Single molecule studies of DNA bending, looping and compacting proteins using optical tweezers and atomic force microscopy

Protein-DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy (AFM), and fluorescence imaging. In this review, we discuss studies that characterize the binding of high mobility group B (HMGB) architectural proteins 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)]. We describe how these HMGB proteins bind, bend, bridge, loop and compact DNA to perform these functions. We also describe how single molecule experiments observe multiple rates for dissociation of HMGB proteins from DNA, while only one rate is observed in bulk experiments. The measured single-molecule kinetics reveals a local, microscopic mechanism by which high mobility group B proteins alter DNA flexibility, along with a second, much slower macroscopic rate that describes the complete dissociation of the protein from DNA. This work was published and has been adapted for this dissertation. Murugesapillai, D., McCauley, M.J., Maher, L.J., 3rd and Williams, M.C. (2017) Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev, 9, 17-40.