* Given the ability of southwestern blotting towards studying the affinity of proteins towards binding to DNA, this information can further be used with regards to uncovering specific protein factors that bind to DNA as well. These protein factors may be involved in controlling gene expression.
* Unlike electrophoretic mobility shift and DNA foot printing, determination of molecular weight of unknown proteins that bind to DNA can occur.  
* Bowen and colleagues not only experimented and demonstrated a procedure for detecting DNA-binding proteins but also procedures for RNA-binding proteins as well as histone-binding proteins.  
* Results can be combined with mass spectrometry to assist in DNA-binding protein identification.
* Isoelectric point determination is possible through the use of 2D-SDS-PAGE instead of the standard one dimension.