2022-11-30 : 15400 3D structures containing nucleic acids | RNAEQ v3.259all
nakb.org
Full Search   

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 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

A notation preceded by "n" (e.g., ntWW) indicates that the interaction is 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).


  • 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.

BASE PAIR
Shear Stretch Stagger
Shear Stretch Stagger
Buckle Propeller Opening
Buckle Propeller Opening
BASE PAIR STEP
Shift Slide Rise
Shift Slide Rise
Tilt Roll Twist
Tilt Roll Twist
HELICAL AXIS
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