Dissertations / Theses: 'DNA. RNA'

1

Buttner, M. "RNA polymerase - DNA interactions in Streptomyces." Thesis, University of Bristol, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.354445.

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2

Nandakumar, Jayakrishnan. "Discrimination of RNA versus DNA by an RNA ligase and distinct modes of substrate recognition by DNA ligases /." Access full-text from WCMC:, 2007. http://proquest.umi.com/pqdweb?did=1428838891&sid=13&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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Antson, Dan-Oscar. "Genotyping RNA and DNA using padlock probes." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5057-1/.

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Gilea, Manuela Aurora. "DNA and RNA synthesis in ionic liquids." Thesis, Queen's University Belfast, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485198.

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The solid-phase synthesis of oligonucleotide derivatives such as phosphorothioates and phosphoroselenoates was investigated. Some ionic liquids containing the trlbexyl(tetradecyl)phosphonium cation and various anions proved to be very effective in dissolving the chalcogens (sulfur and , selenium) and to prepare oligonucleoside chalcogenophosphates. The suitability ofionic liquid-based chalcogen-transfer mixtures for the synthesis of oligonucleoside chalcogenophosphates on solid-phase was evaluated and subsequently the structure-activity relationship studied in detail. The compatibility of ionic liquid-based chalcogen-transfer mixtures with diverse types of solid supports e.g. controlled-pore glass, poly(vinylacetate) and. different synthetic methods. e.g. phosphoramidite and H-phosphonate method makes them useful as replacement of the more expensive and relatively unstable commerciaily avai1able chalcogen-transfer reagents. The distillation of ionic liquids was also studied.

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Zhu, Jian. "The stabilities of RNA and DNA structural elements." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/25194.

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Hill, G. R. "NMR studies of DNA and RNA binding proteins." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604060.

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HMG-D is a 112-residue, non-histone chromosomal protein from Drosophila melanogaster and is a member of the class of non-sequence specific HMGB proteins. The present project was based on the observation that other HMGB complexes that had been solved by NMR had a phenylalanine residue at a key interfacial location (corresponding to position 12 in HMG-D), whereas those like HMG-D that gave few intermolecular NOE cross peaks generally had a tyrosine at this location. This tyrosine was known to be involved in hydrogen-bonding to the DNA in a related complex that had been solved crystallographically. The Y12F mutant of full-length HMG-D was expressed and purified in isotope-labelled form suitable for NMR spectroscopy, and a set of multidimensional triple resonance experiments used to derive assignments for the backbond resonances of the protein both free and in complex with the dA₂bulge DNA. Sidechain assignments for the protein were obtained by a combination of “CCH”-transfer-based experiments and NOE spectra, while nearly complete assignments for the DNA in the complex were obtained from a combination of homonuclear 2D NOESY and TOCSY experiments together with filtered NOESY experiments where just cross peaks between protons both of which were not coupled to heteronuclei were selected. Filtered NOESY-based experiments were used to observe intermolecular NOE cross peaks in isolation, and, in contrast to the case of the wild-type complex, these experiments yielded around 50 intermolecular interactions. Together with an extensive set of assigned intramolecular NOE constraints, these formed the basis for a calculation of the structure of the complex starting from random conformations of both protein and DNA chains, which resulted in an NMR structure for the complex that had good precision over the structured region (residues 3-70 of the protein and stem 1 of the DNA).

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O'Hanlon, Karen Ann. "Studies on the enzyme DNA-dependent RNA polymerase." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266340.

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8

Pritchard, Hannah Louise. "Recognition agents for DNA and RNA quadruplex structures." Thesis, University of Birmingham, 2015. http://etheses.bham.ac.uk//id/eprint/5727/.

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The design and synthesis of a new class of G-quadruplex DNA recognition agents are discussed in this thesis along with their binding abilities to both duplex and G-quadruplex forming DNA. A selection of G-quadruplex binders reported in the literature to date have been reviewed and their interactions with the quadruplex DNA structure analysed. The biisoquinoline ligand used to incorporate into the metal complexes synthesised in this thesis was chosen because of its large aromatic surface area which is ideal for end stacking onto G-quartets. Both the palladium and platinum biisoquinoline complexes bind to quadruplex forming DNA, monitored by UV-vis and circular dichroism. The platinum complex has the most promising DNA binding results showing a selectivity for quadruplex DNA over duplex DNA when examined by gel electrophoresis. Biisoquinoline complex interactions with RNA G-quadruplexes have been investigated to make comparisons of that with DNA. The palladium complex binds less well to parallel quadruplex conformers suggesting its mode of interaction differs from that of the platinum complex. A toxicity assay against two cancer cell lines showed the platinum and palladium complexes to have IC\(_{50}\) values in the nM range. Modifications to the biisoquinoline structure were also attempted in order increase the specificity of the complex to G-quadruplexes by incorporating components that could interact with the quadruplex loops.

