DNA replication is one of the most fundamental processes in all living organisms. Its semi-discontinuous nature dictates that the lagging strand is synthesized in short fragments called Okazaki fragments. In eukaryotes, each Okazaki fragment is initiated by an ~ 30-40 nucleotide-long RNA-DNA hybrid primer that is synthesized by Pol α-primase complex. To ensure genomic stability, the RNA primer has to be excised, any misincorporations by Pol α have to be corrected for and finally the resulting nick has to be sealed generating a contiguous strand. This feat is accomplished by a highly coordinated and regulated process called Okazaki fragment maturation. At the center of this process are 5’ nucleases, which are structure-specific nucleases that catalyze the incision of phosphodiester bonds one nucleotide into the 5’ end of ssDNA/dsDNA junctions. Previous structural and biochemical studies have shed some light on the mechanism of FEN1 substrate recognition, its catalysis and regulation. However, many gaps in our understanding of this remarkable nuclease still persist. Moreover, the choice between the short- and long-flap pathways is still elusive. Finally, the mechanism of the coordination among the different enzymatic activities of the polymerase, the nuclease and the ligase during Okazaki fragment maturation is still debatable. In this work, we set out to study FEN1 substrate recognition, catalysis and regulation using single molecule techniques. We show that FEN1 employs a sophisticated substrate recognition mechanism through which it actively distorts the DNA to ~100˚ bent angle. It also displays a remarkable selectivity towards its cognate substrate and avoids off-target substrate by a lock-down mechanism that commits the enzyme for catalysis on cognate substrates while promoting the dissociation of non-cognate substrates. We further characterized FEN1 reaction from substrate binding/bending to product handoff and built a comprehensive kinetic scheme that shows FEN1 releasing its product in two steps. Finally, we uncovered an unprecedented role of FEN1 in the choice between short- and long-flap pathways.

As one of the most promising solar cell technologies, organic solar cells have unique superiorities distinct from inorganic counterparts, such as semitransparency, flexibility and solution-processability, as well as tunable photophysical properties, which originate from the structural verstailities of organic semiconductors. A major breakthrough in OSCs was the exploration of novel non-fullerene electron acceptor (NFAs): In comparison with traditional fullerene derivative acceptors, NFA possesses several advantages, such as low synthesis cost, tunable absorption range and adjustable energetic level, which effectively provides a wide light-harvesting window with low energetic loss. In recent decades, fused-ring electron acceptors (FREAs) have obtained an irreplaceable status in the development of OSCs. However, there are still initial drawbacks to FREA-based devices including: 1: the degree of molecular packing and the corresponding impact on device performance, which has not been studied in depth; 2: the feasibility of approaches for controlling the bulk heterojunction morphology of the film, which also has not been systemic researched; 3: the presence of bulk (geminate and non-geminate) and surface recombination which significantly affects the efficiency and stability of working devices. In this thesis, I took the above three issues as my main doctoral research subjects. In the first part of the thesis, I shine light onto the strength of π-conjugated backbones in FREA molecular structures, which strongly affect the intramolecular interaction. Herein, two FREA with different conjugated framework (IDT core vs IDTT core) are synthesized and employed as electron acceptors in OSCs. A significantly enhanced power conversion efficiency of 11.2% is obtained from IDTTIC-based devices in comparison with that of IDTIC-based devices (5.6%). After considering the electron-donating part in FREA molecules, I also study the effect of the terminal unit, which has a strong relationship with the intramolecular charge transfer effect and intermolecular interactions. Solvent additives are another powerful strategy to further improve the photovoltaic efficiency. 1-chloronaphthalene (CN) was found to be useful in the PTB7-Th:IEICO-4F system, which show a PCE improvement from 9.5% to 12.8%. Furthermore, by utilizing a small molecule donor, BIT-4F-T, as a third component, an optimum PCE of 14.0% is achieved in the devices based on PTB7-Th:IEICO-4F.

