Dissertations / Theses: 'Triplex DNA'

1

Sayoh, Ibrahim. "Factors affecting DNA Triplex formation." Thesis, University of Southampton, 2016. https://eprints.soton.ac.uk/403876/.

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Triplex-forming oligonucleotides (TFOs) can be used to target DNA in a sequence-specific fashion, and have a number of potential therapeutic and biotechnological applications. TFOs bind within the DNA major groove where they form sequence-specific contacts with exposed groups on the target duplex. Pyrimidine-rich TFOs bind parallel to the target purine strand forming C+.GC and T.AT triplets and usually require conditions of low pH, which are needed for protonation of the third strand cytosines. In contrast, purine-rich TFOs bind antiparallel to the target and form triplexes containing G.GC and A.AT triplets. DNase I footprinting studies with parallel triplexes often reveal enhanced cleavage at the triplex-duplex junction at the 3’-end of the duplex purine strand. This study systematically investigated how this enhanced cleavage is affected by the nature of the base pairs that flank the TFO-binding site. For this we have used the well-characterised TFO-binding site in the tyrT(43-59) fragment and have changed the base at the 3’-end of the homopurine strand from cytosine to each of the other three bases in turn. In each case the footprints were accompanied by enhanced DNase I cleavage at the 3’-triplex-duplex junction on the purine strand, which is thought to be due to local structural changes that render the DNA to be more susceptible to cleavage by the enzyme. The enhancements were generally greater for flanking pyrimidines than purines. Similar experiments investigated the effect of changing the terminal triplet from T.AT to C+.GC, again flanked by each base in turn. Although there were no significant differences in the concentration dependence of the footprints, fluorescence melting experiments showed that triplexes flanked by G and A are more stable than those flanked by C and T. We also used diethylpyrocabonate (DEPC) to probe the reactivity of adenines at the triplex-duplex junction and find that some, but not all, sequence combinations generate enhanced reactivity, suggesting that triplex formation has altered the stacking pattern of adenines on the 3’-side of the TFO binding site. For antiparallel triplex formation, DNase I enhancements were also observed at a number of bands beyond the 5’-end of each TFO’s binding site. This is also attributed to the TFO-induced DNA structural changes that increase the accessibility of the enzyme to the target site. The results of concentration dependence of the footprints are similar to the parallel ones though fragment AC with 17-mer-G TFO had a much lower C50.

2

Ashley, Carolyn. "The role of triplex DNA in the cell." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0018/NQ43508.pdf.

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Dosanjh, Harvinder Singh. "Biophysical studies of triplex and quadruplex DNA systems." Thesis, Institute of Cancer Research (University Of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.409306.

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4

Mayer, Alain. "Synthesis and triplex forming properties of pyrrolidino-DNA /." [S.l.] : [s.n.], 2005. http://www.zb.unibe.ch/download/eldiss/05mayer_a.pdf.

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5

Richards, Sally. "Inhibition of oncogene expression by the formation of Triplex DNA." Thesis, Institute of Cancer Research (University Of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368703.

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Vadhia, Sunil Jayantilal. "The effect of modified nucleosides on DNA duplex and triplex stability." Thesis, University of Southampton, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.484953.

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To date, the single most effective method of improving base pairing affinity and binding of PCR primers, fluorescent probes and triplex forming oligonucleotides (TFO) ',h,';I,,+ destabilising mismatch base pairs has been the incorporation of modified nucleoside into these oligonucleotide structures. As a consequence, significant improvements have been made in the areas of human identity testing, forensic science analysis, pharmacogenetics/pharmacogenomics and anti-gene therapy. In an effort to improve the stability of these DNA duplexes and DNA triplexes further, we have synthesised and incorporated a series of cytosine, 7-deaza adenine, thymine and 3Hfuro-[ 2, 3-d] pyrimidin-2-one base analogues. By using a combination of UV melting analysis and fluorescence melting experiments, we have demonstrated that each of the base analogues gives a significantly higher base pairing affinity and binding selectivity when compared to their corresponding natural base. In addition, we have also incorporated these base analogues into PCR primers (7-deaza adenine) and fluorescent probe sequences (cytosine, 7-deaza adenine, thymine and 3H-furo-[2, 3-d] pyrimidin-2-one). Results from peR experiments show that the 7-deaza adenine base analogue does not adversely the functioning of Taq polymerase during amplification and therefore at the very least behaves similarly to adenine within a PCR primer sequence. In addition, all of the tLUlJre~jCel1tly labelled base analogues (cytosine, 7-deaza adenine, thymine and 3H-furo-[2, pyrimidin-2-one) show a significantly higher level ofbase pairing affinity and binding selectivity a complementary target sequence over a mismatched sequence.

