Applications

EMSA is a highly sensitive, fast and cost-effective technique.

1. Detection of DNA- Protein or RNA-Protein Interactions- to determine if a specific protein binds to a particular DNA or RNA sequence
2. Characterising Binding specificity- defining how changes in sequences affect the binding of proteins or nucleic acids
3. Determination of binding affinity- EMSA calculates how strongly protein binds to the target sequence
4. Identifying protein complexes- EMSA determines whether a protein binding involves cofactors or partner proteins
5. Screening of inhibitors- helps in the recognition of molecules disrupting protein-DNA interactions

Limitations

1. Low Resolution- EMSA defines binding, but provides no clue about the binding site
2. Difficulty with Complexes- if multiple protein molecules bind, then gel shifts become very challenging
3. False Positives and Non- Specific Binding- Sticky proteins at higher concentrations bind non-specifically to DNA, giving false positive results
4. Not Suitable for Very Weak Interactions- If the protein-DNA interaction is very transient or low-affinity, EMSA won't detect it