The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure

Geometric nomenclature and classification of RNA base pairs

“…To illustrate these conventions, we present in Figure 9 examples of two-dimensional representations of RNA motifs with tertiary interactions added+ The left panel shows the loop E of bacterial 5S rRNA from NDB file URL064 (Correll et al+, 1997)+ All bases of this symmetric "internal loop," in fact, are paired+ A104•G72 comprise a trans Hoogsteen/Sugar-edge pair+ This is designated using an open symbol (indicating the trans geometry) comprising a square, placed next to A104 (for the Hoogsteen edge), connected to a triangle, placed next to G72 (for the Sugar-edge)+ The same interaction occurs between A78 and G98, but the orientation is reversed, with the Hoogsteen base, A78, on the right+ The symbols we propose make these relationships immediately clear+ U103•A73 and U77•A99 are trans W+C+/ Hoogsteen pairs, and are indicated by open symbols comprising circles (placed next to the Us) connected to squares (placed next to the As)+ In the U103•A73 pair, the Watson-Crick base (U103) occurs on the left, whereas the situation is reversed for the U77 Fig+ 9) is the highly conserved sarcin/ricin motif (Leontis & Westhof, 1998b)+ This motif also occurs in loop E of eukaryal 5S rRNA and should not be confused with bacterial loop E+ The sequence shown is that of rat 28S rRNA, NDB file UR0002 (Correll et al+, 1998)+ The structure comprises a GAGA hairpin loop (not shown) and an asymmetric "internal loop+" The dotted arrows between C8 and A9 and between A9 and G10 indicate the local strand reversal that occurs at A9+ The positioning of A9 beneath U11 indicates the stacking between these two residues+ The "bulged" base, G10, is actually hydrogen bonded to U11 and lies in the same plane as the U11•A20 trans W+C+/Hoogsteen pair+ This is indicated by placing all three bases at the same horizontal level on the page+ The G10•U11 pair is cis Sugar-edge/ Hoogsteen whereas the G19•A12 and U7•C23 pairs are trans Sugar-edge/Hoogsteen+ Domain IV of SRP 4.5S RNA The SRP motif has been observed as the RNA alone (Jovine et al+, 2000) and in complex to SRP protein 54 Figure 8+ The loop E submotif occurs also in helix 20 of 16S rRNA (Wimberly et al+, 2000), as was predicted (Leontis & Westhof, 1998a)+ Interestingly, the G•G bifurcated pair in 16S rRNA is identical to the pair in the SRP loop (trans bifurcated as in Fig+ 8B)+…”

“…Because the classification facilitates the comparison between different three-dimensional structures to identify common three-dimensional motifs, it further aids in predicting families of isosteric pairings that can substitute for each other in homologous RNA molecules+ Since three-dimensional structures of homologous RNA molecules are more strongly conserved than their individual sequences, covariation data can be used to identify bases involved in tertiary interactions and even indicate the most likely pairing geometry+ This approach was successfully applied for predicting potential sarcinricin motifs (also frequently referred to as "S-turn" or "eukaryal 5S loop E" motifs) and bacterial loop E motifs in 16S and 23S rRNAs (Leontis & Westhof, 1998a, 1998b)+ All these motifs, except for one, were later identified in crystal structures of the ribosome 70S and its subunits (Cate et al+, 1999;Nissen et al+, 2000;Schluenzen et al+, 2000;Wimberly et al+, 2000)+ In ad- dition, a bacterial loop E motif, predicted to occur in domain IV of the 4+5S RNA in the signal recognition particle (Leontis & Westhof, 1998a), was later observed by X-ray crystallography (Batey et al+, 2000;Jovine et al+, 2000)+ Further, used in conjunction with experimental evidence, motif prediction, based on phylogeny and sequence-specific criteria, can be applied to structure prediction of RNA domains+ Recently, such a method combining motif recognition with the NMR signature attached to the three-dimensional structure, led to the rapid identification of a sarcin/ricin (i+e+, eukaryal 5S loop E) motif in a domain of the IRES element in the hepatitic C virus (Klinck et al+, 2000)+…”

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures

“…versus ln(C t ) for self-complementary or ln(C t /4) for nonself-complementary sequences+ Initially, the sequences 59-GCUGAGUGC/CGAAUGACG-59 and 59-GCUGAUUGC/CGAAUGACG-59 were investigated+ In the loop E motif, the GAG/AUG and GAU/AUG submotifs form similar single cross-strand purine stacks (Leontis & Westhof, 1998;Moore, 1999)+ Unfortunately, neither of these oligomers melted in a two-state manner+ The first had a melting transition below 20 8C and the second displayed no hyperchromicity+…”

Molecular Dynamics of Rna Structural Motif. Temperature Enhanced Sampling of the Conformational Space

“…They mediate the specific interactions that induce the compact folding of complex RNAs [4,5], Some of these elements can function as isolated structures, without the context of a larger folded RNA structure. Particularly stable hairpins can form nucleation points for RNA folding.…”