Probing ribosome structure using short oligodeoxyribonucleotides: the question of resolution.

The structure of ribosomal RNA in situ can be probed using short, complementary DNA oligomers. As these oligomers bind to exposed, single-stranded regions of rRNA, the stability of the hybridized complex can be assayed. Differences in binding stability between cDNA probes of similar length and composition may be indicative of the presence of competing structure, such as base-paired rRNA regions, tRNA interactions or protein interactions. In this study the degree to which such interactions can be distinguished is studied. It is found that by using suitable controls, interactions between rRNA and tRNA or rRNA can be discriminated to a resolution of one or two bases. This resolution promises to be important in delineating the higher-order structure of the rRNA.