The molecular basis for oligopyrimidine selectivity in calicheamicin-DNA recognition: Analysis of synthetic oligosaccharides by capillary electrophoresis

The oligopyrimidine DNA-binding selectivity exhibited by the antitumor antibiotic calicheamicin γ₁I is surprising when compared to the common designation of small molecule ligands as either AT- or GC-binders. Initial hypotheses focused on hydrogen bonding and non-covalent interactions as the specificity determinant. However, it has also been proposed that the specificity is due to a shape-selective recognition of pyrimidine sequences of DNA by calicheamicin, based on NMR and biochemical studies.; Synthetic derivatives of the calicheamicin oligosaccharide were designed to probe the molecular basis for pyrimidine sequences in DNA recognition. Binding affinities of the oligosaccharide derivatives for a range of DNA sequences were determined. A new assay has been developed for the quantitative determination of oligosaccharide-DNA interactions using capillary electrophoresis. This technique offers significant advantages in characterization of weak ligand-receptor interactions. It should find wide application as a general solution for the direct determination of ligand-receptor thermodynamics.; The results show that having an iodo-substituted aromatic C-ring, which had been proposed to be the key specific contact, is neither necessary nor sufficient for the calicheamicin oligosaccharide's pyrimidine-selective binding. These experiments support the proposal that the binding selectivity depends on maintaining the overall shape and rigidity of the calicheamicin oligosaccharide. Thus, this binding event is a novel example of structural recognition of mixed DNA sequences by a small molecule, a motif observed normally in protein-DNA complexes.