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Infrared Fluorescent-Based Reagents for Gel Shift Assays

Gel shift EGR image

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.

Other IRDye 700 oligonucleotides as well as IRDye 800 oligonucleotides are available through Integrated DNA Technologies, TriLink BioTechnologies, or Metabion International AG.

Advantages of Infrared
Infrared Radioisotope
Easy access and disposal Regulatory procedures
Disposal limitations
Dye is stable for a long time
Short half-life of the label
Non-hazardous Hazardous
Gel (glass plates) can be easily imaged on the Odyssey Lengthy incubations with autoradiographic film
Detection of the probe is rapid Time-consuming and inconvenient
Gel can be replaced back and run longer Not possible

IRDye 700 infrared dye-labeled EMSA oligonucleotides are supplied as 25 µl of 50 nM double-stranded DNA

Please note: Oligos with an * require up to two weeks for processing and delivery.

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