Hey, I am characterizing a competitive inhibition of a host and viral RNA biding proteins. The RNA binding is not sequence specific but dependent on secondary structure of the RNA. I am looking for a method to identify if the viral protein blocks the host protein from binding RNA in cells.
Any suggestions would be really helpful but I was also specifically considering a filter binding assay or EMSA but I can not isotope label the RNA in my lab. Though I would check if anyone had suggestions.
Thanks for your help!