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Cramer, Janina. "Funktionelle Charakterisierung der RNA-abhängigen RNA-Polymerase des Hepatitis-C-Virus Untersuchung molekularer Mechanismen der Substratspezifität von DNA-abhängigen DNA-Polymerasen /." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=971700796.

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Daniel, Laurianne. "Human Ribosomal DNA and RNA Polymerase I Fate during UV-induced DNA Repair." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1093/document.

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La réparation par excision de nucléotides (NER) garantit l'intégrité du génome lors de l'exposition aux rayons UV. Après irradiation aux UV, un des premiers problèmes rencontrés par la cellule est l'arrêt général de la transcription dû au blocage de l'ARN polymérase II (ARNP2) au niveau des lésions UV. Pour régler ce problème, le NER possède une voie de réparation spécifiquement couplée à la transcription (TCR). Les connaissances concernant le NER ont été obtenu via des études sur la transcription par l'ARNP2. Cependant, dans les cellules à fort métabolisme, plus de 60% de la transcription correspond à la transcription, dans le nucléole, de l'ADN ribosomique (ADNr) par l'ARN polymérase I (ARNP1). De nombreuses protéines sont absence du nucléole, c'est pourquoi certains processus nucléaires ne peuvent avoir lieu dans cette structure. Afin d ‘être répliqué et réparé, l'ADNr se déplace à la périphérie du nucléole. Malgré l'importance de la transcription par l'ARNP1, la réparation de l'ADNr a été peu étudiée chez l'homme. De plus, à notre connaissance, aucune étude ne s'est penchée sur le mécanisme moléculaire du déplacement de l'ADNr à la périphérie du nucléole. Notre étude démontre l'implication de la TCR dans la réparation de l'ADNr après lésions UV induites. De plus, nos recherches ont démontré que l'ARNP1 reste accrochée à l'ADNr et sont tous les deux délocalisés à la périphérie du nucléole après irradiation aux UV. Enfin, nous avons identifié l'actin et la moysine I nucléaires comme facteurs protéiques nécessaire à cette délocalisation
Nucleotide excision repair (NER) guarantees genome integrity and proper cellular functions against UV-induced DNA damage. After UV irradiation, one of the first burden cells have to cope with is a general transcriptional block caused by the stalling of RNA polymerase II (RNAP2) onto distorting UV lesions. To insure UV lesions repair specifically on transcribed genes, NER is coupled with transcription in an extremely organized pathway known as Transcription-Coupled Repair (TCR). Most of the knowledge about TCR has been gathered from RNAP2 transcription. However, in highly metabolic cells, more than 60% of total cellular transcription results from ribosomal DNA (rDNA) transcription, by the RNA polymerase I (RNAP1), which takes place in the nucleolus. Many nuclear proteins are excluded from the nucleolus and because of this some nucleolar processes cannot occur inside this structure. In order to be replicated and repaired rDNAs need to be displaced at the nucleolar periphery. Despite the importance of RNAP1 transcription, repair of the mammalian transcribed rDNA has been scarcely studied. Moreover, to the best of our knowledge no molecular mechanism has been proposed for rDNA displacement. Our study clearly demonstrated that the full TCR machinery is needed to repair UV-damaged rDNA and restart RNAP1 transcription. Our results show that UV lesions block RNAP1 transcription and that RNAP1 is firmly stalled onto rDNAs without being degraded. Our study also describes the displacement of the RNAP1/rDNA complex to the nucleolar periphery after UV irradiation and identifies both nuclear ß-actin and nuclear myosin I as factors required for this displacement

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Mondal, Tanmoy. "Epigenetic Regulation by Noncoding RNA." Doctoral thesis, Uppsala universitet, Genomik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-160326.

