The multiprotein-DNA complex of interest is formed using the site-specifically derivatized DNA fragment.  The complex is then UV-irradiated, initiating covalent cross-linking with proteins in direct physical proximity to the cross-linking agent.  Extensive nuclease digestion is performed to eliminate uncross-linked DNA and convert cross-linked DNA to a cross-linked, radiolabeled nucleotide "tag."

Protocol: Site-Specific Protein-DNA Photo-Cross-Linking: Analysis of Structural Organization of Protein-DNA