Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting

Southwestern blotting was first described by Bowen et al. (1 ) and was used to identify DNA-binding proteins that specifically interact with a chosen DNA fragment in a sequence-specific manner. In this technique, mixtures of proteins such as crude nuclear extracts or partially purified preparations are first fractionated on a sodium dodecyl sulfate (SDS) denaturing gel; the gel is then equilibrated in a SDS-free buffer to remove detergent and the proteins transferred by electroblotting to an immobilizing membrane. During the transfer the proteins renature and hence DNA-binding proteins may subsequently be detected on the membrane by their ability to bind radiolabeled DNA. Fractionation of crude nuclear extracts on an SDS gel followed by electroblotting and analysis for sequence-specific DNA binding directly on the blot combines the advantages of a high-resolution fractionation step with the ability to rapidly analyze for a large number of different DNA-binding specificities.