Binding modes of the distamycin analogue FCE-24517 to d(CGTATACG)2.1H and13C sequence-specific assignments

The interaction of an analogue of distamycin, FCE-24517, with the 'AT-rich' DNA fragment d(CGTATACG)2, was studied in solution by the combined usage of 2D techniques, TOCSY, NOESY, ROESY and C-13/H-1 shift correlation experiments. The formation of tbe complex destroys the C2 symmetry of the double helix, leading to a doubling of the nucleotide resonances. Proton and carbon atoms were assigned in the complex in termsof specific strand and residue. The imino protons of the base pairs, involved in hydrogen bonding and the H-2 protons of adenine moieties, were determinant for defining the binding sites of the drug. The presence of multiple equilibrium reactions was proved by means of NOESY andROESY spectra, where all the chemical-exchange cross peaks were analysed. The FCE-24517 signals in the complex were attributed and some stereospecific assignments performed. Two sets of resonances for FCE wereidentified, showing that tbe drug exists in two different chemical environments, corresponding to two different modes of binding in slow chemical exchange. Significant intermolecular NOE interactions between the drug and the nucleotide have allowed the binding sites in the minorgroove of the DNA fragment to be located.