Table 2.
Predominant base-pairing interactions in RNA helical structures.†
| Base pair | Hydrogen bonds | Sign | Saenger | Leontis-Westhof | Number | ||||
|---|---|---|---|---|---|---|---|---|---|
| Canonical | |||||||||
| G·C | Watson-Crick | N2-H··· O2 | 2.79 (0.17) | − | XIX | cis | W/W | 9500×0.90 | |
| O6· · ·H-N4 | 2.92 (0.18) | ||||||||
| N1-H· · ·N3 | 2.89 (0.13) | ||||||||
| A·U | Watson-Crick | N1· · ·H-N3 | 2.84 (0.14) | − | XX | cis | W/W | 3069×0.93 | |
| N6-H· · ·O4 | 2.97 (0.18) | ||||||||
| Non-canonical | |||||||||
| G·U | wobble | N1-H· · ·O2 | 2.79(0.16) | − | XXVIII | cis | W/W | 1049×0.69 | |
| O6· · ·H-N3 | 2.85(0.16) | ||||||||
| G·A | sheared | N2-H· · ·N7 | 2.89(0.17) | + | XI | trans | H/S | 509×0.59 | |
| N3· · ·H-N6 | 3.03(0.18) | ||||||||
| A·U | Hoogsteen | N6-H· · ·O2 | 2.91(0.21) | + | XXIII | trans | H/W | 354×0.71 | |
| N7· · ·H-N3 | 2.90(0.17) | ||||||||
| U·U | wobble | O2· · ·H-N3 | 2.95(0.24) | − | XVI | cis | W/W | 185×0.54 | |
| N3-H· · ·O4 | 2.87(0.15) | ||||||||
| G·A | Watson-Crick | N1-H· · ·N1 | 2.84(0.17) | − | VIII | cis | W/W | 141×0.85 | |
| O6· · ·H-N6 | 2.91(0.20) | ||||||||
Base pairs described in column 2 by the nomenclature introduced by Lee and Gutell [36] and grouped in columns 6–8 into the structural classes anticipated by Saenger [14] and employed by Leontis and Westhof [23] (see text for details). Hydrogen bonds described in column 4 by the mean values and standard deviations (subscripted values in parentheses) of the distances, in Ångstrom units, between the designated proton donor-acceptor pairs. The signs in column 5, i.e., − or +, respectively denote whether the interacting bases form a pair with opposing faces or share the same face [15]. The entries in the last column correspond to the number of base pairs of a given type and the fraction of those pairs (subscripted numbers expressed as multiplicative factors) with the hydrogen-bonding pattern specified in column 3.