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Electrophoretic Mobility Shift Assay Forum EMSA Forum. Discuss the Electrophoretic Mobility Shift Assay protocols or technique and the assessment of DNA and RNA binding proteins here. Also post questions and troubleshooting about the shift assay.


RNA-protein complex runs faster than the probe

RNA-protein complex runs faster than the probe - Electrophoretic Mobility Shift Assay Forum

RNA-protein complex runs faster than the probe - EMSA Forum. Discuss the Electrophoretic Mobility Shift Assay protocols or technique and the assessment of DNA and RNA binding proteins here. Also post questions and troubleshooting about the shift assay.


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Old 11-14-2008, 06:41 AM
Pipette Filler
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Post RNA-protein complex runs faster than the probe



The RNA-protein complex in my RNA EMSA gels runs faster that the probe, so I can see the probe but in the presence of the protein the band appears below the probe. Has anyone ever seen this anomaly? My probe is 200 nt long and the protein is about 60 kDa, and I resolve them on a native 10% gel. When I do a 2-fold titration of the protein the protein-RNA band shifts up as I lower the concentration of the protein. So there is a shift consistent with the amount of protein present however the shift is below the probe as opposed to above it. Any thoughts?
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Old 07-19-2013, 08:28 AM
Pipette Filler
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Default Re: RNA-protein complex runs faster than the probe

Few years late, but is it possible your protein has RNA exonuclease activity (or is contaminated with such)?
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