BINDING MODES OF THE DISTAMYCIN ANALOG FCE-24517 TO D(CGTATACG)2 - H-1 AND C-13 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 combin ed usage of 2D techniques, TOCSY, NOESY, ROESY and C-13/H-1 shift corr elation experiments. The formation of tbe complex destroys the C2 symm etry of the double helix, leading to a doubling of the nucleotide reso nances. Proton and carbon atoms were assigned in the complex in terms of specific strand and residue. The imino protons of the base pairs, i nvolved in hydrogen bonding and the H-2 protons of adenine moieties, w ere determinant for defining the binding sites of the drug. The presen ce of multiple equilibrium reactions was proved by means of NOESY and ROESY spectra, where all the chemical-exchange cross peaks were analys ed. The FCE-24517 signals in the complex were attributed and some ster eospecific assignments performed. Two sets of resonances for FCE were identified, showing that tbe drug exists in two different chemical env ironments, corresponding to two different modes of binding in slow che mical exchange. Significant intermolecular NOE interactions between th e drug and the nucleotide have allowed the binding sites in the minor groove of the DNA fragment to be located.