Regulatory Protein-DNA Interactions in vivo Analyzed by Ultrafast Photochemical Crosslinking

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Watt W. Webb, School of Applied and Engineering Physics, John T. Lis, Department of Molecular Biology and Genetics, Tadhg P. Begley, Department of Chemistry and Chemical Biology, Bik-Kwoon Tye, Department of Molecular Biology and Genetics, Eric E. Alani, Department of Molecular Biology and Genetics, and Alexander L. Gaeta, School of Applied and Engineering Physics, all of Cornell University are funded with an award from the Collaborative Research in Chemistry Program with funds provided by the Division of Chemistry, the Division of Physics, the Division of Molecular, Cellular Biology and the Office of Multidisciplinary Activities. This multifaceted team will employ ultrafast UV laser crosslinking to lock proteins to their nucleic acid targets instantaneously and covalently during functional activation as it occurs during the cell cycle. These molecular complexes are then resolved by state-of-the-art analytical protein and nucleic acid biochemistry and structural analysis to identify crosslinked amino acids and their nucleotide binding-sites. These researchers will investigate the network of complex DNA-protein interactions regulating gene transcription, replication, and repair using new technologies that allow high temporal and spatial resolution biochemical analysis of elusive DNA-protein interactions in living cells. The ultimate goal of this research is to develop the methods to perform functional genomic experiments on living cells of prokaryotic and eukaryotic systems to establish genome-wide maps of DNA-bound proteins, thus following global gene regulation control through a cell's growth cycle and providing efficient tools for deciphering the complexity of gene regulator networks.In this research, a collaborative approach will be employed to target both the photochemistry and the functional genomics of DNA-binding-proteins. Scientific ideas will be integrated across three disciplines - biology, chemistry, and physics - uniting molecular biologists investigating DNA-protein interactions; chemists studying the photochemistry of DNA; physicists applying ultrashort laser pulse optics; and biophysicists providing the interface for the interdisciplinary research. Students will receive training at all levels from high school to postdoctoral.