7

Veach, Darren R. "SYNTHESIS AND EVALUATION OF 2,2-DIARYL-2,3-DIHYDROPHENANTHRO-[9,10-b]-1,4-DIOXIN PHOTONUCLEASES." University of Cincinnati / OhioLINK, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=ucin991653071.

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Read, Martin. "Molecular modelling and crystallographic studies of quadruplex and triplex DNA drug complexes." Thesis, Institute of Cancer Research (University Of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325536.

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Keppler, Melanie Dawn. "Strategies for increasing the stability of triple helical DNA." Thesis, University of Southampton, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302353.

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Weiser, Michal. "Akcelerace algoritmů pro hledání triplexů v DNA sekvencích." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2012. http://www.nusl.cz/ntk/nusl-236435.

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Triplex forms of DNA act as main factors of some important cell functions. However, their positions within genome and their effect on cell functions are not known well. Triplex search algorithms often don't consider many of triplexs features and the possibility of occurrence of errors. In the other hand the complexity of full featured algorithms is extremely high. This paper shows the way to speed up the algorithm that considers all known triplex features. Parallel aproach allows due to CUDA technology acceleration up to 50.

11

Nam, Kang Hoon. "DNA complexes with adjacent duplex and triplex domains : thermal denaturation and gel mobility shift analysis." Diss., Georgia Institute of Technology, 1997. http://hdl.handle.net/1853/25196.

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12

Zeng, Yingying. "Discrete Assembly of Synthetic Peptide-DNA Triplex Structures from Polyvalent Melamine-Thymine Bifacial Recognition." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1373981452.

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13

Evans, Kathryn. "An NMR study of a natural and a 3'-S-phosphorothiolate modified DNA triplex." Thesis, University of Leeds, 2012. http://etheses.whiterose.ac.uk/4143/.

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Triple helical DNA is formed when purine or pyrimidine bases of a triplex forming oligonucleotide (TFO) occupy the major groove of a homopurine-homopyrimidine double helix, and interact with it via Hoogsteen hydrogen bonding. There is significant interest in triplex structures due to their prevalence in biology as they are the target complex for antigene therapeutic approaches. Triplex structures which comprise a DNA duplex and RNA TFO have previously been found to be more stable than the equivalent all DNA systems. There are synthesis and stability issues surrounding the use of RNA-based TFOs, hence there is interest in developing chemically-modified TFOs which show at least the same duplex-binding affinity. In this project, a 3â�²-S-phosphorothiolate linkage is the modification of interest, which has previously been shown to alter the conformation of deoxyribonucleic acid systems to that of ribonucleic acids. A 12 base pair homopurine-homopyrimidine hairpin duplex that is a target for a TFO was characterised by NMR spectroscopy and high resolution structures were generated. The hairpin was shown to adopt a B-type helix with predominantly south sugar puckers. Similar analysis was performed on a native triplex comprising the hairpin and a pyrimidine TFO. Binding of the third strand was found to cause little structural changes to the hairpin. Two non-adjacent 3â�²-S-phosphorothiolate modifications were then incorporated into the TFO and the effects determined by NMR analysis. The result was very localised conformational changes in the deoxyribose sugars attached to the modifications, as well as those 3â�² to it, from a DNA-like south to an RNA-like north pucker. Finally, UV thermal melting analysis of the target hairpin and triplexes was performed. The stability of the hairpin was found to be pH independent, whereas the triplex structures were only stable at acidic pH. The 3â�²-S-phosphorothiolate modification was found to stabilise the triplex by up to around 7 Â°C and to increase the pH range for triplex formation. It is thought that the increased stability is due to favourable base stacking interactions as a result of the modification.

