Terminology for RNA Basepairs

Figure: Base edges and Base-pair geometric isomerism. (Upper left) An adenosine showing the three base edges (Watson-Crick, Hoogsteen and Sugar-edge) available for hydrogen-bonding interactions. (Lower left) Representation of RNA base as a triangle. The position of the ribose is indicated with a circle in the corner defined by the Hoogsteen and Sugar edge. (Right) Cis and Trans base-pairing geometries, illustrated for two bases interacting with Watson-Crick edges. (Leontis & Westhof, 2001).

Figure: Basepairs geometric families and their annotation. Upper panel: Twelve geometric basepair families resulting from all combinations of edge-to-edge interactions of two bases with cis or trans orientation of the glycosidic bonds. Circles represent Watson-Crick edges, squares Hoogsteen edges, and triangles Sugar edges. Basepair symbols are composed by combining edge symbols, with solid symbols indicating cis basepairs and open symbol, trans basepairs. Lower Left: Symbols for other pairwise interactions. Lower Right: Additional symbols for base-stacking, reversal of chain direction in hairpin loops, syn bases, and bases forming tertiary interactions (Leontis et al., 2002).