Holliday junctions are formed as an intermediate during DNA recombination as the two strands come together. Recombination occurs during meiosis, and also during DNA double strand repair. Trapping this branched intermediate could prevent DNA repair from occurring in cells which would prove beneficial during cancer treatment. There are many enzymes that cleave Holliday junctions. One such enzyme, T7 Endonuclease I, was specifically chosen to detect ligand binding at the core of the junction since its binding and cleavage of cruciforms is well documented. Specialized bifunctional ligands were studied in this project that were designed to bind DNA structures that are held in close proximity to one another. These compounds have two identical binding modules that are connected by a linker of various length and rigidity, with each module binding very weakly; however, when both modules bind the binding affinity is greatly enhanced. The interactions of these compounds with cruciforms are currently being studied.

No description available.

To investigate the localization and targeting of sodium channels in neurons, an efficient means of gene delivery will need to be established. Two amplicon-based viral approaches and a recombinant whole virus approach were attempted in order to package and express RIIA sodium channel tagged with a c-myc epitope (RIIA-myc) with the ultimate purpose of developing a Herpes virus-based model system for targeting studies. / Immunofluorescent staining of transfected epithelial cells was carried out to demonstrate that constructs created for use in these HSV-based approaches were capable of a high level of expression of RIIA-myc. Measurements of $ beta$-galactosidase reporter gene expression observed in cultured cells infected with RIIA amplicon virus suggested successful packaging of amplicon DNA. However, RIIA-myc expression from amplicon virus was not apparent, which may suggest recombination events occurred upon packaging of constructs. Difficulties in selection for recombinants with acyclovir prevented the recombinant whole virus approach from being pursued.

Despite the eradication of smallpox, poxviruses continue to cause human disease around the world. At the core of poxvirus replication is the efficient and accurate synthesis and repair of the viral genome. The viral DNA polymerase is critical for these processes. Acyclic nucleoside phosphonate (ANP) compounds that target the viral polymerase are effective inhibitors of poxvirus replication and pathogenesis. Cidofovir (CDV) is an ANP that inhibits vaccinia virus (VAC) DNA polymerase (E9) DNA synthesis and 3-to-5 exonuclease (proofreading) activities. We determined that point mutations in the DNA polymerase genes of ANP-resistant (ANPR) VAC strains were responsible for CDV resistance and resistance to the related compound, HPMPDAP. Although these resistant strains replicated as well as wild-type VAC in culture, they were highly attenuated in mice. The generation of ANPR VAC strains, in combination with our knowledge of how CDV inhibits E9 activities, allowed us to study the hypothesized role of E9 in catalyzing double-strand break repair through homologous recombination. We provide evidence that VAC uses E9 proofreading activity to catalyze genetic recombination through single-strand annealing reactions (SSA) in infected cells. Both the polarity of end resection of recombinant intermediates and the involvement of polymerase proofreading activity establish these poxviral SSA reactions as unique among homologous recombination schemes. Furthermore, we identified roles for the VAC single-stranded DNA-binding (SSB) protein and nucleotide pools in regulating these reactions. During these later studies we uncovered a differential requirement for the large and small subunits of the VAC ribonucleotide reductase (RR) in viral replication and pathogenesis. Our studies suggest that poxviral RR small subunits form functional complexes with host large RR subunits to provide sufficient nucleotide pools to support DNA replication. We present a model whereby interaction of VAC SSB and RR proteins at replication forks allows for modulation of E9 activity through local nucleotide pool changes, which serves to maximize replication rates while still allowing for recombinational repair. / Virology

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In this thesis the major work described concerns experimental determination of the dissociative recombination (DR) reaction for several molecular ions of astrochemical interest. DR is the process where an electron recombines with a molecular ion to form an excited neutral that disintegrates into two or more neutral fragments to release the gained excess energy. It is very efficient under cold conditions and therefore ubiquitously occurring in interstellar environments such as dark clouds and plays an important role in aeronomical plasmae, lightnings and in man-made plasmas such as in combustion engines and fusion reactors. Although DR reactions are crucial processes in all these environments, product branching fractions of DR reactions have proven to be very unpredictable and present one of the great remaining challenges for theoreticians. The experimental work includes determination of reaction rates and product distribution of DR of complex ions such as protonated alcohols and ethers. The following species have been investigated and are discussed in this thesis: CH3OH2+ (protonated methanol), CD3OD2+ (deuteronated methanol), CD3OCD2+ (methoxymethyl cation), CD3CDOD+ (deuteronated acetaldehyde), CH3CH2OH2+ (protonated ethanol) and (CD3)2OD+ (deuteronated dimethyl ether). The results of these measurements are used in astrochemical model calculations in which the rates used hitherto greatly have been based on educated guesses. Employing the outcome of the DR investigations of the CH3OH2+ and CD3OD2+ ions have shown a great impact on such models. The DR investigations have been followed up by astronomical observations. Theoretical models and laboratory experiments show that methanol should be formed from CO on cold grains. This scenario was tested by astronomical observations of gas associated with young stellar objects (YSOs). Two independent tests were showing consistency with methanol formation on grain surfaces. / I den här avhandlingen redovisas mitt arbete som till stor del baseras på experimentell bestämning av dissociativa rekombinations (DR) processer för molekylära joner av astrokemiskt intresse. DR är en process där en elektron rekombinerar med en molekylär jon som splittras up i två eller fler neutrala fragment för att göra sig av med den extra energi som erhållits. Processen är väldigt effektiv i kalla miljöer varför den är allestädes återkommande i omgivningar som interstellära moln och kometkoman och spelar en betydande roll i aeronomiska plasman, blixturladdningar men även i mänskligt skapade plasman såsom de i förbränningsmotorer och fusionsreaktorer. Det har dock visat sig att produkt distributionsförhållandena från DR reaktioner är mycket oförutsägbara och kvarstår som en av de stora återstående utmaningarna för teoretiker. Det experimentella arbetet består av bestämning av reaktionshastigheter samt produktdistribution för DR av komplexa joner som protonerade alkoholer och etrar. De följande jonerna har blivit undersökta och diskuteras i denna avhandling: CH3OH2+ (protonerad metanol), CD3OD2+ (deuteronerad metanol), CD3OCD2+ (metoxymetyl katjon), CD3CDOD+ (deuteronerad acetaldehyd), CH3CH2OH2+ (protonerad etanol) och (CD3)2OD+ (deuteronerad dimetyleter). Resultaten av mätningarna används i astrokemiska modelberäkningar i vilka reaktionshastigheterna som hittills använts till stor del baserats på kvalificerade gissningar. Insättning av resultaten av CH3OH2+ och CD3OD2+ jonerna har visat sig ha en stor effekt på sådana modeller. DR undersökningarna har följts upp av astronomiska observationer. Teoretiska modeller och laboratorieundersökningar visar att metanol borde kunna formas från CO på kalla iskornsytor, detta scenario har testats med astronomiska observationer av gas som associeras med unga stjärnor. Två oberoende undersökningar visade på förenlighet med metanolformation på kornytor. / At the time of the doctoral defense, the following papers were unpublished  and had a status as follows: Paper 1: Manuscript. Paper 2: In press. Paper 3: Manuscript. Paper 5: Manuscript.

