Southwestern blot

The southwestern blot, is a lab technique that involves identifying as well as characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes. Determination of molecular weight of proteins binding to DNA is also made possible by the technique. The name originates from a combination of ideas underlying Southern blotting and Western blotting techniques of which they detect DNA and protein respectively. Similar to other types of blotting, proteins are separated by SDS-PAGE and are subsequently transferred to nitrocellulose membranes. Thereafter southwestern blotting begins to vary with regards to procedure as since the first blotting’s, many more have been proposed and discovered with goals of enhancing results. Former protocols were hampered by the need for large amounts of proteins and their susceptibility to degradation while being isolated.
Southwestern blotting was first described by Brian Bowen, Jay Steinberg, U.K. Laemmli, and Harold Weintraub in 1979. During the time the technique was originally called "protein blotting". While there were existing techniques for purification of proteins associated with DNA, they often had to be used together to yield desired results. Thus, Bowen and colleagues sought to describe a procedure that could simplify the current methods of their time.  
Method.
Original Method.
To begin, proteins of interest are prepared for the SDS-PAGE technique and subsequently loaded onto the gel for separation on the basis of molecular size. Large proteins will have difficulty navigating through the mesh-like structure of the gel as they can not fit through the pores with the ease that smaller proteins can. As a result, large proteins do not travel very far on the gel in comparison to smaller proteins that travel further. After enough time, this results in distinct bands that can be visualized from a number of post-gel electrophoresis staining procedures. The bands are at different positions on the gel relative to the well that they were loaded into.
Next, proteins are to be renatured followed by the gel being subjected to pressed between two nitrocellulose filters which rely on diffusion to transfer the proteins from the gel to the membrane filters. At this point replicas of the gel have been created of which each serves a particular purpose. One membrane filter can be stained to see the protein bands that were created from gel electrophoresis and the other is used in the actual process of hybridizing with prepared 32P radioactively labeled specific oligonucleotide probes. To detect any protein-DNA interactions, autoradiography is commonly used.  
Southwestern Blot Mapping.
"Southwestern blot mapping" is a time-efficient way of identifying DNA-binding proteins and specific sites on the genomic DNA that they interact with.
Results.
After time is allowed for binding with the oligonucleotide probes, the hope is that some of the proteins on the membrane filter have bound to the probes. Any probe that was not able to bind a protein needs to be removed. Once unbound probe removal has been taken care of, to better visualize the membrane filter, it is subjected to further varying procedures. By corresponding the resulting membrane filter to the second membrane filter that the gel was sandwiched between, the position of the protein in comparison to the molecular weight ladder gives information about the weight of the protein that bound to the probe.