Identification of Defined Sequences in Domain V of E.coli 23S rRNA in the 50S Subunit Accessible for Hybridization with Complementary Oligodeoxyribonucleotides

The accessibility of specific sequences in domain V of E. coli 23s rRNA in the 50S subunit to complementary oligodeoxyribonucleotides (cDNA) has been investigated. The apparent percentage of subunits engaged in complex formation was determined by incubation of radiolabeled cDNA probe with 50S subunits, followed by nitrocellulose membrane filtration of the reaction mixtures and measurement of the bound radiolabeled cDNA probes by liquid scintillation counting of the filters. The site(s) of hybridization were determined by digestion of the RNA in the RNA/DNA heteroduplex by RNase H. The results of this study indicated that single-stranded sequences, 2058-2062, 2448-2454, 2467-2483, and 2497-2505 were available for hybridization to cDNA probes. Bases 2489-2496, which have been postulated to be base paired with 2455-2461 were also accessible for hybridization