Detection of Sequence-Specific Protein-DNA Interactions by the DNA-Footprinting Technique

The initiation of transcription of eukaryotic genes by RNA polymerases is controlled by complex interactions between nonhistone proteins and specific regulatory DNA sequences (promoters and enhancers) (1 ). In order to characterize and purify such transacting protein factors, a sensitive and accurate assay for sequence-specific DNA-binding proteins is the DNA-footprinting technique, which can be used to analyze the interaction of a complex mixture of proteins with a gene regulatory sequence(s) that is known to be important for the expression of that gene.