An Analysis of Large rRNA Sequences Folded by a Thermodynamic Method

Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder 80309-0347, USA.
Folding and Design 02/1996; 1(6):419-30. DOI: 10.1016/S1359-0278(96)00058-2
Source: PubMed


The secondary structure of RNA can be predicted by the thermodynamics-based method of Zuker and Turner. The accuracy of the method's secondary structure predictions for rRNA can be assessed by using as reference the currently available rRNA secondary structure models that have been derived from comparative analysis of rRNA sequence alignments.
We folded 72 23S rRNA sequences with the Zuker-Turner method and scored the resulting secondary structure predictions against the comparative model. Empirically, trends in the score were observed as a function of the phylogenetic memberships of the sequences and as a function of the base pairs secondary structural contexts. Further, three parameters were found that (anti-)correlate with the score.
Three semiquantitative predictors of score were found: % of noncanonical base pairs, % of hairpin loops that were stable tetraloops, and sequence %G + C. The folding of rRNA is a tractable problem and thermodynamics-based folding algorithms, in particular, are useful in the study of this folding problem even for large RNA molecules (e.g. 16S and 23S rRNA).

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    • "Intron and endonuclease nomenclature follows that of Lambowitz & Belfort (1993), and the intergenic open reading frames (ORFs) are numbered according to Foury et al. (1998). The sizes of ribosomal RNAs (rRNA) were inferred from the model elaborated for their equivalents from S. cerevisiae mitochondria (Konings & Gutell, 1995; Fields & Gutell, 1996). "
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    • "Given an RNA sequence and the thermodynamic model, efficient dynamic programming algorithms exist for finding a minimum free energy secondary structure [14-17,13,4]. Energy minimization is not as accurate as comparative analysis [18,13], but unlike comparative analysis, it can be applied to single RNA sequences. "
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    BMC Bioinformatics 02/2006; 7(1):400. DOI:10.1186/1471-2105-7-400 · 2.58 Impact Factor
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    • "We considered any base-pair with a contact distance of 100 nt or less to be "short-range," a contact distance of 101–501 nt to be "mid-range," and a contact distance of 501 or greater to be "long-range." The majority of base-pairs in the 16S and 23S rRNA secondary structure models predicted with comparative analysis were short-range (Table 5), and previous studies have established that short-range base-pairs are predicted more accurately than long-range base-pairs[29,30]. In this section, we: 1) compared the accuracies of the short-range interactions predicted with Mfold 3.1 and Mfold 2.3, 2) compared the number of short-, mid-, and long-range base-pairs in the comparative models with those predicted by Mfold 3.1, and 3) determined the relationship between the base-pair prediction accuracy and the contact distance for 16S rRNA. "
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