TABLE 8.
Comparison of experimentally measured DNA-binding affinities of polyamide hairpin ligands to different DNA sequences with knowledge-based energies
| DNA-binding sequence | 5′-TGGTA-3′ | 5′-TGTTA-3′ | 5′-TATTA-3′ |
|---|---|---|---|
| ImImPy-γ-PyPyPy-β-Dp | |||
| ΔGb (kcal/mol)* | −10.0 | −9.4 | −7.1 |
| Energy† | |||
| Local density | 16.8(3.0) | 25.0(5.8) | 64.0(5.0) |
| Clustering | 25.0(6.4) | 48.5(9.0) | 69.4(7.0) |
| Global density | 19.7(3.8) | 27.1(4.5) | 65.0(6.8) |
| ImPyPy-γ-PyPyPy-β-Dp | |||
| ΔGb (kcal/mol)* | −8.0 | −10.7 | −8.8 |
| Energy† | |||
| Local density | 17.9(2.8) | 15.1(4.5) | 39.0(3.3) |
| Clustering | 38.3(5.9) | 24.6(5.7) | 44.6(7.1) |
| Global density | 27.4(4.2) | 17.0(2.5) | 34.9(4.6) |
*
Data of Pilch et al. (1999) obtained in solution studies at 293 K. ΔGb is the binding free energy, determined from the UV absorption curves.
†
Energies are the average ligand-binding scores and standard deviations (in parentheses) obtained for 10 drug-DNA models based on the known structures of 2:1 polyamide-DNA complexes and assessed with the designated knowledge-based potential.