Analysis of Protein-RNA Interactions by Protein-Induced Fluorescence Enhancement (PIFE)

In this chapter, we provide an overview of a fluorescence technique, known as "Protein-Induced Fluorescence Enhancement" (PIFE), to follow the association between a protein and an RNA. Unlike Förster-type resonance energy transfer (FRET), which requires at least two dyes, PIFE utilizes a single fluorophore attached to the RNA, with an unlabeled protein interacting with the nucleic acid. We discuss how both ensemble and single-molecule PIFE studies can be employed to explore molecular interactions and to measure the strength of the interactions in solution with low sample consumption.