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Lombe, Chipampe Patricia. "Analysis, expression profiling and characterization of hsa-miR-5698 target genes as putative dynamic network biomarkers for prostate cancer: a combined in silico and molecular approach." University of the Western Cape, 2019. http://hdl.handle.net/11394/7026.

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Philosophiae Doctor - PhD
2018, the International Agency for Research on Cancer (IARC) estimated that prostate cancer (PCa) was the second leading cause of death in males worldwide. The number of deaths are expected to raise by 50 % in the next decade. This rise is attributed to the shortcomings of the current diagnostic, prognostic, and therapeutic biomarkers used in the management of the disease. Therefore, research into more sensitive, specific and effective biomarkers is a requirement. The use of biomarkers in PCa diagnosis and management takes advantage of the genetic alterations and abnormalities that characterise the disease. In this regard, a microRNA, hsa-miR-5698 was identified in a previous study as a differentiating biomarker between prostate adenocarcinoma and bone metastasis. Six putative translational targets (CDKN1A, CTNND1, FOXC1, LRP8, ELK1 and BIRC2) of this microRNA were discovered using in silico approaches. The aim of this study was to analyse via expression profiling and characterization, the target genes of hsa-miR-5698 in order to determine their ability to act as putative dynamic network biomarkers for PCa. The study was conducted using a combined in silico and molecular approach. The in silico part of the study investigated the putative transcriptional effects of hsa-miR-5698 on the promotors of its translational targets, the correlation between hsa-miR-5698 and mRNA expression profiles as well as the co-expression analysis, pathway analysis and prognostic ability of the target genes. A number of computational software were employed for these purposes, including, R Studio, Trident algorithm, STRING, KEGG, MEME Suite, SurvExpress and ProGgene. The molecular part of the study involved expression profiling of the genes in two PCa cell line LNCaP and PC3 via qPCR.

15

Riechert-Krause, Fanny [Verfasser]. "Spectroscopic Studies on the Sequence-Selective Interactions of Bioactive Indoloquinolines with Duplex and Triplex DNA / Fanny Riechert-Krause." Greifswald : Universitätsbibliothek Greifswald, 2012. http://d-nb.info/1021841285/34.

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Alvira, Torre Margarita. "Modified oligonucleotides for triple helix studies and for the obtention of structures with biomedical and technological interest." Doctoral thesis, Universitat de Barcelona, 2010. http://hdl.handle.net/10803/80851.

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Oligonucleotides are short fragments of DNA (10-100nt) which are of great interest because their applications in molecular biology, biomedicine and nanotechnology. As a result of their ability to base pairing, oligonucleotides can be used as primers, hybridization probes in biosensors, agents for controlling gene expression, structural material in nanotechnology or as substrates for a variety of biochemical and biophysical studies. Chemical modification of oligonucleotides as well as conjugation to different functional molecules allows for modulation of both therapeutical and biotechnological properties. This thesis is focused in the nucleic acid chemistry field and the main objective is the synthesis of modified oligonucleotides for obtaining structures with therapeutical and/or biotechnological interest. Oligonucleotides capable to form structures other than the canonical DNA double helix have received considerable attention in the last years. The ability of triplex forming oligonucleotides (TFOs) to bind specifically to certain duplex DNA regions provides a strategy for site-directed modification of genomic DNA. Besides, G-quadruplexes are four-stranded DNA structures stabilized by stacking of guanine tetrads which have been found in telomeres and some promoters and play a role in regulation of transcription and translation. In addition, they are also interesting for nanotechnological devices. In this context, the first part of the research work was addressed to synthesize parallel stranded oligonucleotide clamps carrying LNA (locked nucleic acid) residues and study the stability of the triplex formed with DNA and RNA target sequences. Secondly, a novel strategy to obtain parallel clamps using the non-templated chemical ligation of two oligonucleotides by 5’-5’ linkages was developed. For this purpose, several protocols for introduce azido and alkyne moieties in the 5’-end of different sequences were developed so that the modified DNA strands could form a parallel hairpin after their chemical ligation by click chemistry. Thirdly, a system composed of four DNA strands whose 5’ ends are covalently attached was designed to form a monomolecular parallel G-quadruplex, which was used to study the effects of some nucleobase modifications in quadruplex structure. Finally, oligonucleotide conjugates carrying Cu(II) complexes were synthesized to construct arrays of electrochemical oscillators for nanotechnology applications.

