I would like to see RNA-protein interaction following transcription process inside the cell. I am wondering if there is any protocol similar to protein co-immunoprecipitation,which can bind the bead with RNA followed by detection of RNA-bound protein through gel electrophoresis?
CLIP and its variants are techniques that can identify interacting proteins using RNA baits and are being used more commonly in literature. I havent done it myself but it seems to do the job well. If your task is to use the RNA as bait to pull down your interacting protein, then most techniques will involve modifying the RNA with a tag like biotin or an aptamer, Here is a link to a very good nature methods article that provides more options. Article Methods to study RNA–protein interactions
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