see also: RNA Basepair Catalog

No.	Bond Orientation	Interacting Edges	Symbol	Strand Orientation	Abbreviated notation
1	Cis	W-C/W-C		Anti-Parallel	cWW
2	Trans	W-C/W-C		Parallel	tWW
3	Cis	W-C/Hoogsteen		Parallel	cWH
4	Trans	W-C/Hoogsteen		Anti-Parallel	tWH
5	Cis	W-C/Sugar		Anti-Parallel	cWS
6	Trans	W-C/Sugar		Parallel	tWS
7	Cis	Hoogsteen/Hoogsteen		Anti-Parallel	cHH
8	Trans	Hoogsteen/Hoogsteen		Parallel	tHH
9	Cis	Hoogsteen/Sugar		Parallel	cHS
10	Trans	Hoogsteen/Sugar		Anti-Parallel	tHS
11	Cis	Sugar/Sugar		Anti-Parallel	cSS
12	Trans	Sugar/Sugar		Parallel	tSS

Notations preceded by n indicate that the interaction is “near” or close but does not meet the strict criteria for membership.

Figure A: Base edges and Base-pair geometric isomerism. (Upper left) An adenosine showing the three base edges that are available for hydrogen-bonding interactions: Watson-Crick (W-C), Hoogsteen and Sugar-edge. (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 W-C edges. (Leontis & Westhof, 2001).

Figure B: 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 W-C 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 (Leontis et al., 2002).

1. Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512.
2. Leontis NB, Stombaugh J, Westhof E. 2002. The non-W-C base pairs and their associated isostericity matrices. Nucleic Acids Res 30:3497-3531

The 28 possible base-pairs for A, G, U(T), and C involving at least two (cyclic) hydrogen bonds. Hydrogen and nitrogen atoms displayed as small and large filled circles, oxygen atoms as open circles, and glycosyl bonds and thick lines with R indicating ribose C_1' atom. Base-pairs are boxed according to composition and symmetry, consisting of only purine, only pyrimidine, or mixed purine/pyrimidine pairs and asymmetric or symmetric base-pairs. Symmetry elements and are twofold rotation axes vertical to and within the plane of the paper. In the Watson-Crick base-pairs XIX and XX and in base-pairs VIII and XVIII, pseudosymmetry relating only glycosyl links but not individual base atoms is observed. Drawn after compilations in (33,457). [ref: W. Saenger (1984), Principles of Nucliec Acid Structure, 120-121. Springer-Verlag New York Inc., New York.]