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Dissertations / Theses on the topic 'DNA polymerases'

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Published: 4 June 2021

Last updated: 31 July 2024

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1

Leavitt, Markley Carl. "Bacteriophage T5 DNA polymerase relationships of DNA polymerases." Diss., The University of Arizona, 1990. http://hdl.handle.net/10150/185335.

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T5 DNA polymerase, a highly processive single polypeptide enzyme, and PRD1 DNA polymerase, a protein-primed DNA polymerase, have been analyzed for their primary structural features. The amino acid sequence of T5 DNA polymerase reveals a high degree of homology with DNA polymerase I (Pol I) of Escherichia coli and retains many of the amino acid residues which have been implicated in the 3'-5' exonuclease and DNA polymerase activities of that enzyme. Alignment with sequences of polymerase I and T7 DNA polymerase (family A polymerases) was used to identify regions possibly involved in the high processivity of this enzyme. Further amino acid sequence comparisons of T5 DNA polymerase with a large group of DNA polymerases (family B) previously shown to exhibit little similarity to Pol I, indicate certain sequence segments are shared among distantly related DNA polymerases. These shared regions have been implicated in the 3'-5' exonuclease function of Pol I which suggests that the proofreading domains of all these enzymes may be related. Mutations in these segments in T5 DNA polymerase (family A) and PRD1 DNA polymerase (family B) greatly decrease the exonuclease activity of these enzymes but leave the polymerase activities intact. Additionally, an exonuclease deficient T5 DNA polymerase is used in DNA sequencing reactions and yields consistent results with low background contamination on autoradiographs of polyacrylamide/urea gels. PRD1 mutants defective in 3 regions which are highly conserved among family B DNA polymerases, are deficient in DNA polymerase activity but retain exonuclease activity.

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2

SALHI, SAMIA. "Dna polymerase de sulfolobus acidocaldarius : interet de l'etude des dna polymerases thermophiles." Paris 7, 1989. http://www.theses.fr/1989PA077169.

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La copie par la dna polymerase de sulfolobus acidocaldarius d'un dna simple brin uni-amorce de sequence connue a ete etudiee. Les parametres cinetiques affectant cette synthese dependent de la sequence du dna. La temperature de reaction a son importance. Les methodes employees sont la reaction polymerase en chaine, la mutagenese dirigee, le sequencage de sanger

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3

Pospiech, H. (Helmut). "The role of DNA polymerases, in particular DNA polymerase ε in DNA repair and replication." Doctoral thesis, University of Oulu, 2002. http://urn.fi/urn:isbn:9514266692.

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Abstract Analysis of the primary structure of DNA polymerase ε B subunit defined similarities to B subunits of eukaryotic DNA polymerases α, δ and ε as well as the small subunits of DNA polymerase DI of Euryarchaeota. Multiple sequence alignment of these proteins revealed the presence of 12 conserved motifs and defined a novel protein superfamily. The members of the B subunit family share a common domain architecture, suggesting a similar fold, and arguing for a conserved function among these proteins. The contribution of human DNA polymerase ε to nuclear DNA replication was studied using the antibody K18 that specifically inhibits the activity of this enzyme in vitro. This antibody significantly inhibited DNA synthesis both when microinjected into nuclei of exponentially growing human fibroblasts and in isolated HeLa cell nuclei, but did not inhibit SV40 DNA replication in vitro. These results suggest that the human DNA polymerase ε contributes substantially to the replicative synthesis of DNA and emphasises the differences between cellular replication and viral model systems. The human DNA polymerases ε and δ were found capable of gap-filling DNA synthesis during nucleotide excision repair in vitro. Both enzymes required PCNA and the clamp loader RFC, and in addition, polymerase δ required Fen-1 to prevent excessive displacement synthesis. Nucleotide excision repair of a defined DNA lesion was completely reconstituted utilising largely recombinant proteins, only ligase I and DNA polymerases δ and ε provided as highly purified human enzymes. This system was also utilised to study the role of the transcription factor II H during repair. Human non-homologous end joining of model substrates with different DNA end configurations was studied in HeLa cell extracts. This process depended partially on DNA synthesis as an aphidicolin-dependent DNA polymerase was required for the formation of a subset of end joining products. Experiments with neutralising antibodies reveal that DNA polymerase α but not DNA polymerases β or ε, may represent this DNA polymerase activity. Our results indicate that DNA synthesis contributes to the stability of DNA ends, and influences both the efficiency and outcome of the end joining event. Furthermore, our results suggest a minor role of PCNA in non-homologous end joining.

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4

Roettger, Michelle P. "Insight into the Fidelity of Two X-Family Polymerases: DNA Polymerase Mu and DNA Polymerase Beta." Columbus, Ohio : Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1211074588.

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5

Brown, Jessica Ann. "Kinetic Mechanisms of DNA Polymerases." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1290014566.

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6

Morant, Nick. "Novel thermostable DNA polymerases for isothermal DNA amplification." Thesis, University of Bath, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.667735.

