Base pairs and pseudo pairs observed in RNA-ligand complexes.

Previously, a geometric nomenclature was proposed in which RNA base pairs were classified by their interaction edges (Watson-Crick, Hoogsteen or sugar-edge) and the glycosidic bond orientations relative to the hydrogen bonds formed (cis or trans). Here, base pairs and pseudo pairs observed in RNA-ligand complexes are classified in a similar manner. Twenty-one basic geometric families are geometrically possible (18 for base pairs formed between a nucleic acid base and a ligand containing heterocycle and 3 families for pseudo pairs). Of those, 16 of them have been observed in X-ray and/or NMR structures.