Two-dimensional gels and hybridization for studying DNA-protein contacts by cross-linking

DNA-protein covalent cross-linking in combination with two-dimensional gel electrophoresis and hybridization allows mapping of DNA-protein contacts in vivo and determination of the protein's approximate molecular weight [Mw]. Here we present a strategy and detailed protocol for UV cross-linking, purification, two-dimensional gel electrophoresis, and 'protein image' hybridization of cross-linked complexes. This method permits direct study of DNA-protein contacts without constructing artificial in vitro or in vivo systems.