Figure 2 - A flow chart showing a strategy for identifying DNA-binding proteins (e.g., transcription factors) by Southwestern blotting in combination with other methods.

Promoter assays are first performed to identify the promoter regions that are important for regulating transcription of the target gene. Information from promoter studies will be used for designing oligonucleotide primers for electrophoretic mobility shift assay (EMSA), which confirm binding of protein factors with the DNA sequence in an in vitro environment. Southwestern blotting is unique as it is the only technique that shows the molecular weight of the protein factor. On the basis of these studies, one can search databases TransFac and Patch search to identify the protein. To confirm, supershift and chromatin immunoprecipitation (ChIP) assay should then be performed to show the in vitro and in vivo interactions of the protein and the DNA motif using specific antibody.