Use of a sequence-specific DNA-binding ligand to probe the environments of EcoRI restriction endonuclease cleavage sites

The DNAs of bacteriophage lambda and adenovirus were incubated with the sequence-specific DNA-binding ligand 6,4'-diamidino-2-phenylindole. Digestion of the ligand-DNA complexes with EcoRI nuclease and subsequent agarose gel electrophoresis demonstrated that the ligand inhibited nuclease activity at some sites, but not at others. The results suggest that diamidino-2-phynylindole can be used to probe the immediate environments of the EcoRI cleavage sites.