In the last decade, organic photovoltaics (OPVs) have been attracting much attention for their low cost, and feasibility of mass production in large-area modules. Reported power conversion efficiencies (PCE) of organic solar cells have reached more than 10%. These promising PCEs can be realized by uncovering important principles: (1) rational molecular design, (2) matching of the material energy level, (3) favorable morphology of donor-acceptor (D/A) network, (4) higher carrier mobilities, and (5) suppression of charge recombination within the bulk heterojunction (BHJ). Though these key properties are frequently stated, the relationships between these principles remain unclear, which motivates us to fill these gaps. In the beginning, we show that changing the sequence of donor and acceptor units of the benzodithiophene-core (BDT) SM donors critically impacts molecular packing and charge transport in BHJ solar cells. Moreover, we find out that by adding small amount of the external solvent additive, the domain size of the SMFQ1 become relatively smaller, resulting in the FF enhancement of ~70% and thus pushing PCE to >6.5%. To further improve the device performance, we utilize another technique of device optimization: Solvent Vapor Annealing (SVA). Compared with solvent additive, the SVA creates a solvent-saturated environment for SMs to re-arrange and crystalize, leading to PCE of >8%, with nearly-free bimolecular recombination. When the systems are shifted from fullerene acceptors to nonfullerene acceptors, using solvent additives in indacenodithiophene-core (IDT) systems significantly reduces the domain size from >500nm to <50nm and also allows the SM donors to orderly packed, rising the PCE from <1% to 4.5%. Furthermore in a similar IDT-based system, it shows unexpectedly high VOC and low energy loss, and high PCE > 6% can be reached by employing the dimethyl disulfide (DMDS) as the SVA solvent to re-organize the morphology from excessive mixing to ordered phase-separated D/A network. Lastly, taking advantage of the distinct and complementary absorption of fullerene and nonfullerene acceptors, we show that the SM ternary system successfully realizes the high PCE of 11%, good air stability, and scalable property.

Tesis para optar al grado de Magíster en Ciencias, Mención Física / The electron localization function (ELF) is a scalar field that accounts of the excess of electronic kinetic energy due to Pauli repulsion between electrons with the same spin. With this function, it is possible to divide real space in regions (basins) where electronic localization is high and Pauli repulsion is low (up-down electron pairs). From a phenomenological point of view, bifurcation points of the localization domains (points that belong to certain basins of a molecule) can be used to describe the rupture and formation of chemical bonds. Moreover, topological analysis of ELF allows us performing a statistical analysis of the electronic population of basins in a molecule. In this work, by using density functional theory with an hybrid exchange-correlation functional, we describe the electron localization along the intramolecular proton transfer in the Salicidene Methilamine molecule (SMA). First we do it in the ground state, in order to acquire physical insight of the process. Later, by means of time-dependent density functional theory (TD-DFT) in the linear response regime, we perform an equivalent analysis in the first excited state, for which we propose a way to compute ELF in excited states using TD-DFT. We show how the electronic population and other properties of interest of the basins associated with the atoms and bonds involved in the proton transfer change during the reaction. Finally, we choose this system because, after photoexcitation and proton transfer process, SMA suffers a large Stokes shift followed by a "closed" photocycle that ends with the molecule in its original ground state. This makes molecules like SMA good prospects for molecular photoswitches. The main contribution of this thesis is that this is the first time that the ELF developed and successfully used to explain chemical bonding in excited states.

This thesis describes research that has been carried out during the years 2009-2013 as a part of my PhD project related to the method of selected ion flow tube mass spectrometry (SIFT-MS) and its application in interdisciplinary areas of research. SIFT-MS is a method that allows accurate quantification of trace gases and vapours presented in humid air with the focus on human breath; without any sample preparation and in real time. The thesis is divided into several parts. The first part reviews the history of mass spectrometry as a background for the quantitative analytical methods as PTR-MS and SIFT-MS. The second part discusses the detailed history of development of SIFT-MS, starting from principles of selected ion flow tube (SIFT) technique that has been used for study of ion-molecule reactions in the gas phase and forms the basis of SIFT-MS. The next part discusses volatile organic compounds of different biological origin: bacterial, plant and human breath metabolites that can be analyzed in real time using SIFT-MS. The main part "Results and Discussion" is divided into several subsections that serve as commentaries to the enclosed research papers published in peer reviewed journals. The first is a detailed step by step overview of the kinetics of ion molecule reactions which is the basis of...

In the circular Escherichia coli chromosome, two replisomes are assembled at the unique origin of replication and drive DNA synthesis in opposite directions until they meet in the terminus region across from the origin. Despite the difference in rates of the two replisomes, their arrival at the terminus is synchronized through a highly specialized system consisting of the terminator protein (Tus) bound to the termination sites (Ter). This synchronicity is mediated by the polarity of the Tus−Ter complex that stops replisomes from one direction (non-permissive face) but not the other (permissive face). Two oppositely oriented clusters of five Tus–Ters that each block one of the two replisomes create a “replication fork trap” for the first arriving replisome while waiting for the late arriving one. Despite extensive biochemical and structural studies, the molecular mechanism behind Tus−Ter polar arrest activity remained controversial. Moreover, none of the previous work provided answers for the long-standing discrepancy between the ability of Tus−Ter to permanently stop replisomes in vitro and its low efficiency in vivo. Here, I spearheaded a collaborative project that combined single-molecule DNA replication assays, X-ray crystallography and binding studies to provide a true molecular-level understanding of the underlying mechanism of Tus−Ter polar arrest activity. We showed that efficiency of Tus−Ter is determined by a head-to-head kinetic competition between rate of strand separation by the replisome and rate of rearrangement of Tus−Ter interactions during the melting of the first 6 base pairs of Ter. This rearrangement maintains Tus’s strong grip on the DNA and stops the advancing replisome from breaking into Tus−Ter central interactions, but only transiently. We further showed how this kinetic competition functions within the context of two mechanisms to impose permanent fork stoppage. The rate-dependent fork arrest activity of Tus−Ter explains its low efficiency in vivo and why contradictory in vitro results from previous studies have led to controversial elucidations of the mechanism. It also provides the first example where the intrinsic heterogeneity in rate of individual replisomes could have different biological outcomes in its communication with double-stranded DNA-binding protein barriers.

