Table 1.
Hydrogen Bonds of >10% Occupancy between the Templating Residue and the Incoming dNTP
| model | hydrogen bonda | distance (Å)b | angle (°)b | occupancy (%)c |
| control | (tA5)N6–H61...O4(dTTP) | 2.9 ± 0.1 | 167.5 ± 7.1 | 98.1 |
| (dTTP)N3–H3...N1(tA5) | 3.0 ± 0.1 | 163.5 ± 9.6 | 94.2 | |
| intercalation | (tA5*)N6–H6...O4(dTTP) | 3.0 ± 0.2 | 162.7 ± 8.4 | 93.9 |
| (dTTP)N3–H3...N1(tA5*) | 3.1 ± 0.1 | 165.7 ± 7.2 | 84.9 | |
| (tA5*)O4Z-HO4Z...O4(dTTP) | 2.8 ± 0.2 | 170.5 ± 5.4 | 30.8 | |
| (dCTP)N4–H42...N3(tA5*) | 3.1 ± 0.1 | 165.9 ± 7.5 | 67.0 | |
| (dCTP)N4–H42...N1(tA5*) | 3.2 ± 0.1 | 147.0 ± 7.2 | 15.5 | |
| (dATP)N6–H61...N1(tA5*) | 3.1 ± 0.1 | 149.6 ± 9.2 | 31.7 | |
| (syn-dATP)N6–H62...N1(tA5*) | 3.1 ± 0.1 | 155.9 ± 8.1 | 95.2 | |
| (dGTP)N2–H21...N1(tA5*) | 3.1 ± 0.2 | 155.9 ± 10.3 | 59.4 | |
| (tA5*)N6–H6...O6(syn-dGTP) | 3.1 ± 0.2 | 158.0 ± 10.0 | 58.6 | |
| major groove type I | (tA5*)N6–H6...O4(dTTP) | 2.9 ± 0.1 | 168.9 ± 5.2 | 99.7 |
| (tA5*)O4Z-HO4Z...O4(dTTP) | 2.8 ± 0.1 | 169.2 ± 6.4 | 99.6 | |
| (dTTP)N3–H3...N1(tA5*) | 3.1 ± 0.1 | 165.2 ± 8.1 | 96.9 | |
| (dCTP)N4–H41...N1(tA5*) | 3.1 ± 0.2 | 150.6 ± 9.7 | 54.3 | |
| (dCTP)N4–H42...O4Z(tA5*) | 3.1 ± 0.2 | 157.7 ± 10.7 | 24.0 | |
| (tA5*)N6–H6...N1(dATP) | 3.2 ± 0.1 | 167.1 ± 7.1 | 35.3 | |
| (tA5*)O4Z-HO4Z...N1(dATP) | 2.9 ± 0.2 | 168.0 ± 8.1 | 27.0 | |
| (tA5*)O4Z-HO4Z...N7(dATP) | 3.0 ± 0.2 | 155.6 ± 9.6 | 19.2 | |
| (tA5*)O4Z-HO4Z...N1(syn-dATP) | 2.9 ± 0.1 | 162.8 ± 7.8 | 99.6 | |
| (syn-dATP)N6–H62...N1(tA5*) | 3.2 ± 0.1 | 144.6 ± 7.3 | 25.2 | |
| (tA5*)O4Z-HO4Z...O6(dGTP) | 2.8 ± 0.1 | 168.4 ± 6.5 | 100.0 | |
| (dGTP)N1–H1...N1(tA5*) | 3.0 ± 0.1 | 160.8 ± 9.6 | 98.5 | |
| (tA5*)N6–H6...O6(dGTP) | 3.1 ± 0.2 | 163.0 ± 7.9 | 93.3 | |
| (tA5*)O4Z-HO4Z...O6(syn-dGTP) | 2.7 ± 0.1 | 169.8 ± 5.7 | 99.6 | |
| (tA5*)N6–H6...O6(syn-dGTP) | 3.1 ± 0.2 | 167.2 ± 6.7 | 85.2 | |
| (syn-dGTP)N1–H1...O4Z(tA5*) | 3.2 ± 0.1 | 140.2 ± 3.9 | 11.4 | |
| –1 deletion | (dGTP)N1–H1...N3 (tC4) | 3.0 ± 0.1 | 168.2 ± 5.5 | 100.0 |
| (dGTP)N2–H21...O2(tC4) | 2.9 ± 0.1 | 170.0 ± 5.1 | 99.9 | |
| (tC4)N4–H41...O6(dGTP) | 2.9 ± 0.1 | 169.6 ± 6.0 | 99.6 | |
| (dGTP)N1–H1...O2(tC4) | 3.3 ± 0.1 | 149.1 ± 5.1 | 48.4 |
a
Hydrogen bonds are specified in the format (A)B–C...D(E), where A is the residue name of the donor atom, B is the name of the donor atom, C is the name of the hydrogen atom, D is the name of the acceptor atom, and E is the residue name of the acceptor atom.
*
denotes 1S-(–)-B[c]Ph-dA modification. Z denotes the B[c]Ph moiety on the adducted adenine.
b
Average values and standard deviations are provided.
c
The criterion for hydrogen bond occupancy is heavy atom–heavy atom distance ≤ 3.4 Å and heavy atom–hydrogen–heavy atom angle ≥ 135°.