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High throughput transcriptomic analyses have realized us with the fact that eukaryotic genome encodes thousands of noncoding RNAs (ncRNAs) with unknown function. In my thesis, I sought to address epigenetic regulation of transcription by ncRNA using the Kcnq1 imprinted cluster as a model system. Genomic imprinting is an epigenetic phenomenon whereby one of the parental alleles is silenced by epigenetic mechanism in a parent of origin-specific manner. A long ncRNA Kcnq1ot1 regulates imprinting of nearly 8 protein coding genes in the Kcnq1 imprinted cluster. Expression of Kcnq1ot1 is restricted to the paternal chromosome while that of protein-coding genes to the maternal chromosome. Kcnq1ot1 is a 91kb long, moderately stable, nuclear localized and RNAPII encoded transcript. We demonstrated that Kcnq1ot1 RNA itself mediates lineage specific silencing on the paternal chromosome by interacting with chromatin and recruiting the repressive chromatin modifiers to the imprinted gene promoters. Previously we identified an 890bp silencing domain (SD) at the 5´end of the Kcnq1ot1 RNA which is responsible for gene silencing. Targeted deletion of the 890SD in mouse resulted in specific loss of silencing of ubiquitously imprinted genes. We have further shown that Kcnq1ot1 interacts with Dnmt1 and recruit Dnmt1 at the somatic DMRs flanking some of the ubiquitously imprinted genes. We next addressed the stability of the Kcnq1ot1 mediated epigenetic silencing using transgenic mouse where we have conditionally deleted the Kcnq1ot1 RNA at different developmental stages and we found that Kcnq1ot1 RNA is required to maintain the silencing of the ubiquitously imprinted genes. In addition, DNA methylation, which controls imprinting of the ubiquitous genes require Kcnq1ot1 for its maintenance. To characterize the ncRNAs that mediate gene regulation through chromatin interaction we have isolated chromatin associated RNAs (CARs) from sucrose gradient fractioned chromatin. High-throughput sequencing of the CARs resulted in the identification of the 141 intronic and 74 intergenic regions harboring CARs. We characterized one of the intergenic CARs which regulate the transcription of the two neighboring genes by modulating the chromatin marks. In summary current thesis has uncovered unprecedented role of ncRNAs in gene expression via chromatin level regulation.

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Jia, Yiping. "Mechanistic studies of DNA-dependent transcription initiation and RNA synthesis by bacteriophage T7 RNA polymerase /." The Ohio State University, 1998. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487953204281995.

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13

Acharya, Sandipta. "Some Aspects of Physicochemical Properties of DNA and RNA." Doctoral thesis, Uppsala University, Department of Bioorganic Chemistry, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6741.

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This thesis is based on nine research publications (I – IX) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, pK_a values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. Papers I – II showed that the ionization of 2'-OH group is nucleobase-dependant. Paper III showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. Papers IV – VI show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. Paper VII showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. Paper VIII showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. Paper IX showed that the pK_a values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.

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Orban, Mathias. "Die Verteilung transkribierender RNA-Polymerase I auf ribosomaler DNA." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-159198.

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15

Ott, Reina Kristina. "Künstliche Nucleasen - Spaltung von DNA und RNA durch Übergangsmetallkomplexe." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=962774057.

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Tetzlaff, Charles N. "Synthesis and evaluation of acylated DNA and RNA oligomers /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2001.

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Thesis (Ph.D.)--Tufts University, 2001.
Adviser: Clemens Richert. Submitted to the Dept. of Chemistry. Includes bibliographical references (leaves 228-235). Access restricted to members of the Tufts University community. Also available via the World Wide Web;

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17

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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Singh, Shivani Shatrughana. "RNA polymerase-DNA interactions at complex gene regulatory regions." Thesis, University of Birmingham, 2014. http://etheses.bham.ac.uk//id/eprint/4877/.

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RNA polymerase (RNAP) \(\sigma\) factor must recognise and bind to specific DNA elements, usually AT-rich, in order to initiate transcription. At AT-rich regulatory regions or with more than one \(\sigma\) factor binding site; RNAP has to distinguish between different targets to initiate transcription correctly. At two regulatory regions: i) cbpA regulatory DNA with overlapping binding sites for \(\sigma\)70 and 38 associated RNAP and ii) regulatory region for ehxCABD operon with AT content of 71 %, I examined how correct RNAP binding is ensured. For cbpA regulatory region it was found that the shared promoter spacer region played a key role. I identified a location in spacer region that differently affected overlapping cbpA promoters. The base change at this position is sensed by \(\sigma\)70 side chain R451. Alterations in spacer sequence modulate conformation, making it easier, or more difficult, for R451-DNA interactions. Using tethered particle motion analysis, DNA compaction properties of cbpA gene product; CbpA was measured. ehxCABD regulatory region contains many sequences resembling \(\sigma\) factor binding elements. RNAP is capable of binding to the correct promoter elements in this region only in the presence of a chromosome folding protein, H-NS which binds AT-rich DNA. H-NS “coats” ehxCABD regulatory region and enables specific RNAP binding. Finally, many intragenic promoters within ehxCABD operon were identified. We thus propose that H-NS plays a role in silencing this pervasive intragenic transcription.

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Taylor, Laura Margaret. "Aspects of RNA directed DNA methylation in Arabidopsis thaliana." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648263.

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Jeynes, Jonathan Charles Gwilym. "Single walled carbon nanotubes functionalised with RNA or DNA." Thesis, University of Surrey, 2007. http://epubs.surrey.ac.uk/843911/.

