i have do the EMSA assay, and can see weak protein-RNA complex band, the band is so weak that we can't use the sample by mixing the protein and RNA directly for Cryo-EM study and determine the structure of the protein and RNA complex. i have seen a paper that can extract the protein-RNA complex band from the gel, then use this complex for cryo-EM study three years ago. but now i can't find the paper again. have you seen similar paper? or have you done similar assays? thanks
Try electro-elution from the gel
https://www.researchgate.net/method/Electroelution
Dear Wendy Jiang,
do you have any other way to enrich the protein-RNA complex? Can you e.g. use biotinylated RNA for a pull-down with Streptavidin beads? Or does your protein maybe carry a tag? Or can you possibly use a complementary RNA/DNA? Anything that would facilitate affinity purification may work for you.
Good luck!
Markus
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