracycline, the apparent bind ing sites are significantly separated in both the secondary and the three-d imensional structures, suggesting a more regional effect.