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

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).

- Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512.
- 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.]

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

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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