A FUNCTIONAL RIBOSOMAL-RNA TERTIARY STRUCTURE INVOLVES A BASE TRIPLE INTERACTION

Comparative sequence analysis reveals a coordinated set of nucleotide exchanges between the base pair 1092/1099 and the unpaired position 10 72 [(1092/1099)1072] in the L11 binding domain of 23S ribosomal RNA. T his set of exchanges has occurred at least 4 times during evolution, s uggesting that these positions form a base triple. The analysis furthe r suggests an important role for positions (1065/1073), adjacent to 10 72. The covariation at positions (1092/1099)1072 is studied here by an alysis of RNA variants using UV melting and binding of ribosomal prote in L11 and thiostrepton to assay for tertiary folding of this domain. The tertiary structure of the RNA is eliminated by alteration of the u npaired nucleotide (C1072 to U mutation), and binding of L11 and thios trepton are reduced 10-fold compared to the wild type. In contrast, su bstitution of the base pair (CG1092/1099 to UA mutation) allows format ion of the tertiary structure but dramatically alters the pH dependenc e of tertiary folding. The fully compensated set of mutations, (CG)C t o (UA)U, restores the tertiary structure of the RNA to a state almost identical to the wild type. The nature of this base triple and its imp lications for the folding of the RNA and ligand interactions are discu ssed.