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. 2023 Jan 10;5(1):lqac102.
doi: 10.1093/nargab/lqac102. eCollection 2023 Mar.

Identification and characterization of RNA pentaloop sequence families

MdSharear Saon  1 , Charles C Kirkpatrick  1 , Brent M Znosko  1
Affiliations

Identification and characterization of RNA pentaloop sequence families

MdSharear Saon et al. NAR Genom Bioinform. .

Abstract

One of the current methods for predicting RNA tertiary structure is fragment-based homology, which predicts tertiary structure from secondary structure. For a successful prediction, this method requires a library of the tertiary structures of small motifs clipped from previously solved RNA 3D structures. Because of the limited number of available tertiary structures, it is not practical to find structures for all sequences of all motifs. Identifying sequence families for motifs can fill the gaps because all sequences within a family are expected to have similar structural features. Currently, a collection of well-characterized sequence families has been identified for tetraloops. Because of their prevalence and biological functions, pentaloop structures should also be well-characterized. In this study, 10 pentaloop sequence families are identified. For each family, the common and distinguishing structural features are highlighted. These sequence families can be used to predict the tertiary structure of pentaloop sequences for which a solved structure is not available.

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Figures

Figure 1.
Figure 1.
Secondary structure of a pentaloop with nucleotides numbered.
Figure 2.
Figure 2.
Distance tree (generated by Archaeopteryx 0.9901 beta (65)) created from an all-against-all sequence representative structure analysis. Each branch on the right is indicating a sequence representative structure (cluster representative structures are asterisked) where the structures within a cluster are magnified and color-coded according to the legend.
Figure 3.
Figure 3.
Cluster representative structure for each of the 10 clusters (A–J). 3D structures were created by DSSR-Jmol (66). If determined to be a feature of the cluster, stacking interactions (black arrows), glycosidic conformation, sugar pucker and base pairing (dashed lines) are shown for each cluster. Additional hydrogen bonds are not shown for clarity. Degenerate sequence (underlined section of the sequence represents the hairpin residues) and name of the representative structure for each cluster are shown below each cluster representative structure.
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