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Base Interactions


Base Pairs:Leontis-Westhof Classification

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

Base Pairs:Saenger Classification

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 C1' 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.]


Base-Phosphate

No. Interacting Edge Symbol Notation
1 Sugar 1BPh
2 Sugar or W-C 2BPh
3 W-C 3BPh
4 W-C 4BPh
5 W-C 5BPh
6 W-C 6BPh
7 Hoogsteen 7BPh
8 Hoogsteen 8BPh
9 Hoogsteen 9BPh
10 Hoogsteen 0BPh

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

Proposed nomenclature for BPh interactions and superpositions of idealized BPh interactions observed in RNA 3D crystal structures for each base. H-bonds are indicated with dashed lines. BPh categories are numbered 0 to 9, starting at the H6 (pyrimidine) or H8 (purine) base positions. BPh interactions that involve equivalent functional groups on different bases are grouped together, e.g. [0BPh (A,C,G,U) 5BPh (G,U)], [6BPh (A,C), 7BPh (A,C) and 9BPh (C,U)].
Zirbel C L et al. Nucl. Acids Res. 2009;37:4898-4918


Base Stacking

s35 is a stacking interaction in which the first base uses its 3 face, and the second base uses its 5 face. Similarly, in s53, s33, s55, s stands for stacking and the two number stand for the face used by the first base and second base in the interaction respectively.

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