campus seminar: Capture of DNA/RNA-protein interactions by chemical crosslinking mass spectrometry

A highly complex and dynamic interaction network of proteins and nucleic acids confers the viability of cells by driving essential cellular processes like gene expression, DNA replication, recombination and repair. As such, a longstanding focus of research is to elucidate how proteins bind to DNA and/or RNA, to pinpoint key players, potential hubs of deregulation and predispositions to various diseases. By employing chemical crosslinking mass spectrometry, we can identify DNA and RNA interaction sites within proteins at amino acid resolution in vivo. In combination with high-resolution structural techniques, crosslink site information can contribute to the understanding of the structures of DNA/RNA-protein complexes, which may ultimately provide clues to their functions. Our recent studies in Escherichia coli and HeLa cells discovered thousands of proteins interacting with nucleic acids, revealing surprising hints to potential multifunctionality of proteins. Using the crosslinking reagent nitrogen mustard, we overcome the limited crosslinking efficiency of conventional UV irradiation, enabling the transition from interaction site identification to cell-wide crosslink quantification. These advances provide new opportunities to study the dynamics of DNA/RNA-protein interactions in vivo.