Southwestern blot

Southwestern blotting, based along the lines of Southern blotting (which was created by Edwin Southern) and first described by B. Bowen and colleagues in 1980, involves identifying and characterizing DNA-binding proteins (proteins that bind to DNA) by their ability to bind to specific oligonucleotide probes. The proteins undergo gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting.

The name southwestern blotting is based on the fact that this technique detects DNA-binding proteins, since DNA detection is by Southern blotting and protein detection is by western blotting.

However, since the first southwestern blottings, many more have been proposed and discovered. Large amounts of proteins and their degradation when being isolated hampered previous protocols.

"Southwestern blot mapping" is performed for rapid characterization of both DNA-binding proteins and their specific sites on genomic DNA. Proteins are separated on a Sodium Dodecyl Sulfate (SDS), polyacrylamide gel (PAGE), 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.