Probing RNA-Protein Interactions by Psoralen Photocrosslinking

RNA molecules can fold into extensive structures containing regions of double-stranded duplex, hairpins, internal loops, bulged bases, and pseudo-knotted structures (1 ). Owing to the complexity of RNA structure, the rules governing sequence-specific RNA-protein recognition are not well understood. RNA-protein interactions are vital for many regulatory processes, especially in gene regulation where proteins specifically interact with binding sites found within RNA transcripts. In the absence of high-resolution crystallographic and nuclear magnetic resonance data, new methods are needed to determine the topology of RNA-protein complexes under physiological conditions. We have devised a new method based on psoralen photochemistry to identify specific contacts in RNA-protein complexes (2 ,3 ).