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DNA polymerases play a fundamental role in the transmission and maintenance of genetic information and have become an important in vitro diagnostic and analytical tool. The Loop-mediated isothermal DNA amplification (LAMP) method has major applications for disease and pathogen detection and utilises the unique strand-displacement activity of a small group of thermostable DNA polymerases. The Large (Klenow-like) Fragment of Geobacillus stearothermophilus DNA polymerase I (B.st LF Pol I) currently serves as the enzyme of choice for the majority of these isothermal reactions, with few alternatives commercially available. An increasing need for point-of-care nucleic acid diagnostics is now shifting detection methods away from traditional laboratory based chemistries, such as the polymerase chain reaction (PCR), in favour of faster, and often simpler, isothermal methods. It was recognised that in order to facilitate these rapid isothermal reactions there was a requirement for alternative thermostable, strand-displacing DNA polymerases and this was the basis of this thesis. This thesis reports the successful identification of polymerases from Family A, chosen for their inherent strand-displacement activity, which is essential for the removal of RNA primers of Okazaki fragments during lagging-strand DNA synthesis in vivo. Twelve thermophilic organisms, with growth temperature ranges between 50oC and 80oC, were identified and the genomic DNA extracted. Where DNA sequences were unavailable, a gene-walking technique revealed the polA sequences, enabling the Large Fragment Pol I to be cloned and the recombinant protein over-expressed in Escherichia coli. A three-stage column chromatography purification permitted the characterisation of ten newly identified Pol I enzymes suitable for use in LAMP. Thermodesulfatator indicus (T.in) Pol I proved to be the most interesting enzyme isolated. Demonstrating strong strand-displacement activity and thermostability to 98oC, T.in Pol I is uniquely suitable to a newly termed heat-denaturing LAMP (HD-LAMP) reaction offering many potential advantages over the existing LAMP protocol. The current understanding of strand-displacement activity of Pol I is poorly understood. This thesis recognised the need to identify the exact regions and motifs responsible for this activity of the enzyme, enabling potential enhancements to be made. Enzyme engineering using site-directed mutagenesis and the formation of chimeras confirmed the importance of specific subdomains in strand-separation activity. With this knowledge, a unique Thermus aquaticus (T.aq) Pol I mutant demonstrated sufficient strand-displacement activity to permit its use in LAMP for the first time. The fusion of Cren7, a double-stranded DNA binding protein, to Pol I for use in LAMP is also reported. Although the fusion construct was found to reduce amplification speed, enhancements were observed in the presence of increased salt concentrations and it is suggested here as a means for future enzyme development.

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7

Elshawadfy, Ashraf Mohamed. "Engineering archaeal DNA polymerases for biotechnology applications." Thesis, University of Newcastle Upon Tyne, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.606814.

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The DNA polymerase from the archaeon Pyrococcus furiosus (Pfu- Pol) is commonly used in the polymerase chain reaction (PCR). The enzyme has high thermostability and is very accurate due to the presence of 3'---5'exonuclease (proofreading) activity. Unfortunately, the polymerase has relatively low processivity, limiting its ability to amplify long stretches of DNA relatively quickly. In this project, two approaches have been used in an attempt to improve the performance and processivity of Pfu DNA polymerase in PCR applications. In the first, the overall positive charge of the protein has been increased; predicted to increase electrostatic interactions between the negatively charged DNA and the more positively charged proteins. In the second, we have prepared a set of Pfu-Pol mutants in an attempt to make Pfu-Pol more similar to KODl; a polymerase isolated from a related hyperthermophilic archaeon Thermocococcus kodakaraensis. KODl is known to have a higher processivity than Pfu-Pol and both share a 3'---5' proof reading exonuclease activity. A PCR-based protocol was used to introduce the desired mutations.

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8

Wardle, Josephine. "Recognition of deaminated bases by DNA polymerases." Thesis, University of Newcastle Upon Tyne, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443025.

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9

MENTEGARI, ELISA. "DNA damage tolerance by specialized DNA polymerases in humans and plants." Doctoral thesis, Università degli studi di Pavia, 2018. http://hdl.handle.net/11571/1243288.

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10

Plaskon, Randolph Richard. "DNA curvature and fluctuational base pair opening in the promoter regions of escherichia coli." Diss., Georgia Institute of Technology, 1988. http://hdl.handle.net/1853/25323.

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11

DONALDSON, ROBERT WILLIAM. "PHOSPHORYLATION OF DNA POLYMERASE ALPHA IN NORMAL AND ROUS SARCOMA VIRUS TRANSFORMED RAT FIBROBLASTS." Diss., The University of Arizona, 1987. http://hdl.handle.net/10150/184054.

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Immunochemical and immunohistochemical techniques were used to determine the role of post-translational modifications in the regulation of DNA polymerase α in Rat-1(tsLA24/RSV) cells. Immunoaffinity purification following sucrose gradient fractionation showed two immunospecific polypeptides of Mᵣ ≃ 185,000 and 220,000 only in those fractions exhibiting DNA polymerase α activity. The Mᵣ ≃ 220,000 polypeptide was shown to be phosphorylated, primarily at serine residues. Incubation of cell lysates with immobilized alkaline phosphatase reduced enzyme activity and subsequent readdition of ATP, but not ATP-γ-S, restored activity suggesting the involvement of an endogenous serine protein kinase. This kinase may be a cAMP dependent protein kinase because prior incubation of the catalytic subunit stimulated DNA polymerase α activity 3-4 fold. In the absence of serum growth factors or pp60ˢʳᶜ, DNA polymerase α activity and semi-conservative DNA replication rates in growth arrested cells were severely depressed. However, both polymerase activity and DNA synthetic rates were subsequently restored by either activation of pp60ˢʳᶜ by temperature shift or by serum addition. DNA polymerase α protein was found primarily in the nucleus of all cells in log phase, growth arrested or subsequently stimulated cultures, independent of whether the cells were replicating DNA. Stimulation by either pp60ˢʳᶜ or serum did not alter DNA polymerase α localization within the cell nor lead to a preferential synthesis of Mᵣ ≃ 220,000 peptide or proteolytic conversion of the Mᵣ ≃ 220,000 peptide to smaller peptides, but did result in phosphorylation of the Mᵣ ≃ 220,000 polypeptide. This phosphorylation was not apparent in serum deprived, growth arrested cells. It is suggested that pp60ˢʳᶜ acts to initiate DNA synthesis through the temporal activation of DNA polymerase α through a mechanism similar to that used by serum growth factors and that phosphorylation by a serine protein kinase serves an important function.

