SOLUTION STRUCTURE STUDIES OF THE COBALT COMPLEX OF A BLEOMYCIN FUNCTIONAL-MODEL BOUND TO D(CGCAATTGCG)(2) BY 2-DIMENSIONAL NUCLEAR-MAGNETIC-RESONANCE METHODS AND RESTRAINED MOLECULAR-DYNAMICS SIMULATION

The interaction between the cobalt(III) complex of a bleomycin functio nal model (AMPHIS-NET) and the oligonucleotide d(CGCAATTGCG)(2) and th e structural features of the 1:1 ligand-DNA complex have been determin ed by high-resolution two-dimensional nuclear magnetic resonance metho ds and restrained molecular dynamics calculations. The intermolecular nuclear Overhauser effect (NOE) cross-peaks between Ligand protons and the DNA minor groove protons suggest that the cobalt(III) complex of AMPHIS-NET binds in the minor groove of DNA at the central AATT site. The NOE connectivities also clearly indicate that the H-8 pyridine pro ton and the H-2 imidazole proton in the metal-binding domain interact with the H-4' sugar proton of C-19 and the H-4' sugar proton of A(5), respectively, which defines a structure where the metal binding moiety of Co(III) AMPHIS-NET participates in binding to the DNA and extends into the region two base pairs beyond the central AATT site in the min or groove. This binding model is in accord with the consistently obser ved nondiffusion DNA cleavage in locations two to three residues beyon d the end of AT-rich binding sites induced by the corresponding iron(I I) complexes of AMPHIS-NET and other AMPHIS-lexitropsin hybrids of the bleomycin functional model compounds.