Structure of daunomycin complexed to d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy

The anthracycline antibiotic daunomycin, having four fused rings and an amino sugar, is being used in the treatment of acute leukemia. Binding to DNA is generally believed to be essential for its activity. We have studied the interaction of daunomycin with DNA hexamer sequence d-(TGATCA)2 by titrating up to two drug molecules per duplex using nuclear magnetic resonance spectroscopy. The solution structure of 2:1 drug to DNA complex based on two dimensional nuclear Overhauser enhancement (NOE) spectroscopy and molecular dynamics calculations has been studied. The change in conformation of drug molecule on binding to DNA, deoxyribose conformation and glycosidic bond rotation has been obtained. The absence of sequential NOE connectivities at d-T1pG2 and d-C5pA6 sites shows that the drug chromophore intercalates between these two base pairs. This is substantiated by intermolecular NOEs observed between nucleotide base protons and aromatic ring protons of drug molecule. A set of 17 intermolecular NOE interactions allowed the structure to be derived by restrained molecular dynamics simulations, which have been compared with that obtained by X-ray analysis. Several specific interactions between the drug and DNA protons are found to stabilize the formation of drug-DNA complex.