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12

Keith, Brian. "Investigating thermostable DNA polymerases for PCR-based applications." Thesis, University of Newcastle upon Tyne, 2014. http://hdl.handle.net/10443/2372.

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Thermostable DNA polymerases are essential components of the polymerase chain reaction (PCR), a technique widely applied across the entire biosciences. The work presented in this thesis improves understanding of the function and properties of these enzymes with the aim of developing improved formulations for biotechnological applications. The accuracy with which polymerases replicate DNA is essential for their application in PCR. A plasmid-based DNA polymerase fidelity assay, based on a gapped plasmid template containing the lacZα gene, has been developed. This technique, a marked improvement on previous methods, enables straightforward determination of any polymerase’s fidelity. The functions of two loops in archaeal family-B DNA polymerases, located in the thumb domain responsible for double-stranded DNA binding, have been elucidated, revealing a role in the control of polymerase and proof-reading exonuclease activities. Site-directed mutagenesis, combined with kinetic and binding experiments, was used for this purpose. The family-B DNA polymerase from the archaeon Pyrococcus furiosus has low processivity, limiting its ability to amplify long stretches of DNA. The processivity of this enzyme was increased by changing a number of amino acids to those observed in the more processive polymerase from Thermococcus kodakarensis. Several mutants have been identified with increased processivity and improved performance in PCR. Reverse transcription PCR (RT-PCR) typically requires the use of a mesophilic reverse transcriptase to generate cDNA from RNA, which is then amplified by a thermostable DNA polymerase in PCR. Through the use of compartmentalised self-replication (CSR) and rational design, generation of a DNA polymerase with reverse transcriptase activity capable of single tube RT-PCR was attempted.

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13

Gilroy, Louise. "Thermostable DNA polymerases in replication, repair and biotechnology." Thesis, University of Newcastle upon Tyne, 2014. http://hdl.handle.net/10443/2508.

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Many archaea contain a unique DNA polymerase, DNA Pol D. This enzyme is a heterodimer composed of a large subunit (polymerase) and a small subunit (3’- 5’ proof reading exonuclease). The enzyme from Pyroccocus furiosus is inhibited by the presence of uracil in template strands. This research has shown that a single uracil located as far as 134 bases ahead of the primertemplate junction causes inhibition of replication. Further, using replication fork mimics, it is shown that, as expected, uracil on a template strand being copied by Pol D causes inhibition. Surprisingly, though, the presence of uracil on a complementary non-copied strand is also inhibitory. A model for uracil recognition by Pol D is proposed. The biochemical properties of the individual, large and small, subunits of the Pol D heterodimer were analysed. Both subunits were found to possess activity when expressed alone although the activity was greatly reduced compared to the Pol D heterodimer. It was not possible to regain the level of activity observed in the Pol D holoenzyme by mixing the two subunits in vitro. This finding contributed to the hypothesis that the carboxyl-terminal region of the large subunit contains an Fe-S cluster that is lost when the protein is purified aerobically. Attempts were made to express Pol D in archaeal hosts and purify the protein with the correct metallo-status; regrettably, these were not successful. Two thermostable bacterial family-B (pol II) DNA polymerases were cloned and expressed in E.coli and their biochemical properties analysed. The enzymes were found to possess many properties that make them amenable to biotechnology: polymerase activity, 3’-5’ proofreading activity, high fidelity rates and the ability to bypass uracil located in template strand DNA. Unfortunately, thermostability assays revealed that the polymerases denatured on exposure to temperatures ~85°C, making them unsuitable in the PCR. Thus, further manipulation is required to determine whether the polymerases have applications in biotechnology.

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14

Killelea, Tom. "Archaeal family B DNA polymerases : structure function relations." Thesis, University of Newcastle upon Tyne, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.548029.

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15

Fowler, Jason David. "Investigation of Noncanonical DNA Polymerases and Their Mechanisms." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1250701062.

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16

Rytkönen, A. (Anna). "The role of human replicative DNA polymerases in DNA repair and replication." Doctoral thesis, University of Oulu, 2006. http://urn.fi/urn:isbn:9514281381.

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Abstract The maintenance of integrity of the genome is essential for a cell. DNA repair and faithful DNA replication ensure the stability of the genome. DNA polymerases (pols) are the enzymes that synthesise DNA, a process important both in DNA replication and repair. In DNA replication DNA polymerases duplicate the genome during S phase prior to cell division. Pols α, δ, and ε are implicated in chromosomal DNA replication, but their exact function in replication is not yet completely clear. The mechanisms of different repair pathways and proteins involved are not yet completely characterised either. The deeper understanding of DNA repair and replication mechanisms is crucial for our understanding on the function of the cell. The mechanism of repair of DNA double strand breaks (DSBs) by non-homologous end joining (NHEJ) was studied with an in vitro assay. DNA polymerase activity was found to be involved in NHEJ and important in stabilising DNA ends. Antibodies against pol α, but not pol β or ε, decreased NHEJ significantly, which indicates the involvement of pol α in NHEJ. In addition, the removal of proliferating cell nuclear antigen (PCNA) slightly decreased NHEJ activity. The division of labour between pols α, δ, and ε during DNA replication was studied. Results from UV-crosslinking, chromatin association, replication in isolated nuclei, and immunoelectron microscopy (IEM) studies showed that there are temporal differences between the activities and localisations of the pols during S phase. Pol α was active throughout S phase, pol ε was more active at early S phase, whereas the activity of pol δ increased as S phase advanced. These results suggest that pols δ and ε function independently during DNA replication. Pol ε could be crosslinked to nascent RNA, and this labelling was not linked to DNA replication, but rather to transcription. Immunoprecipitation studies indicated that pol ε, but not pols α and δ, associated with RNA polymerase II (RNA pol II). Only the hyperphosphorylated, transcriptionally active RNA pol II was found to associate with pol ε. A large proportion of pol ε and RNA pol II colocalised in cells as determined with immunoelectron microscopy. The interaction between pol ε and RNA pol II suggests that they are involved in a global regulation of transcription and DNA replication.

