I'm wondering what is the best technique for studying RNA-protein interactions !!! I'm trying to find the sequence specific part of my protein (for binding to its RNA target) and right now I'm using Electrophoresis Mobility Shift Assay (EMSA) as well as UV-cross linking. After a long time trying to optimize the assay it still gives me very confusing results which are not very reproducible either. So Does any body know another approach that I can take on the side. Can NMR be applied for this purpose !?
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