Photogeneration of hydroxyl radicals for footprinting

Hydroxyl radicals yield footprints of DNA-ligand interactions that are uniform in intensity and display single base pair resolution. It is shown here that brief illumination of dilute aqueous solutions of hydrogen peroxide with a standard uv transilluminator can be used to generate hydroxyl radicals for footprinting studies. Photogenerated hydroxyl radicals are used to footprint netropsin, a drug that interacts with the minor groove of DNA. The method presented eliminates two of the reagents used in conventional Fenton-reaction-based hydroxyl radical footprinting. It has the further advantage that the extent of cleavage of the DNA can be precisely regulated by controlling the illumination time. Because light is used to drive the reaction, photogenerated hydroxyl radicals can be used to footprint DNA-ligand interactions under experimental conditions of temperature and pressure inaccessible to Fenton-reaction chemistry.