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In a project I'm working on, we are designing a system where specific RNAs bind to proteins - an important part of this is to test whether the RNA binds when we modify the proteins in some way. What assays are there to test whether a specific (or non-specific) RNA is binding to a protein?

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I would reccomend an electrophoretic mobility shift assay (EMSA), one procedure for which can be found here.

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