Abstract
BackgroundHighly hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex RNA molecules, such as transfer-RNAs, ribozymes and ribosomal RNAs.ResultsWe describe the graph theoretical identification and searching of highly hydrogen bonded base triples, where each base is involved in at least two hydrogen bonds with the other bases. Our approach correlates theoretically predicted base triples with literature-based compilations and other actual occurrences in crystal structures. The use of ‘fuzzy’ search tolerances has enabled us to discover a number of triple interaction types that have not been previously recorded nor predicted theoretically.ConclusionsComparative analyses of different ribosomal RNA structures reveal several conserved base triple motifs in 50S rRNA structures, indicating an important role in structural stabilization and ultimately RNA function.
Highlights
Hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex RNA molecules, such as transfer-RNAs, ribozymes and ribosomal RNAs
We present a survey, that cross-references the patterns in the NAIL database [14], the Protein Data Bank (PDB) [15] and the records in NCIR [13], and is able to deliver a catalogue of base triples of a specific type in existing crystal structures
Fourteen or approximately 24% of these patterns were discovered for multiply hydrogen bonded base triples that were either not currently represented in NCIR (Figure 2A), not represented in NAIL (Figure 2B) or not found in either resource (Figure 2C)
Summary
Hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex RNA molecules, such as transfer-RNAs, ribozymes and ribosomal RNAs. It is clear that three-dimensional (3D) structure is as fundamental to the functionality of complex RNA molecules as it is for proteins. It is clear that multiply hydrogen bonded triples, which consist of at least two hydrogen bonding interactions per base, will be especially stable and the structural conservation of such triples is likely to be significant. They are expected to be influential constituents of RNA structure and are of primary interest in this work. A library of 840 theoretically computed base triples has been compiled and is accessible as part of the NAIL
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