Table 8 Non Watson-Crick hydrogen bonds commonly observed in free-RNA helices
Step | Cross/Intra-strand | Groove face | Base (atom) involved | DA | HA | DHA |
|---|---|---|---|---|---|---|
|  | Donor, Acceptor | (Å) | (Å) | ( ° ) | ||
RR | Â | Â | Â | Â | Â | Â |
AA/UU | Cross | m | A(C2,H2),U(O2) | 3.4(0.2) | 3.0(0.2) | 101.3(7.5) |
GA/UC | Cross | M | A(C2,H2),U(O2) | 3.4(0.3) | 3.0(0.3) | 97.8(6.4) |
GG/CC | Intra | M | C(N4,H41),C(N4) | 3.4(0.2) | 3.0(0.2) | 101.3(7.9) |
RY | Â | Â | Â | Â | Â | Â |
AC/GU | Intra | M | C(N4,H42),A(N6) | 3.3(0.1) | 3.1(0.2) | 95.1(5.1) |
AC/GU | Cross | M | A(N6,H61),G(O6) | 3.4(0.2) | 2.9(0.2) | 114.8(6.1) |
AU/AU | Cross | M | A(N6,H61),A(N6) | 3.2(0.2) | 2.7(0.2) | 114.8(5.5) |
YR | Â | Â | Â | Â | Â | Â |
CA/UG | Intra | M | A(N6,H62),C(N4) | 3.4(0.2) | 2.9(0.2) | 108.7(6.5) |
CA/UG | Cross | m | G(N2,H22),A(N9) | 3.6(0.1) | 3.3(0.1) | 98.2(4.6) |
C G/CG* | Intra | M | C(N4,H42),G(O6) | 3.5(0.2) | 3.1(0.2) | 106.8((7.6) |
CG/C G* | Intra | M | C(N4,H42),G(O6) | 3.5(0.2) | 3.1(0.2) | 104.1(6.7) |
CG/CG* | Cross | m | G(N2,H22),G(N9) | 3.6(0.1) | 3.3(0.1) | 98.0(5.0) |
CG/CG* | Cross | m | G(N2,H22),G(N9) | 3.6(0.1) | 3.3(0.1) | 96.2(4.6) |
UA/UA* | Intra | M | A(N6,H62),U(O4) | 3.3(0.2) | 2.9(0.2) | 104.6(6.2) |
UA/UA* | Intra | M | A(N6,H62),U(O4) | 3.3(0.2) | 2.8(0.2) | 108.1(7.7) |
UA/UA | Cross | M | A(N6,H61),A(N6) | 3.5(0.2) | 3.2(0.2) | 97.1(3.5) |