Symbolic generation and clustering of RNA 3-D motifs.

Non canonical G.A. base pairs play important structural and functional roles in ribonucleic [sequence: see text] acids (RNA). In particular, the 3'-A-G-5' motif and three of its sequence variants have a relatively high occurrence in 16S and 23S ribosomal RNA. Extensive 3-D modeling of these variants has allowed to support a previously proposed 3-D model and to identify another series of conformations consistent with phylogenetic data. The library of 3-D conformations generated by the MC-SYM program was then used to produce 3-D conformations of the small ribonucleotide r(GGCGAGCC)2. This new library includes the conformation determined by nuclear magnetic resonance spectroscopy.