Hydroxyl Radical Footprinting of ProteinDNA Complexes

This unit details the use of hydroxyl radicals to characterize protein–DNA interactions. This method may be used to assess the exact location of contacts between a protein and its cognate DNA and details of the complex structure. We describe several methods to prepare DNA templates for footprinting and ways to avoid many of the pitfalls associated with the use of hydroxyl radical footprinting. In addition, we describe in detail one example of the application of this technique.