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17

Biles, Benjamin Daniel. "Family B DNA polymerases : applications to biotechnology and role in DNA repair." Thesis, University of Newcastle Upon Tyne, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413940.

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18

Jung, Guhung. "Structure-function analysis of PRD1 DNA polymerase; nucleotide sequence, overexpression and in vitro mutagenesis of the PRD1 DNA polymerase gene." Diss., The University of Arizona, 1989. http://hdl.handle.net/10150/184654.

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A small lipid-containing bacteriophage PRD1 specifies its own DNA polymerase which utilizes terminal protein as a primer for DNA synthesis. The PRD1 DNA polymerase gene has been sequenced and its amino acid sequence deduced. This protein-primed DNA polymerase consists of 553 amino acid residues with a calculated molecular weight of 63,300. Thus, it is the smallest DNA polymerase ever isolated from prokaryotic cells. Comparison of the PRD1 DNA polymerase with other DNA polymerases whose sequences have been published, yielded segmental but significant homologies. These results strongly suggest that many prokaryotic and eukaryotic DNA polymerase genes regardless of size have evolved from a common ancestral gene. The results further indicate that those DNA polymerases which use either an RNA or protein primer are related. We propose to classify DNA polymerases on the basis of their evolutionary relatedness. In order to overexpress PRD1 DNA polymerase in E. coli cells, the 2kb Hae II fragment was isolated from phage genomic DNA. This fragment was then cloned into pEMBLex3 expression vector. Phagemid pEMBLex3 contains lambda pR promoter and cI857 gene as a repressor. A specific 57 bp deletion was performed by using uracil containing ss DNA and oligonucleotide spanning each region to remove an unwanted non-coding region. After this deletion, the PRD1 DNA polymerase gene is totally under the control of the vector promoter and SD sequence. Upon heat induction, a protein with an apparent size of 68 kdal was overexpressed as an active PRD1 DNA polymerase. The expression of DNA polymerase was about 1% of total E. coli protein. The PRD1 DNA polymerase is a small multifunctional DNA polymerase and has three major conserved amino acid sequences which are shared among many DNA polymerases including human DNA polymerase alpha. Therefore, the PRD1 DNA polymerase provides an useful model system to study structure-function analysis of DNA polymerases. Four specific amino acid changes generated in conserved regions by the site-directed mutagenesis, in order to investigate their functional roles. Based on complementation test, three conserved regions are functional domains of PRD1 DNA polymerase.

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19

Fiala, Kevin Andrew. "A kinetic and biochemical approach to understanding the mechanisms of novel DNA polymerases." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187048005.

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20

Jozwiakowski, Stanislaw Konstanty. "Fidelity of eukaryotic and archaeal family-B DNA polymerases." Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1110.

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DNA polymerases are essential for replication, recombination and repair of DNA. However these enzymes have multiple applications in biotechnology. Since PCR has been developed, thermostable DNA polymerases have become important for numerous PCR based applications. Currently these enzymes are used routinely in laboratories all over the world. The fidelity of DNA polymerases is a key feature for PCR. We have developed a fidelity assay, based on a gapped plasmid template containing the lacZα gene reporter, allowing easy and straightforward measurement of the accuracy of DNA synthesis by DNA polymerases in vitro. Previous studies on the family-B DNA polymerase from Pyrococcus furiosus demonstrated that fidelity is controlled by D473, an amino acid located in the loop of the fingers domain. It was observed that the mutation D473G had a strong error-prone phenotype and Pfu-Pol D473G can be successfully used for random mutagenesis. To test if eukaryotic family-B DNA polymerases use the same aspartic acid residue to control fidelity we prepared the D799G mutant of a proteolytic fragment of polymerase epsilon from Saccharomyces cerevisiae. Unfortunately we did not observe the expected modulation of the fidelity of DNA synthesis for the D799G polymerase epsilon variant. Overexpression of the multi-subunit family-B DNA polymerases from Saccharomyces cerevisiae was found to be extremely demanding. Therefore, we decided to modify the thermostable family-B DNA polymerase from Thermococcus gorgonarius to obtain variants containing the loop region of the fingers domain from family-B DNA polymerases of Saccharomyces cerevisiae. We have observed no change in DNA synthesis accuracy when the loop region was transferred from high fidelity yeast replicative polymerase delta. However when the loop region was transferred from Saccharomyces cerevisiae error-prone family-B DNA polymerase zeta we observed a strong error-prone phenotype, in some instances, loop swapping with polymerase zeta is complicated by alignment ambiguity, so several variants were prepared. The primary sequence alignment of the fingers domain of eukaryotic polymerases zeta suggests no strong consensus within the loop region. Therefore, we decided to replace the major part of the fingers domain of the family-B polymerase from Thermococcus gorgonarius with the equivalent functional module from Saccharomyces cerevisiae polymerase zeta. The main aim of such a rearrangement was to test if the module from the error-prone DNA polymerase zeta has the potential to decrease fidelity. The chimeric polymerase variant was indeed found to be a very inaccurate DNA polymerase. To our surprise we also discovered that the polymerase variant possesses reverse transcriptase activity. Several further modifications allowed us to significantly improve reverse transcriptase activity of the chimeric polymerase variant.

