Skip to main content Accessibility help
×
Home

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

  • PATRICIA BABIN (a1), MICHAEL DOLAN (a1), PAUL WOLLENZIEN (a1) and ROBIN R. GUTELL (a2)

Abstract

Comparative sequence analysis complements experimental methods for the determination 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 with the opportunity to identify new base triples in 16S rRNA. The three-dimensional conformations for one of our strongest candidates involving U121 (C124:G237) and/or U121 (U125:A236) (Escherichia coli sequence and numbering) are analyzed here with different molecular modeling tools. Molecular modeling shows that U121 interacts with C124 in the U121 (C124:G237) base triple. This arrangement maintains isomorphic structures for the three most frequent sequence motifs (approximately 93% of known bacterial and archaeal sequences), is consistent with chemical reactivity of U121 in E. coli ribosomes, and is geometrically favorable. Further, the restricted set of observed canonical (GU, AU, GC) base-pair types at positions 124:237 and 125:236 is consistent with the fact that the canonical base-pair sets (for both base pairs) 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 for the prediction of specific secondary and tertiary structure base pairing where there is a network of correlated base changes.

Copyright

Corresponding author

Reprint requests to: Paul Wollenzien, Department of Biochemistry, Box 7622, North Carolina State University, Raleigh, North Carolina 27695-7622, USA; e-mail: wollenz@bchserver.bch.ncsu.edu.

Keywords

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

  • PATRICIA BABIN (a1), MICHAEL DOLAN (a1), PAUL WOLLENZIEN (a1) and ROBIN R. GUTELL (a2)

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed