Use IRDye® Labeled Oligonucleotides for Safer, Faster Fluorescent Gel Shift Assays

The EMSA (electrophoretic mobility shift assay) is used to study protein:DNA complexes and interactions. Protein:DNA complexes migrate more slowly than unbound linear DNA on a non-denaturing gel, causing a “shift.”

Also called “gel shift” or “gel retardation” assays, EMSA can be used to analyze sequence-specific recognition of nucleic acids by proteins.

Traditional, radioactive EMSA protocols can be easily adapted to near-infrared fluorescence EMSA detection by using IRDye end-labeled oligonucleotides and imaging with the Odyssey® CLx or Odyssey Classic Infrared Imaging System, providing a safe and sensitive alternative.

Comparison of Detection Methods for Fluorescent Gel Shift Assay

For more information on the EMSA workflow and a sample protocol for infrared fluorescent mobility shift assays, visit our website.

Detect EMSA (Gel Shift Assays) on your Odyssey® CLx or Classic Infrared Imager

Gel shift assays or electrophoretic mobility shift assays (EMSA) provide a simple method to study DNA:protein interactions. This assay is based on the principle that a DNA-protein complex will have different mobility during electrophoresis than non-bound DNA. These shifts can be visualized on a native acrylamide gel using labeled DNA to form the DNA-protein binding complex.

Do you know that you can easily adapt your existing mobility gel shift assay protocols by replacing the radiolabeled oligonucleotides with IRDye® end-labeled oligonucleotides?

And using the Odyssey CLx or Classic Infrared Imager, you can complete your EMSA in about 90 minutes – saving valuable research time.

Figure 1.
EMSA performed with IRDye 700 AP-1 oligos. Reprinted with permission from Electrophoretic Mobility Shift Assay (EMSA) Using IRDye Oligonucleotides.

And when you are ready to image, there is no need to remove the gel from the glass plates. This makes gel handling easier and allows running the gel further, if needed, after scanning is completed. Possible deformations or tearing of the gel while separating plates are also eliminated.

For more information, refer to our Technical Note on Infrared EMSA detection.