TABLE 1.
Polyamide 3 binding affinities and inhibition constants
| Construct | Site position relative to T+1 | Kd (nM)a | TBP inhibition IC50 (nM)b | Relative transcriptionc | Transcription inhibition IC50 (nM)d |
|---|---|---|---|---|---|
| U−20 | −26 to −20 | NDe | >200f | 0.79 | 50 |
| U−15 | −21 to −15 | ND | >200 | 0.78 | 75 |
| U−10 | −16 to −10 | 4.0 | >200 | 0.96 | 50 |
| U−2 | −8 to −2 | 4.6 | 17.5 | 1.10 | 25 |
| U−1 | −7 to −1 | 5.1 | 12.5 | 0.38 | 20 |
| U+1 | −6 to +1 | 6.0 | 10.0 | <0.05 | ND |
| D+6 | +6 to +12 | 2.7 | 10.0 | 0.52 | 20 |
| D+8 | +8 to +14 | 4.7 | 35 | 0.65 | 50 |
| D+10 | +10 to +16 | 2.0 | >200 | 0.41 | >200 |
| D+15 | +15 to +21 | ND | ND | 0.97 | 75 |
a
Determined by quantitative DNase footprinting under equilibrium conditions.
b
Polyamide concentration required for half-maximal occupancy of TBP, as determined by DNase footprinting.
c
Transcription in the absence of polyamides relative to wild type.
d
Polyamide concentration required for 50% inhibition of transcription (see Fig. 7).
e
ND, not determined.
f
>200, no inhibition observed up to 200 nM polyamide.