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?