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Within this thesis, many building blocks that are necessary to fabricate nano-scale biotechnology devices are examined. In this rapidly expanding field, carbon nanotubes (CNTs) have been identified as a key component. In particular, the biomedical applications of CNTs functionalised with DNA or RNA, utilising dielectrophoresis as a nano-manipulating tool, is investigated. The use of RNA and RNase A to generate chemically unmodified and pure single walled CNTs in a simple two step procedure is described. RNA is shown to efficiently wrap and solubilise CNTs while RNase effectively strips the RNA from the CNT, providing a convenient purification technique. The mechanism of binding of DNA to carbon nanotubes (CNTs) is shown to be much more efficient when the DNA is single-stranded rather than a double-stranded helix, while parameters (e.g. pH) are optimised for the most efficient CNT solubilisation with RNA. The compatibility of RNA-CNT composites with mammalian cells in tissue culture is also investigated. Flow cytometry and confocal microscopy show it is highly likely that RNA-CNTs composites are internalised into mammalian cells, while laser heating did not effectively kill cells. This is presumably because the power was too low or not enough CNTs were internalised in the cells. DNA-CNT composites are used to electrically sense the binding of biomolecules which have been trapped between micro-electrodes by dielectrophoresis. In a fluid cell, it is shown that solutions affect the flow of current through the CNTs, as an ionic solution increases the resistance in relation to deionised water, whereas with no CNTs, the opposite is true. Moreover, a rise in the resistance is also seen as proteins bind to CNTs. The nano-manipulation of DNA was studied with dielectrophoresis. It is shown that poly(dG)-poly(dC) (GC) collects at higher frequencies than poly(dA)-poly(dT) (AT) indicating that GC is a better conductor than AT. It was also found that different lengths of DNA polarise at about the same frequency, while shorter lengths need a higher field intensity to trap them.

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Antonopoulos, Ioanna H. "CHARACTERIZING RNA TRANSCRIPTION AND DNA REPLICATION VIA RAMAN CRYSTALLOGRAPHY." Case Western Reserve University School of Graduate Studies / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=case1428076280.

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Sfyrakis, Konstantinos. "Computer simulation and advanced visualisation of DNA." Thesis, University of Surrey, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368378.

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Pan, Hu. "Structural and biochemical studies of DNA primase from Bacillus stearothermophilus." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302122.

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Zhang, Zhouwei. "Investigation of DNA and RNA markers by novel technologies demonstrates DNA content intratumoral heterogeneity and long non-coding RNA aberrations in breast tumors." ScholarWorks @ UVM, 2014. https://scholarworks.uvm.edu/graddis/323.

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BACKGROUND: Breast cancer is the most commonly diagnosed cancer and second leading cancer death cause among females in the U.S.A. About 1 in 8 women in U.S will develop invasive breast cancer over the course of her lifetime. In 2013, 234,580 new invasive breast cancer cases are expected to occur in women within the US and approximately 64,640 non-invasive carcinomas in situ were diagnosed in 2013, most of which were ductal carcinoma in situ (DCIS). Along with technological advances, a wide variety of candidate biomarkers have been proposed for cancer diagnosis and prognosis, including DNA content and non-coding RNA. Current techniques for detecting DNA content abnormalities in formalin-fixed, paraffin-embedded (FFPE) tissue samples by flow cytometric analysis have used cells recovered from ≥50Âµm whole tissue sections. Here, in our first study, a novel core punch sampling method was investigated for assessing DNA content abnormalities and intratumoral heterogeneity in FFPE specimens. Secondly, long non-coding RNAs (lncRNAs) has been examined. LncRNA participates in a broad spectrum of biological activities by diverse mechanisms and its dysregulation is associated with tumorgenesis. Some lncRNAs may function as oncogenes (O) and others as tumor suppressor genes (TSG). To date, lncRNA has been investigated primarily by qRT-PCR and RNA sequencing. This study has examined the relationship of lncRNA expression patterns to breast tumor pathology by chromogenic in situ hybridization (CISH). METHODS: Firstly, FFPE breast carcinoma specimens were selectively targeted using 1.0 mm diameter punch needles. Extracted cores were assayed by flow cytometry using a modified-Headley method. Secondly, the lncRNA expression levels of 6 lncRNAs: HOTAIR, H19, KCNQ1OT1, MEG3, MALAT11 and Zfas1, was examined by RNAscope® CISH using FFPE breast tissue microarrays (TMAs) comprising normal adjacent epithelia (NA), DCIS, and invasive carcinoma (IC) from 46 patients. LncRNA associate polycomb complex protein EZH2 was evaluated by immunohistochemistry (IHC). LncRNA data was also compared to standard breast tumor data including ER, PR, Her2 and Ki67 IHC. SYSTAT version 11 statistical package was used to perform for all the tests. RESULTS: Following optimization experiments of the core punch flow cytometric approach, DNA index and percent S-phase fraction intratumoral heterogeneities were detected in 10/23 (44%) and 11/23 (47%) specimens respectively. The lncRNA CISH study utilized a TMA that contained 36 spots of NA breast tissues, 34 DCIS spots and 43 IC spots. HOTAIR CISH staining was significantly stronger in IC than DCIS (p CONCLUSION: Core-punching is an effective alternative to whole specimen sectioning and shows that macro-level genomic heterogeneity is common even within a single FFPE block. The interrelationship of DNA content heterogeneity to other forms of heterogeneity requires further study. RNAscope CISH supports bright-field microscopy investigations of lncRNA expression in FFPE tissue specimens. HOTAIR, H19 and KCNQ1OT1 may be potential breast cancer biomarkers, both HOTAIR and H19 may be a marker for DCIS at increased risk of progression to invasive cancer. HOTAIR, in particular, may be a predictor for invasive cancer grade.

