Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots

DNA-transcription factor interactions in eukaryotic systems have been documented by a broad gamut of biochemical techniques including deoxyribonuclease I (DNase I) footprinting and Southwestern (SW) assays. In spite of their wide applicability, each of these approaches provides only partial information about DNA-protein complexes. DNase I footprinting identifies the extent and location of the binding site within the DNA but does not yield information about the protein(s) involved. On the other hand, the SW assay can reveal the relative size of active protein species in crude extracts, facilitating their identification, but fails to localize their binding site within the probing DNA sequence. Coupling SW and in situ (on-blot) DNase I footprinting methodologies has the dual potential of accurately determining the molecular mass of individual DNA-binding transcription factors and precisely mapping their cognate binding sites.