Protection of specific sites in 16 S RNA from chemical modification by association of 30 S and 50 S ribosomes

The accessibility of specific sites in 16 S RNA in 30 S and 70 S ribosomes was measured by reaction of 30 S and 70 S ribosomes, containing ³²P-labeled 16 S RNA, with the guanine-specific reagent kethoxal. The oligonucleotides surrounding the sites of kethoxal substitution were isolated and quantitated by diagonal electrophoresis. A total of 22 reactive sites could be positively located in the 16 S RNA chain, providing new information about the primary and secondary structure of 16 S RNA. The reactivity of sites in the 5′-terminal 600 nucleotides was the same in 30 S and 70 S ribosomes. Two regions, near the middle of the chain and at the 3′ terminus, respectively, were strongly protected in 70 S ribosomes, suggesting that these regions of the 16 S RNA may be located at the 30 S-50 S subunit interface. One site, located about 550 nucleotides from the 3′ terminus, becomes more reactive in 70 S ribosomes, indicating an allosteric transition in this region of the 30 S subunit upon formation of the 70 S ribosome.