Bi-functional photo-crosslinking (BFPX) for genome-wide study of protein-nucleic acid interactions

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Bi-functional photo-crosslinking (BFPX) for genome-wide study of protein-nucleic acid interactions For a given cell at a certain state, what proteins bind to the genomic DNA and where they bind in the genomic sequence are fundamental questions to understanding cellular functions and disease mechanisms. To address these questions, a variety of techniques have been developed to capture protein-DNA complexes for analyses and identifications. However, most of the current technologies depend on the capture of protein- DNA complexes by formaldehyde crosslinking. Increasing evidence suggests that formaldehyde fixation could be a major problem undermining the effectiveness of the current approaches. This is largely due to the highly reactive and non-specific damages to proteins by formaldehyde and its inability to crosslink DNA to proteins. DNA captured by formaldehyde is not covalently linked to protein but trapped in fixed protein complexes, which can lead to the capture of a large amount of non-specific DNA fragments which will mask the real signals (). Direct UV crosslinking of protein to DNA and RNA have recently been reported, but these approaches are limited by the low crosslinking efficiency and the use of short wavelength UVC (~250 nm) that damages proteins and nucleic acids. There is a critical unmet research need for molecular tools and technologies that can capture protein-DNA complexes in cells with high efficiency, selectivity (i.e., only targeting DNA-bound proteins) and stability (to enable robust isolation of protein-DNA complexes for subsequent analyses). The proposed research seek to develop a class of bi-functional photo-crosslinking probes (BFPX) that are cell and nuclear permeable, inert to cellular molecules in the absence of UV, bind and enrich on DNA or RNA, and under illumination with long wavelength UVA (~360nm), become activated to form covalent adduct to DNA or RNA and at the same time to crosslink nearby proteins bound to DNA or RNA through highly efficient photochemical reactions. These molecular probes will serve as powerful tools for robust capture of protein-DNA and protein-RNA complexes in a wide range of in situ studies of protein- nucleic acid interactions.