In order to determine whether there is an orientation preference of pyrrole-imidazole (Py-Im) polyamide dimers with respect to the 5′-3′ direction of the backbone in the DNA helix, equilibrium association constants (Ka) were determined for a series of six-ring hairpin polyamides which differ with respect to substitution at the N and C termini. Affinity cleaving experiments using hairpin polyami...