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21

Gill, Sukhvinder. "Cren- and euryarchaeal DNA polymerases : interactions with deaminated bases." Thesis, University of Newcastle Upon Tyne, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.493030.

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The family B DNA polymerase from the euryarchaeote, Pyrococcus furiosus (PFU-Pol), has been shown to recognize template strand uracil and stall DNA synthesis four bases ahead, thus preventing the permanent fixation of the mutation. This recognition is due to the presence of a special pocket in the N-terminal domain of the enzyme. This study confirmed the recognition of hypoxanthine, the deaminated product of adenine, by PFU-Pol. Primer extension assays demonstrated that template strand hypoxanthine leads to stalling of DNA synthesis, four bases demonstrated that template strand hypoxanthine leads to stalling of DNA synthesis, four bases in front of the base, exactly the same position as seen for uracil.

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22

Curti, Elena. "Structure function studies of selected RNA and DNA polymerases." Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414158.

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23

Ong, Jennifer Lee. "Directed evolution of DNA polymerases with altered substrate specificities." Thesis, University of Cambridge, 2004. https://www.repository.cam.ac.uk/handle/1810/284037.

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Zurita, Leal Andrea Cristina. "Translesion DNA polymerases and genome maintenance in Trypanosoma brucei." Thesis, University of Glasgow, 2017. http://theses.gla.ac.uk/8897/.

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Many DNA repair pathways have been documented in Trypanosoma brucei but less attention has been paid to damage tolerance, a reaction in which lesion bypass is needed, in particular to ensure continued genome replication. Such bypass is promoted by translesion DNA polymerases (TLS Pols). T. brucei has ~15 TLS polymerases candidate genes, only two of which have been functionally examined to date. Understanding the roles provided by TLS Pols could reveal new aspects of T. brucei biology. Here, I examine the activities of TLS Pol Nu (PolN), TbPolZ and TbPolQ (HelQ) in bloodstream cells. RNAi against TbPolN results in slowed growth after ~24 hours, which is associated with altered DNA content, changed cell morphology and sensitivity to DNA damage. Surprisingly, growth and morphology defects are reduced after ~48 hours, without apparent RNAi reversion. In addition, depletion of the protein seems to lead to an aberrant distribution of the chromosomes, as visualised by telomere fluorescent in situ hybridization. TbPolN epitope tagging demonstrates a discrete localisation of the protein at the periphery of the nucleus in the absence of damage, with a more widespread, but non-uniform localisation after damage. EdU labelling and γH2A analysis after TbPolN knockdown reveal a decrease in proliferating cells, which accumulate nuclear DNA damage. Finally, we show that TbPolN interacts with a nuclear putative non-canonical PolyA polymerase. Taken together, these data suggest TbPolN may be involved in T. brucei nuclear DNA maintenance. RNAi of TbPolZ (zeta) did not impair growth but resulted in increased sensitivity to methyl methanesulphonate (MMS) damage and UV radiation, suggesting a possible role in the response against both genotoxic agents. Generation of TbPolZ null mutants confirmed that the protein is non-essential and plays a role in genotoxic damage repair. Surprisingly, TbPolZ epitope tagging not only showed a nuclear signal, but a mitochondrial signal was also detected. These data were supported by immunoprecipitation, where mitochondrial proteins were obtained as potential interaction partners. These data suggest a contribution of TbPolZ to both nuclear and kinetoplast genome maintenance. Targeted RNAi of the third putative TLS-related factor, TbHelQ, was unsuccessful. Despite this, sequence analysis of the protein indicates that its current annotation as a PolQ homologue is inaccurate, since the predicted protein is not a joint polymerase-helicase like in other eukaryotes, but only a putative helicase. Hence, it is suggested it should be renamed TbHelQ. Immunoprecipitation and colocalisation analyses indicate a possible role of TbHelQ in homologous recombination, given the potential interaction of the factor with BRCA2 and other factors involved in this repair process. Notably, the predicted interactome of TbHelQ differs from that of TbPolN, suggesting discrete functions in T. brucei. Taken together, these data reveal widespread and variant functions of three putative TLS DNA polymerases in the parasite genome biology, suggesting a possible role in the maintenance of genome integrity in T. brucei.

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Li, Jian. "Mechanism of DNA Homologous Recombination through Studies of DNA Sliding Clamps, Clamp Loaders, and DNA Polymerases." Ohio University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1374835449.

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rob, abdur. "Protein-Nucleic Acid Interactions in Nuclease and Polymerases." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/chemistry_diss/54.