<p>Double-stranded DNA breaks are potentially lethal lesions that can be repaired in mitotic cells by either homologous recombination (HR) or non-homologous end- joining (NHEJ) pathways. In the HR pathway, the broken DNA molecule is repaired using either the sister chromatid or the homolog as a template. Mitotic recombination events involving the homolog often result in loss of heterozygosity (LOH) of markers located distal to the crossover. In humans that are heterozygous for a mutation in a tumor suppressor gene, mitotic recombination leading to LOH can be an early step in cancer development.</p><p> In my thesis research, I analyzed mitotic recombination in the yeast Saccharomyces cerevisiae using oligonucleotide-containing microarrays to detect LOH of single-nucleotide polymorphisms (SNPs). In analyzing cells treated with ionizing radiation, I performed the first whole-genome analysis of LOH events done in any organism (Chapter 2). I showed that irradiated cells had between two and three unselected LOH events. I also showed that crossovers were often associated with non- reciprocal exchanges of genetic information (gene conversion events) and that these conversion events were more complex than predicted by standard models of homologous recombination.</p><p> In Chapter 3, I describe my mapping of spontaneous crossovers in a 1.1 Mb region of yeast chromosome IV. This analysis is the first high-resolution mitotic recombination map of a substantial fraction (about 10%) of a eukaryotic genome. I demonstrated the existence of recombination "hotspots" and showed that some of these hotspots were homolog-specific. Two of the strongest hotspots were formed by closely- spaced inverted repeats of retrotransposons. I demonstrated that the hotspot activity was a consequence of a secondary DNA structure formed by these repeats. Additionally, the majority of spontaneous LOH events reflect DNA lesions induced in unreplicated chromosomes during G1 of the cell cycle, indicating that G1-initiated lesions threaten genome stability more than G2-initiated lesions.</p><p> In Chapter 4, I describe mitotic crossovers associated with DNA replication stress induced by hydroxyurea (HU) treatment. Surprisingly, most HU-induced crossovers had conversion tracts indicative of DNA lesions initiated in G1. Additionally, HU- induced recombination events were very significantly associated with solo delta elements, a 330 bp sequence that is repeated several hundred times in the yeast genome.</p> / Dissertation

The site frequency spectrum of mutations (SFS) and linkage disequilibrium (LD) are the two major sources of information in population genetics studies. In this study we focus on the levels of LD and the SFS and on the effect of sample size on summary statistics in 10 Scandinavian populations of Norway spruce. We found that previous estimates of a low level of LD were highly influenced by both sampling strategy and the fact that data from multiple loci were analyzed jointly. Estimates of LD were in fact heterogeneous across loci and increased within individual populations compared with the estimate from the total data. The variation in levels of LD among populations most likely reflects different demographic histories, although we were unable to detect population structure by using standard approaches. As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in line with recent studies in other conifers that have revealed a more complex and variable pattern of LD than earlier studies suggested and with studies in trees and humans that suggest that Tajima's D is sensitive to sample size. This has large consequences for the design of future association and population genetic studies in Norway spruce.

Bibliography: p. 75-84. / 84 p., [20] leaves, [36] leaves of plates : ill. (chiefly col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Identifies key interactions between Polycomblike and other members of the Polycomb group and suggests a model for the role of Polycomblike within the group. / Thesis (Ph.D.)--University of Adelaide, Dept. of Genetics, 2000?

Bibliography: p. 75-84. / 84 p., [20] leaves, [36] leaves of plates : ill. (chiefly col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Identifies key interactions between Polycomblike and other members of the Polycomb group and suggests a model for the role of Polycomblike within the group. / Thesis (Ph.D.)--University of Adelaide, Dept. of Genetics, 2000?