Table 1.
Tm values of different triplet combinations determined by fluorescence melting
| X = | BAU | MeP | APP | S | |
|---|---|---|---|---|---|
| pH 5.0 | X.AT | 63.5 | 43.9 | 48.3 | 61.5 |
| X.TA | 53.6 | 49.8 | 48.4 | 63.5 | |
| X.GC | 53.3 | 63.5 | 50.8 | 60.4 | |
| X.CG | 53.6 | 47.2 | 63.5 | 66.5 | |
| pH 5.5 | X.AT | 63.9 | 43.7 | 48.1 | 62.0 |
| X.TA | 52.8 | 49.5 | 48.3 | 63.9 | |
| X.GC | 53.0 | 63.9 | 48.1 | 60.6 | |
| X.CG | 51.5 | 46.3 | 63.9 | 66.4 | |
| pH 6.0 | X.AT | 62.4 | 40.4 | 45.7 | 60.5 |
| X.TA | 50.7 | 47.0 | 46.4 | 62.4 | |
| X.GC | 49.0 | 62.4 | 45.3 | 57.7 | |
| X.CG | 48.0 | 44.5 | 62.4 | 64.5 | |
| pH 6.5 | X.AT | 58.2 | n.d. | 38.8 | 54.1 |
| X.TA | 42.9 | 39.1 | 40.4 | 58.2 | |
| X.GC | 42.6 | 58.2 | 37.3 | 50.3 | |
| X.CG | 40.2 | 37.7 | 58.2 | 59.6 | |
| pH 7.0 | X.AT | 48.8 | n.d. | n.d. | 43.2 |
| X.TA | n.d. | n.d. | n.d. | 48.8 | |
| X.GC | n.d. | 48.8 | n.d. | 39.7 | |
| X.CG | n.d. | n.d. | 48.8 | 49.8 | |
| pH 7.5 | X.AT | 37.4 | n.d. | n.d. | n.d. |
| X.TA | n.d. | n.d. | n.d. | 37.4 | |
| X.GC | n.d. | 37.4 | n.d. | n.d. | |
| X.CG | n.d. | n.d. | 37.4 | 37.8 |
The values in bold correspond to those for TFO-1 at its intended target (employing BAU.AT, MeP.GC, APP.CG and S.TA triplets). For all the other cases, 1 bp in the target was changed opposite one of the modified bases, as shown in Figure 1 using duplexes 2–5 (1.2 opposite S, duplex 2; 3.4 opposite BAU, duplex 3; 5.6 opposite MeP, duplex 4; 7.8 opposite APP, duplex 5). n.d. indicates that no melting transition was detected (Tm < 30°C). Each value is the average of three determinations, which usually differed by <0.5°C.