Structural analysis of protein-RNA interactions with mass spectrometry.

We present a high-resolution mass spectrometric footprinting approach enabling the identification of amino acids in the protein of interest interacting with cognate RNA. This approach is particularly attractive for studying large nucleoprotein complexes that are less amenable to crystallographic or nuclear magnetic resonance analysis. Importantly, our methodology allows examination of protein-RNA interactions under biologically relevant conditions using limited amounts of protein and nucleic acid samples.