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HIV-1 integrase (integrase) catalyzes the insertion of viral DNA into human chromosomes and is a focus for development of anti-integrase inhibitors to combat HIV infection. Integrase catalyzes two steps, a DNA-end cleavage reaction (3’-processing), and a DNA-end joining reaction (strand transfer). Together, these steps result in viral DNA integration into the genome of the host cell, resulting in persistent infection. Better understanding of the mechanism of integration and interactions of the viral and host DNA with integrase are required for optimal inhibitor development. Recombinant integrase protein was purified and activity was evaluated in a biochemistry assay under bulk conditions to optimize 3’-processing and strand transfer activity. Integrase binding to DNA was then measured under these conditions, using quartz crystal microbalance. This technique will also be used to characterize the disruption of integrase binding to DNA by inhibitors. Finally, integrase/DNA complexes will be visualized by atomic force microscopy to explore their interaction. This study addresses gaps in knowledge of viral DNA and HIV-1 integrase interactions as well as the effects of inhibitors on DNA binding.
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