Table 1. Effect of base substitutions on the formation and stability of M-DNA with 0.2 mM ZnCl2.
| DNA | pKa | pHm B- to M-DNA | pHm M- to B-DNA |
|---|---|---|---|
| Control 54% GC |
T = 9.9; G = 9.4 |
8.4 |
8.3 |
| c-src 73% GC |
– |
8.2 |
7.9 |
| 2-Aminoadenine |
– |
8.6 |
8.0 |
| 7-Deazaadenine |
– |
8.2 |
8.0 |
| 5-Methylcytosine |
– |
8.5 |
8.2 |
| Hypoxanthine |
H = 8.8 |
8.1 |
7.8 |
| Uracil |
U = 9.3 |
8.3 |
8.1 |
| 5-Bromouracil |
5BrU = 8.2 |
8.0 |
7.8 |
| 5-Fluorouracil |
5FU = 7.8 |
7.9 |
7.7 |
| 5-Bromouracil/hypoxanthine |
5BrU = 8.2/H = 8.8 |
7.8 |
7.6 |
| Poly(dG)•Poly(dC) |
– |
7.8 |
7.6 |
| Poly[d(GGCC)] |
– |
8.2 |
7.8 |
| Poly[d(GC)] |
– |
8.5 |
8.3 |
| Poly(dA)•Poly(dT) |
– |
8.1 |
7.8 |
| Poly[d(AT)] |
– |
8.6 |
8.4 |
| Poly[d(AU)] |
U = 9.3 |
8.4 |
8.1 |
| Poly[r(AU)] | U = 9.3 | 8.5 | 8.1 |
The pHm is defined as the pH at which 50% conversion occurs either for B- to M-DNA or M- to B-DNA. The pKa is for the imino protons of T- or G-type bases.