2024-04-10 : 17516 3D structures containing nucleic acids | RNAEQ v3.330all

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 |

- 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 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).

- 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.

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