DNA-SEQUENCE PREFERENCES OF SEVERAL AT-SELECTIVE MINOR-GROOVE BINDING LIGANDS

We have examined the interaction of distamycin, netropsin, Hoechst 33258 and berenil, which are AT-selective minor groove-binding ligands, with synthetic DNA fragments containing different arrangements of AT base pairs by DNase I footprinting. For fragments which contain multiple blocks of (A/T)(4) quantitative DNase I footprinting reveals that AATT and AAAA are much better binding sites than TTAA and TATA, Hoechst 33258 shows the greatest discrimination between these sites with a 50-fold difference in affinity between AATT and TATA, Alone amongst these ligands, Hoechst 33258 binds to AATT better than AAAA, These differences in binding to the various AT-tracts are interpreted in terms of variations in DNA minor groove width and suggest that TpA steps within an AT-tract decrease the affinity of these ligands. The behaviour of each site also depends on the flanking sequences; adjacent pyrimidine-purine steps cause a decrease in affinity, The precise ranking order for the various binding sites is not the same for each ligand.