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DNA polymerase binds to the double stranded DNA and extends the primer strand by adding deoxyribonucletide to the 3’-end. Several reactions in the polymerase active site have been reported by Kornberg in addition to the polymerization. We observed DNA polymerase I can act as a pyrophosphatase and hydrolyze deoxyribonucletide. In performing the pyrophosphatase activity, DNA polymerase I requires to interact with RNA. RNA in general, was found to activate the DNA polymerase I as pyrophosphatase. This hydrolysis causes depletion of dNTP and inhibits DNA polymeration synthesis in vitro. In this RNA-dependent catalysis, DNA polymerase I catalyzes only dNTP but not rNTP. We have also observed that many other DNA polymerases have this type of the RNA-dependent pyrophosphatase activity. Our experimental data suggest that the exonuclease active sites most likely play the critical role in this RNA-dependent dNTP hydrolysis, which might have a broader impact on biological systems. On the basis of the crystal structure of a ternary complex of RNase H (Bacillus halodurans), DNA, and RNA, we have introduced the selenium modification at the 6-position of guanine (G) by replacing the oxygen (SeG). The SeG has been incorporated into DNA (6 nt. - 6 nucleotides) by solid phase synthesis. The crystal structure and biochemical studies with the modified SeG-DNA indicate that the SeDNA can base-pair with the RNA substrate and serve as a template for the RNA hydrolysis. In the crystal structure, it has been observed that the selenium introduction causes shifting (or unwinding) of the G-C base pair by 0.3 Å. Furthermore, the Se-modification can significately enhance the phosphate backbone cleavage (over 1000 fold) of the RNA substrate, although the modifications are remotely located on the DNA bases. This enhancement in the catalytic step is probably attributed to the unwinding of the local duplex, which shifts scissile phosphate bond towards the enzyme active site. Our structural, kinetic and thermodynamic investigations suggest a novel mechanism of RNase H catalysis, which was revealed by the atom-specific selenium modification.

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27

Sikorsky, Jan A. "Effect of DNA base modification on polymerase chain reaction efficiency and fidelity." Huntington, WV : [Marshall University Libraries], 2005. http://www.marshall.edu/etd/descript.asp?ref=554.

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28

Rangarajan, Subhashree Friedman Simon H. "Design, synthesis and evaluation of new intercalator analogs targeting human telomerase." Diss., UMK access, 2006.

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Thesis (Ph. D.)--School of Pharmacy and Dept. of Chemistry. University of Missouri--Kansas City, 2006.
"A dissertation in pharmaceutical science and chemistry." Advisor: Simon H. Friedman. Typescript. Vita. Description based on contents viewed Nov. 9, 2007; title from "catalog record" of the print edition. Includes bibliographical references (leaves 292-317). Online version of the print edition.

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29

Yunnan, Jiang. "Testing the occurrence of forward hyper-translocation during the promoter escape transition / Jiang Yunnan." Connect to online version, 2009. http://ada.mtholyoke.edu/setr/websrc/pdfs/www/2009/381.pdf.

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30

Sherrer, Shanen Michelle. "Mutagenic and Kinetic Effects of Various DNA Lesions on DNA Polymerization Catalyzed by Y-Family DNA Polymerases." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1313178275.

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31

Showalter, Alexander Keith. "KINETIC STUDIES OF TWO ERROR-PRONE DNA REPAIR ENZYMES: POSSIBLE MECHANISMS FOR VIRAL MUTAGENESIS." Connect to this title online, 2002. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1016207119.

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Thesis (Ph. D.)--Ohio State University, 2002.
Title from first page of PDF file. Document formatted into pages; contains xii, 97 p.; also contains graphics (some col.). Includes abstract and vita. Advisor: Ming-Daw Tsai, Dept. of Chemistry. Includes bibliographical references (p. 92-97).

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32

Bergen, Konrad [Verfasser]. "Structural insights into DNA polymerases encountering aberrant substrates / Konrad Bergen." Konstanz : Bibliothek der Universität Konstanz, 2015. http://d-nb.info/1078230455/34.

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33

Cozens, Christopher. "An adaptive path from DNA to RNA and ANA polymerases." Thesis, University of Cambridge, 2012. https://www.repository.cam.ac.uk/handle/1810/252281.

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34

Kinsman, Thomas Stephen. "Processivity and thermostability of archaeal DNA polymerases : application in PCR." Thesis, University of Newcastle upon Tyne, 2014. http://hdl.handle.net/10443/2606.

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The polymerase chain reaction (PCR) is one of the most widely used techniques in the biosciences, and has found extensive use in a variety of processes including gene cloning and mutagenesis. The PCR requires the use of a thermostable DNA polymerase that is able to tolerate the multiple heat/cool steps that occur during each cycle of the reaction. Archaeal family B DNA polymerases have found extensive use in this process, as in addition to their high thermostability they also contain a 3’-5’ exonuclease or proofreading activity, which increases the fidelity of replication. A polymerase that exhibits high processivity, defined as the number of nucleotides added per association with the DNA, is also desirable from a commercial perspective as it will reduce the amount of time taken to replicate any given amplicon. In this thesis, the processivity of a variety of commercially available archaeal Pol B enzymes is determined, which reveals significant differences in the processivity of polymerases closely related in sequence. The PCR performance of Pfu-Pol and Tkod-Pol, representing poorly and highly processive enzymes respectively is investigated, which reveals that Tkod-Pol is less efficient at replicating long amplicons (> 1000 bp) than Pfu-Pol, attributed to the increased thermostability of the latter. Based on this observation, an attempt is made to enhance the processivity of Pfu-Pol to improve the PCR performance of this enzyme.

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35

Henfrey, R. D. "In vitro transcription of exogenous plant DNA." Thesis, University of Hertfordshire, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.381604.

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36

Kim, Hong-Yeoul Carleton University Dissertation Biology. "Determinants of the E. coli polymerase I- independent and polymerase I- dependent pathways of replication of an incompatibility N group plasmid replicon." Ottawa, 1993.

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37

Chun, Chiu-shun, and 秦超舜. "REV7-mediated polyubiquitination and degration of human REV1." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B42841343.

