Abstract
Three minor-groove binding ligands have been used to study the characteristics of two d(GA·CT) n DNAs embedded in longer DNA fragments. The binding of mithramycin, netropsin or Thia-Net to these sequences has been studied using DNAse I footprinting. None of these ligands appeared to bind to d(GA·CT) 5 nor to d(GA·CT) 22 extensively, although with mithramycin some protected bonds were detected at the very edge of these sequences. In general, these small ligands did not enhance the DNAse I cleavage patterns at the alternating d(GA·CT) n flanking sequences located near DNA regions where the drug was bound. The d(GA·CT) n sequences could act as a rigid block in which it is not easy to propagate structural changes, whereas other sequences flanking the binding sites showed cleavage enhancements.
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