Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling

Comparative sequence analysis complements experimental methods for the dete rmination of RNA three-dimensional structure, This approach is based on the concept that different sequences within the same gene family form similar higher-order structures. The large number of rRNA sequences with sufficient variation, along with improved covariation algorithms, are providing us wi th the opportunity to identify new base triples in 16S rRNA. The three-dime nsional conformations for one of our strongest candidates involving U121 (C 124:G237) and/or U121 (U125:A236) (Escherichia coli sequence and numbering) are analyzed here with different molecular modeling tools. Molecular model ing shows that U121 interacts with C124 in the U121 (C124:G237) base triple . This arrangement maintains isomorphic structures for the three most frequ ent sequence motifs (approximately 93% of known bacterial and archaeal sequ ences), is consistent with chemical reactivity of U121 in E. coli ribosomes , and is geometrically favorable. Further, the restricted set of observed c anonical (GU, AU, CC) base-pair types at positions 124:237 and 125:236 is c onsistent with the fact that the canonical base-pair sets (for both base pa irs) that are not observed in nature prevent the formation of the 121 (124: 237) base triple, The analysis described here serves as a general scheme fo r the prediction of specific secondary and tertiary structure base pairing where there is a network of correlated base changes.