Table 2.
H-Bond Percentage for the Different Conformations in the Single Mismatch Sequencesa
| RNA-CCG |
RNA-GCC |
DNA-CCG |
DNA-GCC |
|||||||||
| H-bond percentage (%) | AA | AS/SA | AA | AS/SA | AA | AS/SA | AA | AS/SA | ||||
| C(N3)–C(N4:H41) | 50.5 | 47.8 | 95.5 | 87.9 | ||||||||
| C(O2)–C(N4:H41) | 28.5 | 6.2 | 12.7 | 9.0 | ||||||||
| C(N4)–C(N4:H41) | 20.7 | 2.6 | 35 | 8.2 | 16.1 | 20.5 | 33.2 | 17.3 | ||||
| C(N3)–C(N4:H42) | 15.5 | 16.2 | 64.4 | 48.8 | ||||||||
| C(O2)–C(N4:H42) | 11.0 | 15.1 | ||||||||||
| RNA-CCG |
RNA-GCC |
DNA-CCG |
DNA-GCC |
|||||||||
| H-bond percentage (%) | AA | AS | SA | AA | AS | SA | AA | AS | SA | AA | AS | SA |
| G(O6)–G(N2:H21) | 18.4 | (28.9) | 29.0 | 34.8 | (14.8) | 17.8 | 52.3 | |||||
| G(O6)–G(N2:H22) | 6.8 | 17.0 | 70.0 | 10.2 | ||||||||
| G(N2)–G(N1:H1) | 11.7 | 21.8 | ||||||||||
| G(O6)–G(N1:H1) | (86.5) | 88.0 | 14.5 | (65.4) | 70.1 | (87.0) | 88.9 | 7.0 | (79.1) | 80.4 | ||
| G(OP2)–G(N2:H22) | (92.4) | 92.0 | (96.4) | 96.3 | (11.3) | 8.8 | (9.3) | 10.1 | ||||
| G(N7)–G(N2:H21) | (67.0) | 67.8 | (97.4) | 97.4 | (84.5) | 81.4 | (97.1) | 96.7 | ||||
| G(N7)–G(N1:H1) | (34.5) | 31.1 | (11.8) | 9.1 | (24.1) | 23.0 | ||||||
a
AA stands for anti–anti and AS (SA) for anti–syn (syn–anti) conformations. The mismatch (Figure 1) is B5–B14 (with B representing G or C bases). For AA, the value represents the total H-bond. The values under AS/SA in C-rich sequences represent the average of AS and SA. In G-rich sequences, in the AS and SA columns, the values in brackets correspond to B14(N3)–B5(H41) and those outside the brackets to the complementarys B5(N3)–B14(H41). All of the calculations use a 3.5 Å distance cutoff and a 135° angle cutoff. Percentages less than 2% are not listed.