NMR AND MOLECULAR MODELING STUDIES OF THE INTERACTION OF BERENIL AND PENTAMIDINE WITH D(CGCAAATTTGCG)2

The interaction of two anti-trypanosomal agents, berenil and pentamidi ne, with the A+T-rich dodecamer d(CGCAAATTTGCG)2 has been examined by high-resolution H-1-NMR. optical spectroscopy, and molecular modeling. Proton assignments for the free DNA and each DNA-ligand complex were obtained using nuclear Overhauser enhancement spectroscopy and total c orrelation spectroscopy. Complexation induces large changes in chemica l shift for protons in the DNA minor groove for the A5-T9 segment, and intermolecular NOEs reveal contacts between the DNA bases and each li gand. The asymmetric binding site for berenil indicated by the NMR dat a suggests that at least two overlapping sites are involved. Rapid exc hange between symmetrically-equivalent binding sites, via dissociative rearrangement, is consistent with retention of twofold degeneracy for both the ligand and the DNA host. Calculations of binding energy conf irm that this DNA duplex contains overlapping sites of similar binding affinity. In contrast, the larger pentamidine molecule occupies a sit e that spans four or five bp, with asymmetric binding to the minor-gro ove 5'-ATTT sequence. The B-type conformation of the DNA is not altere d substantially by either ligand.