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. 1998 Apr 1;26(7):1689–1699. doi: 10.1093/nar/26.7.1689

Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4.

J M Hancock 1, A P Vogler 1
PMCID: PMC147449  PMID: 9512540

Abstract

Variable regions within ribosomal RNAs frequently vary in length as a result of incorporating products of slippage. This makes constructing secondary structure models problematic because base homology is difficult or impossible to establish between species. Here, we model such a region by comparing the results of the MFOLD suboptimal folding algorithm for different species to identify conserved structures. Based on the reconstruction of base change on a phylogenetic tree of the species and comparison against null models of character change, we devise a statistical analysis to assess support of these structures from compensatory and semi-compensatory (i.e. G.C to G.U or A.U to G.U) mutations. As a model system we have used variable region V4 from cicindelid (tiger beetle) small subunit ribosomal RNAs (SSU rRNAs). This consists of a mixture of conserved and highly variable subregions and has been subject to extensive comparative analysis in the past. The model that results is similar to a previously described model of this variable region derived from a different set of species and contains a novel structure in the central, highly variable part. The method we describe may be useful in modelling other RNA regions that are subject to slippage.

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Selected References

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