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Shen, Ying. "Studies on the mechanisms of RNA-driven DNA repair and modification." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/45969.

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Our previous studies have demonstrated that RNA can serve as a template for double-strand break (DSB) repair in the yeast Saccharomyces cerevisiae using synthetic RNA-containing oligonucleotides (oligos). Following this initial work, we show that the RNA tract of RNA-containing oligos can be copied into DNA to transfer a genetic change at the chromosomal level also in the bacterium Escherichia coli and in human cells. Exploiting the use of oligos containing ribonucleoside monophosphates (rNMPs), we developed a molecular approach to generate RNA/DNA hybrids of chosen sequence and structure at the chromosomal level in both yeast and E. coli cells. Such technique allows us to study how rNMPs present in the DNA genome of cells are tolerated by cells, what factors recognize and target rNMPs in DNA and to what extent the embedded rNMPs may alter genome integrity. Here we proved that mispaired rNMPs embedded into genomic DNA, if not removed, serve as templates for DNA synthesis during chromosomal replication and produce a genetic change. We discovered that mispaired rNMPs that are embedded in genomic DNA are not only targeted by ribonucleases H (RNases H) but also by the mismatch repair (MMR) system both in yeast and in E. coli. Our data reveal novel substrates for the MMR system, and also uncover an unpredicted competition between RNase H and MMR for the RNA/DNA mispairs.

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Zhou, Min. "Characterisation of ADAM expression in human myeloma cells." Thesis, University of Sheffield, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312273.

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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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Walter, Heidi-Kristin [Verfasser], and H. A. [Akademischer Betreuer] Wagenknecht. ""DNA/RNA Traffic Lights 2.0" - Entwicklung von wellenlängenverschiebenden DNA- und RNA-Sonden unter Verwendung von "Click"-Modifikationen / Heidi-Kristin Walter ; Betreuer: H.-A. Wagenknecht." Karlsruhe : KIT-Bibliothek, 2016. http://d-nb.info/1122461534/34.

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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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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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Choudury, Sarah G. Choudury. "Identification and characterization of proteins required for RNA-directed DNA Methylation, including the RNA binding protein ALY1." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543508792612526.

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Mast, Christof. "Polymerization and replication of DNA/RNA in a thermal trap." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-175178.

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Chen, Cai. "Quantitative studies of RNA editing and nucleosomal DNA-protein interactions." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1417523347.

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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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35

Sigurgeirsson, Benjamín. "Analysis of RNA and DNA sequencing data : Improved bioinformatics applications." Doctoral thesis, KTH, Genteknologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-184158.

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Massively parallel sequencing has rapidly revolutionized DNA and RNA research. Sample preparations are steadfastly advancing, sequencing costs have plummeted and throughput is ever growing. This progress has resulted in exponential growth in data generation with a corresponding demand for bioinformatic solutions. This thesis addresses methodological aspects of this sequencing revolution and applies it to selected biological topics. Papers I and II are technical in nature and concern sample preparation and data anal- ysis of RNA sequencing data. Paper I is focused on RNA degradation and paper II on generating strand specific RNA-seq libraries. Paper III and IV deal with current biological issues. In paper III, whole exomes of cancer patients undergoing chemotherapy are sequenced and their genetic variants associ- ated to their toxicity induced adverse drug reactions. In paper IV a comprehensive view of the gene expression of the endometrium is assessed from two time points of the menstrual cycle. Together these papers show relevant aspects of contemporary sequencing technologies and how it can be applied to diverse biological topics.

QC 20160329

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Lee, Sally. "Architecture of RNA polymerase II and RNA polymerase III pre-initiation transcription complexes /." Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/9213.

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Dofková, Květoslava. "Analýza genů pro ribozomální RNA u variet Brassica napus (řepka olejka)." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2011. http://www.nusl.cz/ntk/nusl-216749.

