Gel shift assays, or electrophoretic mobility shift assays (EMSA), provide a simple method to study DNA-protein interactions. Existing mobility shift assay protocols can be easily converted to infrared fluorescent assays by replacing the existing DNA oligonucleotides with IRDye® infrared dye end-labeled oligonucleotides. Binding and electrophoresis conditions are the same as any other EMSA detection method.
A DNA oligonucleotide end-labeled with IRDye 700 infrared dye is a good substrate for protein binding. Using the Odyssey Infrared Imaging System, IRDye infrared dye labeled DNA detection is linear within a 50-fold dilution range from 9.1 fmol to 0.18 fmol. Infrared assays can be completed in less than two hours with no gel transfer or film exposure. The gel doesn’t even have to be removed from the glass plates for imaging. Plus, the gel can be placed back into the electrophoresis unit and run longer, if necessary.
