Table 1.
# | Sequence | Site | Dye locn | % Δ int | Kd, nM |
---|---|---|---|---|---|
1 | dImImPyγImPyPyβDp | head | T37 | 10 ± 5 | 7.8 ± 1.6 |
2 | dImImPyPyγPyImPyPyβDp | head | T37 | 34 ± 2 | 2.3 ± 0.3 |
3 | dImImPyImγPyPyβPyβDp | tail | T37 | 25 ± 3 | 50 ± 15 |
4 | dImImβImγPyPyPyPyβDp | tail | T37 | 38 ± 3 | 140 ± 30 |
5 | dImPyPyPyγPyImImPyβDp | head | T34 | 22 ± 4 | 11.4 ± 1 |
6 | dImPyPyβPyPyPyγ-PyPyβPyPyPyPyβTab | n/a | T3 | 5.5 ± 1.5 | 4.8 ± 0.6 |
Im = imidazole, dIm = desamino-imidazole, Py = pyrrole, β= beta alanine, γ= gamma turn, Ta = 3,3’-diamino-N-methyldipropylamine, Dp = N,N-dimethylaminopropylamine. Site refers to the expected binding location based on recognition rules. Dye locn refers to the position of the TAMRA dye. % Δ int refers to the percent change in fluorescence intensity between the free DNA and PA-bound DNA. Unless otherwise noted, DNA binding to all PAs was measured with HP1 in 10 mM HEPES, 50 mM NaCl, pH 7.4, 25°C.
Kds were measured with HP2 and 200 µM nt calf thymus DNA, an additive carrier necessary to achieve reliable isotherms with this PA. Such carriers are used frequently in the literature and are known to decrease non-specific interactions between nucleic acids and proteins or small molecules [38; 39].