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Brassica napus (AACC, 2n = 38) is an allotetraploid species derived from the parentel diploid species Brassica rapa (AA, 2n = 20) and Brassica oleracea (CC, 2n = 18). The aim of thesis was to carry out the genetic and epigenetic analysis of high-copy rRNA genes (or rDNA) in several varieties of hybrid species B. napus. The experiments involved determining the ratio of parental genes in hybrids, sequencing and methylation analysis of the promoter region of rDNA. Using Southern hybridization, it was revealed significant variability in the number of parental rDNA units between each variety. Data from sequence analysis were in good agreement with the results of Southern blot. Genetic recombination between parental rDNA units was revealed in one variety by DNA sequencing of promotor region. To study methylation, bisulfite sequencing was performed. It was found out that rDNA units of B. rapa origin have a higher value of methylation than units originated from B. oleracea.

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Vystrčilová, Jana. "Tolerance poškození DNA novými, biologicky aktivními komplexy platiny." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2011. http://www.nusl.cz/ntk/nusl-216799.

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The anti-tumor activity of platinum based drugs is mediated by their ability to attack DNA. Platinum complexes can alter the structure of DNA by modifying the bases, mainly guanines. The biological consequnces of such interactions are compromising replication and transcription. RNA polymerase complex can stall at a damaged site in DNA and mark the lesion for repair by proteins that are utilized to execute nucleotide excision repair, a pathway commonly associated with the removal of bulky DNA damage from the genome. This RNA polymerase-induced repair pathway is called transcription-coupled nucleotide excision repair. Main goal of this thesis was to study RNA polymerases tolerance of DNA damage by novel, biologically active platinum (II) complexes involving derivatives of aromatic cytokinines as the ligands; cis-[Pt(2-chloro-6-(4-methoxybenzylamino)-9-isopropylpurin)2Cl2](PR-001), cis-[Pt(2-chloro-6-(benzylamino)-9-isopropylpurin)2Cl2](PR-002 )and cis-[Pt(2-(3-hydroxypropylamino)-6-(benzylamino)-9-isopropylpurin)2Cl2](PR-005). DNA templates (constructs) that contain a single, site-specific DNA lesion and support transcription by human RNA polymerase II and bacteriophage T7 RNA polymerase were prepared. The method is making use of polymerase chain reaction (PCR) and biotin-streptavidin interactions and paramagnetic particles to purify the final product. Synthetic oligomers duplexes (75-mer, 56-mer and 15-mer) are ligated to 5´-biotin pCI-neo-G-lessT7 PCR fragment, the 15-mer is either unmodified or modified with a site-specific lesion of PR-005 and cisplatin. We also studied the inhibition of RNA polymerases activity on globally modified plasmid pCI-neo and pUC 19 by novel platinum complexes and cisplatin. We found that bifunctional adducts of complex PR-005 contrary to adducts of PR-001 and PR-002 effectively decrease amount of full lenght transcripts produced by both, human and bacterial RNA polymerases. This result can be explained by a sterical block, induced to DNA by intrastrand cross-link of PR-005 with bulky aromatic ligands.

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39

Fredriksson, Mona. "Using Minisequencing Technology for Analysing Genetic Variation in DNA and RNA." Doctoral thesis, Uppsala University, Department of Medical Sciences, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4789.

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In this thesis, the four-color fluorescence tag-microarray minisequencing system pioneered by our group was further developed and applied for analysing genetic variation in human DNA and RNA. A SNP marker panel representing different chromosomal regions was established and used for identification of informative SNP markers for monitoring chimerism after stem cell transplantation (SCT). The success of SCT was monitored by measuring the allelic ratios of informative SNPs in follow-up samples from nine patients with leukaemia. The results agreed with data obtained using microsatellite markers. Further the same SNP marker panel was used for evaluation of two whole genome amplification methods, primer extension preamplification (PEP) and multiple displacement amplification (MDA) in comparison with genomic DNA with respect to SNP genotyping success and accuracy in tag-array minisequencing. Identical results were obtained from MDA products and genomic DNA.

The tag-microarray minisequencing system was also established for multiplexed quantification of imbalanced expression of SNP alleles. Two endothelial cell lines and a panel of ten coding SNPs in five genes were used as model system. Six heterozygous SNPs were genotyped in RNA (cDNA) from the cell lines. Comparison of the relative amounts of the SNPs alleles in cDNA to heterozygote SNPs in genomic DNA displayed four SNPs with significant imbalanced expression between the SNP alleles. Finally, the tag-array minisequencing system was modified for detection of splice variants in mRNA from five leukaemia cell lines. A panel of 20 cancer-related genes with 74 alternatively splice variants was screened. Over half of the splice variants were detected in the cell lines, and similar alternative splicing patterns were observed in each cell line. The results were verified by size analysis of the PCR product subjected to the minisequencing primer extension reaction. The data from both methods agreed well, evidencing for a high sensitivity of our system.

