5 - Photofootprinting DNA in Vitro and in Vivo

Abstract

This chapter discusses photofootprinting DNA in vitro and vivo. Photofootprinting refers to the use of light or light-activated molecules to footprint nucleic acids. The chapter discusses the most widely used photofootprinting technique, termed ultraviolet footprinting photons to footprint nucleic acids. The use of UV light to footprint nucleic acids has several important advantages over other footprinting techniques. The UV footprinting technique is based on the premise that changes in the structure of DNA, or the formation of protein-DNA complexes, will alter UV damage rates along the DNA helix. The UV footprinting technique was developed on the premise that protein-DNA contacts and altered structures of DNA will alter UV damage rates by affecting the ability of DNA to adopt geometry necessary to form a UV photoproduct. UV footprinting measures the ease with which bases along the DNA helix can unwind and bend to form UV photoproducts. Agents that inhibit these structural deformations in DNA inhibit UV damage rates whereas agents that facilitate these deformations enhance UV damage rates.