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38

Bhattacharjee, Sonali. "The role of Fml1 and its partner proteins Mhf1 and Mhf2 in promoting genome stability." Thesis, University of Oxford, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.711640.

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39

Chun, Chiu-shun. "REV7-mediated polyubiquitination and degration of human REV1." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B42841343.

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40

Johnson, Allison Anne. "Fidelity of replication by the mitochondrial DNA polymerase and toxicity of nucleoside analogs /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004298.

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41

Holzberger, Bastian [Verfasser]. "From Multi-fluorinated DNA Polymerases to Insights into DNA Synthesis by NMR spectroscopy / Bastian Holzberger." Konstanz : Bibliothek der Universität Konstanz, 2012. http://d-nb.info/1026847125/34.

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42

Bakhtina, Marina M. "Application of chemical probes to study the kinetic mechanism of DNA polymerases." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1148915981.

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43

Cooper, Christopher D. O. "Isolation and characterisation of a novel archaeal DNA polymerase." Thesis, University of Oxford, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.589621.

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DNA replication is a key process required by organisms during cell division, with a concomitant requirement for genome synthesis by DNA polymerases. Biotechnological exploitation of thermostable DNA polymerases for DNA amplification by the Polymerase Chain Reaction (PCR), provides a significant market for novel enzymes or those with improved properties. An approach was taken to isolate alternative thermostable DNA polymerases, by enriching thermophilic bacteria from a novel thermal environment, aerobically spoiling silage. In addition, a novel DNA polymerase (Abr polBl) was cloned from the thermoacidophilic archaeon, Acidianus brierleyi, with the intention of characterising its in vivo role and application to PCR. Protein sequence analysis suggested a proofreading (high fidelity) DNA synthesis activity most related to polBl DNA polymerases from Crenarchaeota. Abr polBl was heterologously expressed in bacteria and protein purified to homogeneity. Biochemical assays confirmed high-temperature DNA polymerase and 3'-5'exonuclease activities of Abr polBl, with an accompanying proofreading ability. Sequence analysis, processivity, strand displacement and lesion bypass activities indicated potential roles in genome replication and DNA repair. Abr polBl could not amplify DNA under a range of PCR conditions, presumably following its low intrinsic thermostability. Biophysical analyses confirmed irreversible unfolding of Abr polBl at temperatures required for PCR. Supplementation with organic compounds and ionic salts stabilised Abr polBl, promoting retention of conformational stability and DNA synthesis activity following thermal incubation, but could not promote DNA amplification with Abr polB 1.

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44

Nayak, Dhananjaya. "Conformational mechanisms in T7 RNA polymerase transcription a dissertation /." San Antonio : UTHSC, 2008. http://learningobjects.library.uthscsa.edu/cdm4/item_viewer.php?CISOROOT=/theses&CISOPTR=44&CISOBOX=1&REC=11.

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45

Chiu, Joyce Biotechnology &amp Biomolecular Sciences Faculty of Science UNSW. "Protein engineering of DNA polymerase I: thioredoxin dependent processivity." Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Sciences, 2005. http://handle.unsw.edu.au/1959.4/23077.

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DNA polymerases are found in a diverse range of organisms, prokaryotes, eukaryotes, viruses and bacteriophage. T7 DNA polymerase is a replicative enzyme from E. coli bacteriophage T7. It relies on the thioredoxin binding domain (TBD) of phage gene 5 protein (gp5) and E. coli thioredoxin (Trx) for processive replication of phage DNA. Although T7 DNA polymerase is processive, it is also thermolabile. In order to design a thermostable and processive DNA polymerase, the structural stabilities of the TBD and Trx were studied in respect to their binding affinity and affect on enzyme processivity. An artificial operon was designed for coexpression of subunits of T7 DNA polymerase. By means of a 9??His-tag at the amino terminus of gp5, T7 DNA polymerase complex was purified by one-step nickel-agarose chromatography, with subunits gp5 and Trx co-eluting in a one to one molar ratio. Purified T7 DNA polymerase was assayed for polymerase activity, processivity and residual activity and compared to the commercial T7 DNA polymerase. The two enzymes were not identical with commercial T7 DNA polymerase being less processive at 37??C. Mass spectrometry of the two enzymes identified a mutation of Phe102 to Ser in the Trx subunit (TrxS102) of commercial T7 DNA polymerase. The Ser102 mutation, was found near the carboxyl terminal helix of Trx. TrxS102 was less stable than wild type Trx. In the study of the TBD structural stability, a hybrid polymerase was constructed by inserting the TBD motif into the homologous position in the Stoffel fragment of Taq DNA polymerase. The hybrid enzyme was coexpressed with Trx from an artificial operon; however, the TBD inserted retained a mesophilic binding affinity to Trx. The chimeric polymerase required 100 molar excess of Trx for processive polymerase activity at 60??C. TBD structural deformation at elevated temperatures was hypothesized to be the cause of the change in the subunit stoichiometry. Mutagenesis of TBD would be required to increase its thermostability. An efficient, rapid high throughput mutagenesis method (SLIM) was invented and would be appropriate for further studies.

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46

Newmister, Sean Alexander. "Purification and characterization of novel X and Y-family DNA polymerases." Connect to resource, 2007. http://hdl.handle.net/1811/28381.

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Thesis (Honors)--Ohio State University, 2007.
Title from first page of PDF file. Document formatted into pages: contains 29 p.; also includes graphics. Includes bibliographical references (p. 28-29). Available online via Ohio State University's Knowledge Bank.

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47

Richardson, Tomas Takuyoshi. "Recognition of, and response to, deaminated bases by archaeal DNA polymerases." Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1357.