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Tomkuvienė, Miglė. "Methyltransferases as tools for sequence-specific labeling of RNA and DNA." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2013. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2013~D_20131209_091531-59976.

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Investigation of RNA and DNA function often requires sequence-specific incorporation of various reporter and affinity probes. This can be achieved using AdoMet-dependent methyltransferases (MTases) as they can be active with synthetic AdoMet analogues equipped with transferable chains larger than the methyl group. These chains usually carry reactive groups that can be further chemically appended with required reporters. For this, azide-alkyne 1,3-cycloaddition (AAC), also called “click”, reaction is particularly attractive. This work shows that the HhaI cytosine-5 DNA MTase (variant Q82A/Y254S/N204A) catalyzes efficient sequence-specific transfer of hex-2-ynyl side chains containing terminal alkyne or azide groups from synthetic cofactor analogues to DNA. Both the enzymatic transfer and subsequent “click” coupling of a fluorophore can be performed even in cell lysates. For RNA labeling, the activity of an archaeal RNA 2‘-O-MTase C/D ribonucleoprotein complex (RNP) with synthetic cofactors was investigated. It was shown that synthetically reprogrammed guide RNA sequences can be used to direct the C/D RNP-dependent transfer of a prop-2-ynyl group to predetermined nucleotides in substrate RNAs. Followed by AAC this can be used for programmable sequence-specific labeling of a variety of RNA substrates in vitro. These new possibilities for specific labeling of nucleic acids can be adopted in biochemistry, biomedical, nanotechnology, etc. research.
Tiriant DNR ir RNR, neretai svarbu prijungti įvairius reporterinius ar giminingumo žymenis griežtai apibrėžtose (sekos) vietose – t.y. specifiškai. Tam galima pasitelkti fermentus metiltransferazes (MTazes). Natūraliai jos naudoja kofaktorių AdoMet, tačiau gali būti aktyvios ir su sintetiniais jo analogais, turinčiais ilgesnes nei metil- pernešamas grandines. Jei šios grandinės turi galines funkcines grupes, prie jų vėliau cheminių reakcijų pagalba galima prijungti norimus žymenis. Tam itin patogi azidų-alkinų cikloprijungimo (AAC), dar vadinama „click“, reakcija. Šiame darbe parodyta, kad DNR citozino-5 MTazė HhaI (variantas Q82A/Y254S/N204A) efektyviai katalizuoja sekai specifinę heks-2-inil- grandinių, turinčių galines alkinil- arba azido- grupes, pernašą nuo sintetinių kofaktorių ant DNR. Naudojant šią MTazės-kofaktorių sistemą bei AAC, visą specifinio DNR žymėjimo procesą galima atlikti netgi ląstelių lizate. RNR žymėjimui ištirtas archėjų RNR 2‘-O-MTazės C/D ribonukleoproteininio komplekso aktyvumas su sintetiniais kofaktoriais. Parodyta galimybė sintetiškai keičiant kreipiančiąją RNR, prop-2-inilgrupės pernašą nukreipti į norimas įvairių substratinių RNR sekos vietas ir po to AAC reakcijos pagalba prijungti fluoroforą. Taigi, sukurtas naujas molekulinis įrankis, leidžiantis be suvaržymų pasirinkti norimą pažymėti RNR seką. Šios naujos specifinio nukleorūgščių žymėjimo galimybės gali būti pritaikytos biochemijos, biomedicinos, nanotechnologijų ir kitose tyrimų srityse... [toliau žr. visą tekstą]

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41

Francis, Rawle Friedman Simon H. "Inhibition of human telomerase by targeting its transitory RNA/DNA heteroduplex." Diss., UMK access, 2005.

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Thesis (Ph. D.)--School of Pharmacy and Dept. of Chemistry. University of Missouri--Kansas City, 2005.
"A dissertation in pharmaceutical sciences and chemistry." Advisor: Simon H. Friedman. Typescript. Vita. Description based on contents viewed June 23, 2006; title from "catalog record" of the print edition. Includes bibliographical references (leaves 327-353). Online version of the print edition.

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42

Cooke, L. A. "Preparation and evaluation of novel phosphoramidites for labeling DNA and RNA." Thesis, Queen's University Belfast, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.557306.

