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Base Pair Geometry Standards

The Leontis-Westhof classification system annotates basepairs according to the interacting edge used on each base (Watson-Crick, Hoogsteen, Sugar), and bond orientation (Cis, Trans). The classification table is shown below, along with diagrams explaining the edge pairings and bond orientations (Figures A, B). See also: RNA Basepair Catalog

No. Bond Orientation Interacting Edges (i, j)* Symbol Strand Orientation Notation*
1 Cis Watson-Crick/Watson-Crick Anti-Parallel cWW
2 Trans Watson-Crick/Watson-Crick Parallel tWW
3 Cis Watson-Crick/Hoogsteen Parallel cWH (or cHW)
4 Trans Watson-Crick/Hoogsteen Anti-Parallel tWH (or tHW)
5 Cis Watson-Crick/Sugar Anti-Parallel cWS (or cSW)
6 Trans Watson-Crick/Sugar Parallel tWS (or tSW)
7 Cis Hoogsteen/Hoogsteen Anti-Parallel cHH
8 Trans Hoogsteen/Hoogsteen Parallel tHH
9 Cis Hoogsteen/Sugar Parallel cHS (or cSH)
10 Trans Hoogsteen/Sugar Anti-Parallel tHS (or tSH)
11 Cis Sugar/Sugar Anti-Parallel cSS
12 Trans Sugar/Sugar Parallel tSS
*For six of twelve classes, the correct Leontis-Westhof notation depends upon the order of identified nucleotides:
  • tHS: nucleotide i pairs via Hoogsteen edge, nucleotide j pairs via Sugar edge.
  • tSH: nucleotide i pairs via Sugar edge, nucleotide j pairs via Hoogsteen edge.

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).

  • Leontis NB and Westhof E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512. DOI
  • Leontis NB, Stombaugh J, Westhof E. (2002) The non-W-C base pairs and their associated isostericity matrices. Nucleic Acids Res 30:3497-3531 DOI
  • Stombaugh, J., C.L. Zirbel, E. Westhof, and N.B. Leontis (2009) Frequency and isostericity of RNA base pairs. Nucleic acids research, 37:2294-2312. DOI

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).

  • W. Saenger (1984), Principles of Nucleic Acid Structure, pp. 120-121. Springer-Verlag New York Inc., New York.
  • D. Voet and A. Rich (1970), The Crystal Structures of Purines, Pyrimidines and Their Intermolecular Complexes Progress in Nucleic Acid Research and Molecular Biology vol 10, pp 183-265. DOI

The standard reference frame described in the tables and references below is commonly used for nucleic acid conformational analysis, to describe the characteristics of base-pairs, base-pair steps, and base-pair geometry relative to the local helical axis. In the schematic diagrams within the tables, the shaded edge facing the viewer denotes the minor-groove side of a base or base pair.

Shear Stretch Stagger
Shear Stretch Stagger
Buckle Propeller Opening
Buckle Propeller Opening
Shift Slide Rise
Shift Slide Rise
Tilt Roll Twist
Tilt Roll Twist
x-displacement (dX) y-displacement (dY) Helical Rise
x-displacement y-displacement As for Rise above
Inclination Tip Helical Twist
Inclination Tip As for Twist above

Images source: X3DNA-DSSR Website

  • Olson WK et al. (2001) A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry. Journal of Molecular Biology 313: 229-237 DOI
  • Lu, X-J and Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Research 31: 5108-5121 DOI
  • Lu, X-J and Olson WK (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures Nature Protocols 3: 1213-1227 DOI