A method called "South Western blot mapping" for rapid characterization of both DNA binding proteins and their specific sites on genomic DNA is described. Proteins are separated on a sodium dodecyl sulfate (SDS) polyacrylamide gel, renatured by removing SDS in the presence of urea, and blotted onto nitrocellulose by diffusion. The genomic DNA region of interest is digested by restriction enzymes selected to produce fragments of appropriate but different sizes, which are subsequently end-labeled and allowed to bind to the separated proteins. The specifically bound DNA is eluted from each individual protein-DNA complex and analyzed by acrylamide gel electrophoresis. Evidence that tissue-specific DNA binding proteins may be detected by this technique is presented. Moreover, their sequence-specific binding allows the purification of the corresponding selectively bound DNA fragments and may improve protein-mediated cloning of DNA regulatory sequences.