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Phosphoramidite derivatives of a nucleoside analogue bearing photoswitchable ortho-, meta- and para azobenzene moieties were prepared and used to incorporate the azobenzene groups into DNA.8mers. The photochemical E-Z isomerisation of the azobenzene-appended 8mers was investigated by UV/vis spectroscopy and RP-HPLC. In order to investigate the stabilities of the irradiated-8mers towards thermal Z - E isomerisation, Arrhenius and Eyring parameters for the photoisomerisation were determined. The meta-isomer was found to be the most thermally stable. An initial investigation into the stability of duplexes containing a para-azobenzene-modified 8mer was carried out using melting studies. The duplex-forming activity of the oligonucleotide was modulated by the E- Z photoisomerisation of the para-azobenzene residue. A divergent methodology for the preparation of a novel structural class of photoswitchable oligonucleotide has been described. A novel anthracene methyl phosphoramidite derivative suitable for the preparation of end- labelled oligonucleotides under solid-phase directed-Arbusov conditions was prepared and its reactivity investigated. A comparison of the utility of this anthracene methyl phosphorarnidite with a related benzyl phosphorarnidite in a model reaction with the 5'-hydroxyl of support-bound decathymidylate was made. Directed Michaelis-Arbusov reactions of the putative phosphite triester intermediates with primary and secondary amines in the presence of 0.01 M iodine gave the corresponding phosphoramidate diesters in high yields. This reactivity was also demonstrated using commercially available phosphoramidites for the preparation of inter-nucleotide phosphoramidates bearing terminal primary amines. Derivatisation of these primary amine-functionalised oligomers was accomplished in solution-phase following treatment with the meta-azobenzene NHS ester.

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43

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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44

Xiong, Chen. "Enzymatic modification of DNA and RNA 3'-termini for click ligation." Thesis, University of Southampton, 2014. https://eprints.soton.ac.uk/367127/.

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45

Li, Tianzi li. "Promoter DNA Melting by RNA Polymerase Holoenzyme Containing Various Sigma Factors." Cleveland State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=csu1474639635315205.

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46

NandyMazumdar, Monali. "RfaH CONTACTS TO DNA, RNA POLYMERASE AND RIBOSOME ACTIVATE GENE EXPRESSION." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1482155208767278.

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47

Varshney, Dhaval. "Regulation of RNA polymerase III transcription by DNA methylation and chromatin." Thesis, University of Glasgow, 2012. http://theses.gla.ac.uk/3114/.

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Mammalian genomes contain huge numbers of short interspersed elements (SINEs). An extreme case is provided by the human genome, which carries ~106 copies of Alu SINEs that together account for ~10% of total chromosomal DNA. SINEs spread by retrotransposition, which depends on their transcription by pol III. This transcription is heavily suppressed. Silencing is thought to involve DNA methylation and packaging the SINEs into chromatin structures that deny access of transcription factors. It has been argued that this may be of great importance to prevent SINEs from competing with essential genes for a limited pool of transcription machinery. Our investigation of this has revealed some unexpected findings. This study has also investigated the effects of SWI/SNF chromatin remodellers on tRNA transcription.

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48

Ikeda, Shuji. "Studies on the Design of Parallel-Stranded DNA and Functional RNA." Kyoto University, 2000. http://hdl.handle.net/2433/180986.

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Novoa, Carolina. "RecQ-like helicase SGS1 counteracts DNA : RNA hybrid induced genome instability." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/60964.

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Dividing cells are constantly under threat from both endogenous and exogenous DNA damaging stresses that can lead to mutations and structural variations in DNA. One contributor to genome instability is three-stranded DNA:RNA hybrid structures called R-loops. Though R-loops are known to induce DNA damage and DNA replication stress, it is unclear whether they are recognized and processed by an established DNA repair pathway prior to inducing DNA breaks. Canonically, DNA repair proteins work downstream of R-loop-induced DNA damage to stimulate repair and suppress genome instability. Recently, the possibility that some DNA repair pathways actively destabilize R-loops, thus preventing unscheduled DNA damage has emerged. Here we identify the helicase SGS1 as a suppressor of R-loop stability. Our data reveals that SGS1 depleted cells accumulate R-loops. In addition, we define a role for transcription in genome instability of cells lacking SGS1, which is consistent with an R-loop based mechanism. Hyper-recombination in SGS1 mutants is dependent on transcript length, transcription rate, and active DNA replication. Also, rDNA instability in sgs1Δ can be suppressed by ectopic expression of RNaseH1, a protein that degrades DNA:RNA hybrids. Interestingly, R-loops are known to form at rDNA loci. We favour a model in which SGS1 contributes to the stabilization of stalled replication forks associated with transcription complexes, and unresolved DNA:RNA hybrids. Finally, we showed that knockdown of the human Sgs1 orthologue BLM in HCT116 cells also led to the accumulation of more R-loops than control HCT116 cells. In summary, our data supports the idea that some DNA repair proteins involved in replication fork stabilization might also prevent and process R-loops.
Science, Faculty of
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Klasens, Bianca Ilona Fenna. "The HIV-1 RNA genome and regulation of reverse transcription and polyadenylation." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2000. http://dare.uva.nl/document/84233.

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Dissertations / Theses on the topic 'DNA. RNA'

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