Date of Award

Spring 2008

Document Type



Life & Environmental Sciences

First Advisor

Kyle Strode

Second Advisor

Ron Wilde

Third Advisor

Dan Gretch


Human immunodeficiency virus nucleocapsid protein (HIV-1 NC) is known to have both structural and nucleic acid chaperone functions in the replication cycle of the retrovirus. As a nucleic acid chaperone, NC protein interacts with TAR RNA and TAR DNA structures during the minus-strand transfer step of reverse transcription. The aim of this study is to use single molecule florescence resonance energy transfer (SM-FRET) spectroscopy to study biotin-immobilized TAR DNA hairpins at various concentrations of NC protein. The resulting data will subsequently be used to determine whether cooperative binding occurs between the NC protein and the TAR DNA hairpins. The results of this study are inconclusive; however, refinement of the experimental technique may provide conclusive data regarding cooperative binding in NC protein-TAR DNA interactions.