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The archaea comprise one of the three domains of life and are often characterised by a propensity for physically- and geochemically-extreme environments. Under such conditions spontaneous DNA deamination events, which ordinarily occur at stochastically insignificant rates, increase in frequency to the point where specialised recognition pathways are required to maintain genomic stability. Archaeal DNA polymerases are unique in their capacity to recognise and respond to deaminated bases, such as uracil and hypoxanthine. For example, the family B DNA polymerases of archaea possess a well-characterised uracil-binding pocket, which, helps prevent replicative bypass of deaminated bases and thus proliferation of fixed mutations. This thesis aims to elucidate additional features of the deaminated base recognition pathways of archaeal DNA polymerases. Here we present studies that concern both the family B and more enigmatic family D DNA polymerases of archaea. Methods employed for investigation of these enzymes include mobility shift assays, targeted mutagenesis, primer extension, exonuclease and uracil-DNA glycosylase assays, as well as time-resolved and steady-state fluorescence analysis. Furthermore, through genetic manipulation of Thermococcus kodakarensis, this work seeks to address previously unanswered questions regarding DNA replication and repair in the archaea. The in vivo studies of deaminated base recognition presented in chapter 5 raise intriguing questions about fundamental aspects of the molecular and cellular biology of archaea.

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48

Ivanova, Iglika Gencheva. "Single stranded DNA re-synthesis at uncapped telomeres requires replication polymerases." Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1338.

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Telomeres are specialised DNA-protein structures capping or protecting the chromosome ends fromshortening,degradation and fusions. Telomere uncapping occurs when some of the proteins associated with telomeres lose their integrity. For example in yeast a point mutation in the gene encoding the telomere binding protein Cdc13called cdc13-1,leads to conditional telomere uncapping at temperatures above 26º C. In this thesis I have utilised the cdc13-1model system to study repair after telomere uncapping. De-protection of the telomere triggers resection of the AC rich strand in 5’ to 3’ direction and formation of single stranded DNA(ssDNA). Checkpoint proteins are readily recruited to the damage and halt the cell cycle. However nossDNA re-synthesishas been observed in cdc13-1cells with uncapped telomeres. Here I will show that the ssDNA damage in cdc13-1cells recruits polymerase α,εandδand the clamp PCNA but in normal circumstancesefficientrepair is not observed. Only when telomeres are recapped the ssDNA could be re-synthesisedand this depended on the polymerase δsubunit Pol32 but did not require the non-essential subunits Dpb3 and Dpb4from polymerase ε. Interestingly, ssDNA re-synthesisat uncapped telomeres could be stimulatedthroughmild osmotic pressureand required both polymerase δand ε. Furthermore mild osmotic pressurecould also rescue cells damaged with methyl methanesulfonate but not with UV light or hydroxyurea. My data suggeststhat single stranded DNA re-synthesis may bespecifically inhibited or compete with resection when telomeres are uncapped and that osmotic pressurestimulated re-synthesisby regulating polymerases α, εand/or δ.

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49

Firth, Andrew Graeme. "Synthesis and Characterisation of Fluorescent RibonucleotideSubstrates for DNA Dependent RNA Polymerases." Thesis, University of York, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507614.

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50

Jarosz, Daniel F. "Novel function and regulation of mutagenic DNA polymerases in Escherichia coli." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/39742.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2007.
Vita.
Includes bibliographical references.
The observation that mutations in the Escherichia coli genes umuC+ and umuD+ abolish mutagenesis induced by UV-light strongly supported the counterintuitive notion that such mutagenesis is an active rather than passive process. Biochemical studies have revealed that umuC+ and its homolog dinB+ encode novel, low to moderate fidelity DNA polymerases with the ability to catalyze synthesis on imperfect DNA templates in a process termed translesion synthesis (TLS). Similar enzymes exist in nearly all organisms, constituting the Y-superfamily of DNA polymerases. Although DinB is the only Y-family DNA polymerase conserved among all domains of life, its precise function has remained elusive. Here we show that AdinB E. coli strains are sensitive to DNA damaging agents that form lesions at the N2 position of guanine. In vitro bypass studies of an N2-guanine adduct by DinB demonstrate considerable preference for correct nucleotide insertion and an increased catalytic proficiency on the lesion-bearing template relative to undamaged DNA. Moreover, DinB and its mammalian and archaeal orthologs possess similar substrate specificities. Mutation of a single residue in the active site ofE. coli DinB suggests that its enhanced activity is coupled to lesion recognition and that its TLS function is required for resistance to DNA damaging agents in vivo.
(cont.) Regulation of the mutagenic potential of DinB is critical for maintenance of genomic integrity. We present evidence indicating that abortive TLS products generated by a DinB variant are subject to the proofreading function of DNA polymerase III. Moreover, both the TLS activity and -1 frameshift mutator potential of DinB are modulated in a highly sophisticated manner by the DNA damage-inducible proteins RecA and UmuD2. These biochemical data, coupled with genetic analyses and molecular modeling, indicate that DinB is a specialized and remarkably controlled translesion DNA polymerase. In addition, we present evidence that the umuC+participates in several novel biological functions in addition to its established role in TLS. A novel umuC gain-of-function allele confers striking resistance to hydroxyurea and umuC+ mediates the expression of genes and physiological responses under conditions of SOS induction. Taken together, these observations hint at at a largely uncharacterized function of Y-family polymerases in sculpting physiological responses, including active mechanisms of cell death, in response to environmental stress.
by Daniel F. Jarosz.
Ph.D.

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