G • U base pairing patterns

This application exemplifies how theoretical methods were used to extend the MC-SYM database. The symmetrical tandem of G U mismatches is a motif that was identified in ribosomal RNAs. The secondary structure and a selected spanning tree of the motif are shown in Figure 11. The list of possible G U base pairing patterns that involve two hydrogen bonds are shown in Table 5. Two of these patterns, XXVII (reverse Wobble) and XXVIII (Wobble), were described in Saenger and both were found in RNA and DNA X-ray crystallography and NMR spectroscopy three-dimensional structures. 

Figure 11 Symmetrical tandem of G U mismatches, (a) Secondary structure. The arrows indicate the selected edges in the spanning tree, (b) MC-SYM script corresponding to the spanning tree in (a). The ANY-ANY list corresponds to combinations of C3 -, C2 -endo, anti, and syn nucleotide conformations. The XXVII relational list corresponds to the reverse Wobble G U base pairing pattern (see Table 5). The indicates that all examples of a given list are tested by MC-SYM...

Table 5 G U Base Pairing Patterns Involving Two Hydrogen Bonds. The nitrogen atoms are indicated by small bullets and the oxygen atoms by circles. The riboses are indicated by the letter R ...

Using the new database, MC-SYM produced consistent three-dimensional structures that contained the reverse Wobble, the Wobble, and the XXXI G U base pairing patterns. The three MC-SYM three-dimensional structures of symmetrical tandem of G U mismatches, refined using AMBER 4.1, are shown in Figure 12. In the case of class structures that include the reverse Wobble base pairing pattern, the guanosines were... 

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See also in sourсe #XX -- [ , ]

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