SINGLE-MOLECULE STUDIES OF UNUSUAL KINETICS IN BIOLOGICAL AND SYNTHETIC POLYMERS
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For all life forms including bacteria, transition metals like Zn are essential but their excess is also detrimental. Host cells can sequester metals to curb bacterial proliferation during infection, while metal stress can also be effective bactericidal treatments. For growth and survival, bacteria have evolved exquisite mechanisms to regulate metal uptake and efflux. Studying bacteria has thus produced mechanistic paradigms not only for understanding metal homeostasis in general but also for developing antibiotic treatments. One such paradigm is the ‘set-point’ mechanism that bacteria use to regulate cellular concentrations of a variety of transition metals. There, a set of transcription regulators, so-called metalloregulators, sense cellular free metal concentration [Mn+]free, without interacting with each other, to regulate metal uptake and efflux genes to maintain [Mn+]free “set” by their respective metal-binding affinities.In Chapter 2 we study E. coli, a model bacterium, which has evolved complex machineries to combat phenomena such as nutritional immunity that disrupt cellular metal homeostasis. Here the metalloregulators, Zur (uptake) and ZntR (efflux), sense and maintain the cytoplasmic [Zn]free, responding in a set-point mechanism. Using a combination of live-cell single-molecule tracking and in vitro single-molecule FRET measurements, we uncovered a first-of-its-kind “through-DNA” mechanism for interaction between Zur and ZntR at chromosomal recognition sites, leading to a [ZntR]-dependent enhancement of Zur unbinding from DNA. We have identified potential sequences around Zur recognition motifs where ZntR could bind and interact with Zur. Identification of similar potential binding motif overlaps for other uptake/efflux pairs in E. coli, and in other organisms, expands the relevance of this work. These findings provide insights into understanding metal homeostasis and for developing antibiotic treatments. Proteins inside bacteria constantly experience force which can affect protein-DNA interactions and gene regulation. These forces may affect the mechanisms in which the transcription regulators dissociate from DNA and are therefore a direction that complements the discovery of these transcriptional regulation pathways. Although these goals are not within the scope of this thesis, in Chapter 3 we make a transition towards force spectroscopy, specifically using magnetic tweezers to study living polymerizations. In Chapter 3 we study the force dependence of the real-time dynamics of chain growth polymerizations of single synthetic polymers. Using magnetic tweezers and focusing on ring-opening metathesis polymerization, we had previously visualized real-time polymer growth at the single-polymer level. The presence of a constant but variable force during the polymerization allowed us to investigate the force dependence of these polymerization reactions. We discovered a biphasic force dependence of the polymerization kinetics; here low forces initially suppressed the polymerization kinetics followed by an acceleration at higher forces. These results provide additional insights into understanding and manipulating polymerization reactions and there by contributing to the development of polymeric materials with interesting physical and mechanochemical properties.