[19] Hydroxyl radical footprinting

Publisher Summary This chapter provides an overview on hydroxyl radical footprinting. Hydroxyl radical footprinting of DNA has evolved over the last several years into a facile and powerful technique for studying DNA structure and complexes of DNA with other molecules. The chapter describes the chemistry and history behind these techniques. In a footprinting experiment, a strand of DNA is subjected to cleavage by some reagent, both in the presence and absence of a DNA-binding ligand. Comparison of the cleavage patterns yields information on the structure of the DNA-ligand complex. Footprinting can also be used to obtain thermodynamic information on DNA-ligand complexes through footprint titration experiments.