Capillary electrophoretic mobility shift assay (CEMSA) of a protein-DNA complex

The utility of capillary electrophoresis in the study of DNA-protein binding is demonstrated, using the minimal DNA binding domain of the oncoprotein c-Myb (R2R3) and a specific target DNA sequence as a model system. The capillary electrophoresis method is based on simple UV detection at 260 nm with a linear polymer buffer and a coated capillary, and requires no labeling or derivatization of the DNA. A specific protein-DNA complex is observable as a retarded peak, which increases with increasing protein concentration with a corresponding reduction in the free DNA peak. With DNA and protein preparations of known concentrations, a test for sequence-specific binding can be completed within 10 min.