| Summary: | Protein-DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers and atomic force microscopy (AFM). In this work, we characterize the binding of high mobility group B (HMGB) architectural proteins and HIV-1 viral protein R to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function. These roles vary from the maintenance of chromatin structure and facilitation of ribosomal RNA transcription [yeast high mobility group 1 (HMO1) protein] to regulatory and packaging roles [human mitochondrial transcription factor A (TFAM) and yeast mitochondrial protein Abf2p]. Vpr is packaged into virions and is essential for maintaining HIV-1 virulence. The functions of Vpr remain mysterious, though in vivo functions attributed to Vpr include nuclear transport of the HIV-1 pre-integration complex (PIC) and facilitating reverse transcription. In this thesis, we describe how these HMGB and Vpr proteins bind, bend, bridge, loop and compact DNA, and we relate these properties to their functions.
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