2015/04/14 by Adam J. M. Wollman, Wollman, Adam J. M., Helen Miller +5
Biochemistry, Genetics and Molecular Biology · #Advanced Biosensing Techniques and Applications #Advanced Electron Microscopy Techniques and Applications #Advanced Fluorescence Microscopy Techniques #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Physical sciences
paper · pdf · doi:10.48550/arxiv.1504.03488
openalex publication_date 2015/04/14 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
DNA-interacting proteins have roles multiple processes, many operating as\nmolecular machines which undergo dynamic metastable transitions to bring about\ntheir biological function. To fully understand this molecular heterogeneity,\nDNA and the proteins that bind to it must ideally be interrogated at a single\nmolecule level in their native in vivo environments, in a time-resolved manner\nfast to sample the molecular transitions across the free energy landscape.\nProgress has been made over the past decade in utilising cutting-edge tools of\nthe physical sciences to address challenging biological questions concerning\nthe function and modes of action of several different proteins which bind to\nDNA. These physiologically relevant assays are technically challenging, but can\nbe complemented by powerful and often more tractable in vitro experiments which\nconfer advantages of the chemical environment with enhanced detection\nsingle-to-noise of molecular signatures and transition events. Here, we discuss\na range of techniques we have developed to monitor DNA-protein interactions in\nvivo, in vitro and in silico. These include bespoke single-molecule\nfluorescence microscopy techniques to elucidate the architecture and dynamics\nof the bacterial replisome and the structural maintenance of bacterial\nchromosomes, as well as new computational tools to extract single-molecule\nmolecular signatures from live cells to monitor stoichiometry, spatial\nlocalization and mobility in living cells. We also discuss recent developments\nfrom our lab made in vitro, complementing these in vivo studies, which combine\noptical and magnetic tweezers to manipulate and image single molecules of DNA,\nwith and without bound protein, in a new superresolution fluorescence\nmicroscope.\n