Angiogenesis is a physiological process by which new blood vessels develop from preexisting vasculature. The process of converting endothelial cells into fully developed blood vessels involves multiple coordinated cellular events that occur through the collaboration that exists between a variety of growth factors, receptors and adhesion molecules. The immunoglobulin-containing and proline rich receptor-1 (IGPR-1) is an IgSF containing adhesion molecule that has been recently identified as a novel regulator of angiogenesis in vitro. In this study, we provide evidence that IGPR-1 promotes cell survival in porcine aortic endothelial cells (PAE) and plays a role in the inhibition of p38 MAPK in vitro. Deletion of the extracellular domain of IGPR-1 abolished IGPR-1’s ability to inhibit phosphorylation of p38 MAPK and promote the survival of endothelial cells. Likewise, mutation of serines 186 (A186-IGPR-1) and 220 (A220-IGPR-1) on the cytoplasmic domain of IGPR-1 was also found to reduce both the promotion of cell survival and inhibition of p38 MAPK. These findings suggest that both domains of IGPR-1 are important for endothelial cell survival and the activation p38 MAPK.

Numerous short flapped DNA structures are created during the semi-discontinuous replication. These toxic intermediates are quickly resolved to produce a fully intact duplex of replicated DNA. Structure specific nuclease are key to resolving these structures, and show a high degree of specificity for their cognate substrate structures while being essentially insensitive to nucleotide sequence. Herein I demonstrate through confocal based single molecule experiments that the 5’ structure specific nuclease Flap Endonuclease 1 (FEN1) achieves its substrate specificity by coupling the bending of DNA substrate with structuring of the active site in a way that non-cognate structures binding is significantly destabilized and enzymatic features are incapable of structuring in the absence of particular substrate features, in particular a single nucleotide 3’ flap the FEN1 induces in nearly all DNA substrates. Debate remained over whether DNA was bound via a conformational capture or induced fit mechanism, and so I proceed to investigate the dynamics of the DNA itself in solution. Conclusions about conformational capture or induced fit remain elusive, however I did determine that DNA structures are rigidified by charge repulsion, an effect lessened by the salt concentration, which functions to shield the negative charge of DNA from itself. Additionally unstacking of the DNA in nicked structures incurs a significant free energy penalty, which FEN1 overcomes by its hydrophobic wedge motif, lending credence to an induced fit mechanism.

No description available.

Mining operations have led to an increase in polycyclic aromatic compound (PAC) concentrations in the Alberta oil sands area. However, the toxicity of most PACs and PAC mixtures is not well characterized. Some PACs and PAC mixtures are known to be mutagenic, though there is limited research on the genotoxicity of PACs from the Alberta oil sands to wildlife. This thesis tested the hypothesis that anthropogenic sources of PACs from the Alberta oil sands are mutagenic to wildlife. The objectives were: 1) to determine whether wildlife with increased exposure to PACs had increased mutations, and 2) to determine whether an anthropogenic source of PACs is mutagenic in a controlled lab setting. For the first objective, we used a single-molecule polymerase chain reaction (SM-PCR) assay to detect microsatellite mutations in river otters with differing liver tissue PAC concentrations in the Athabasca oil sand region (AOSR; Alberta, Canada). For objective two, an in vitro mammalian mutagenicity assay with the FE1 MutaMouse epithelial cell line (FE1) was used to determine the mutagenic potential of a bitumen extraction by-product, tailings pond bitumen. We found that PAC exposure in the AOSR was positively correlated with elevated microsatellite mutations in river otters. From the in vitro study, tailings pond bitumen extracts did not induce lacZ mutations in the FE1 cells. Differences in detection methods between the two assays and PAC profiles between the otter tissue and tailings pond bitumen are suspected reasons for contradictory results. Further investigation of the different sources and PAC profiles within the AOSR environment and wildlife food web will provide insights on what types of PACs are mutagenic. Cytotoxicity, observed following exposure to tailings pond bitumen extracts, also suggests other toxicity pathways should be considered when investigating the toxicity of bitumen from the AOSR. Overall, this thesis provided data on the potential mutagenicity of PACs in the AOSR, which can be used to elucidate potential molecular mechanisms of toxicity in wildlife exposed to oil processing contaminants.