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301 The accuracy of ribosomal RNA comparative structure models Robin R Gutell*, Jung C Lee? and Jamie J Cannone? The determination of the 16S and 23S rRNA secondary structure 2. The mappings and associations between each of these models was initiated shortly after the first complete 16S and structural elements, and the permissible arrangements 23S rRNA sequences were determined in the late 1970s. The and composition of the nucleotides that form that element structures that are common to all 16S rRNAs and all 23S rRNAs (a ‘many-to-one problem’). were determined using comparative methods from the analysis of thousands of rRNA sequences. Twenty-plus years later, the 3. The organization and arrangement of these structural 16S and 23S rRNA comparative structure models have been elements with one another, both locally and globally across evaluated against the recently determined high-resolution crystal the entire RNA structure. structures of the 30S and 50S ribosomal subunits. Nearly all of the predicted covariation-based base pairs, including the regular 4. The thermodynamic energetics associated with the proper base pairs and helices, and the irregular base pairs and tertiary folding of the RNA molecule. interactions, were present in the 30S and 50S crystal structures. 5. Other factors influencing RNA folding, including protein Addresses binding (e.g. chaperones and ribosomal proteins) and the *Institute for Cellular and Molecular Biology, and Section of Integrative rates of folding during transcription. Biology, University of Texas, 2500 Speedway, Austin, Texas 78712-1095, USA; e-mail: robin.gutell@ 6. The relative contributions of these rules to the process ?Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Te