I having an issue seeing my EMSA probes on an acrylamide gel. I've annealed complimentary 35 bp oligos to use as probes. When I run them out to see them on a 6% acrylamide gel they don't show up. The probes do show up on an agarose gel. Also the ladder shows up nicely on both. I haven't tagged them. I'm using the Molecular Probes kit that uses a sybr green stain to visualize DNA and sybr Ruby to visualize the protein. I have no idea what is going on.
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