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Shrestha, Prakash. "FOLDING DYNAMICS OF G-QUADRUPLEXES DURING TRANSCRIPTION AND IN A NANO-CONFINEMENT." Kent State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1514906810383603.

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Koirala, Deepak P. "Mechanochemistry, Transition Dynamics and Ligand-Induced Stabilization of Human Telomeric G-Quadruplexes at Single-Molecule Level." Kent State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=kent1397919270.

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Zrůna, Michal. "Vyhledávání triplexů v DNA sekvencích." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2012. http://www.nusl.cz/ntk/nusl-236546.

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20

Cassidy, Sarah Anne. "Stabilisation of DNA triple helices." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242535.

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Rusling, David Anthony. "DNA recognition by triple helex formation." Thesis, University of Southampton, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.494720.

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22

Washbrook, Elinor. "Alternate strand DNA triple helix formation." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242223.

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23

Paes, Hazel Margaret. "The kinetics of DNA triple helices." Thesis, University of Southampton, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242691.

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24

Chandler, Simon Paul. "DNA sequence recognition by triple helix formation." Thesis, University of Southampton, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296164.

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25

Makube, Neo. "The triple-helical DNA four-way junction." Doctoral thesis, University of Cape Town, 1999. http://hdl.handle.net/11427/26926.

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This Thesis will show that third strands can be incorporated into the four-way junctions combining the properties of the triple helices and those of branched structures within one system without compromising either of the two. It is now known that folding into secondary and tertiary structures by nucleic acids is crucial for their biological functions. However, what remain to be clarified are the mechanisms involved in the folding of nucleic acids into -noncanonical structures. It requires a thorough understanding of the chemical and physical properties of the structure in question. This in tum will improve the design of new secondary and tertiary structures that may add to the DNA nanotechnology. With this aim, thermodynamic and structural properties of two triple-helical DNA fourway junctions (JTIT3 and JT2T4) are reported and discussed. JTIT3 and JT2T4 differ only in the polarity of the third strands (and/or position of the loops). Both junctions contain the same Watson-Crick double-helical four-way junction, named Js, as a core structure. Js was constructed from four 20-mer oligomers, two of which consists of purines and the other two strands pyrimidines. Extending each of the pyrimidine strands of Js at the 3' end by four cytosines followed by twenty pyrimidine bases results in JTIT3. Similarly, JT2T4 is formed by extending the same pyrimidine strands at the 5' end. The junctions are named according to the position of the C4-loops. JTIT3 and JT2T4 are further simplified into JT1, JT2, JT3 and JT4. Lowering the pH from 12 to 2 allows the oligomers to fold sequentially from random coil into the double-helical four-way junction, Js, and finally into the triple-helical four-way junction. The analysis of the structures discussed is based on the biochemical methods such as native polyacrylamide gel electrophoresis and chemical footprinting using osmium tertroxide as a probe. The analysis is also based on the physical methods, UV spectroscopy and DSC. The native polyacrylamide gel electrophoresis has been used to verify the formation of the complete four-way junctions. Chemical footprinting has been used to detect the formation of the junctions as well as to indicate the conformations these junctions assume under different pH and/or salt conditions. The phase diagrams enthalpies and entropies of the structures are determined mainly by DSC. The results indicate that all the junctions are highly sensitive to salt concentrations and/or pH. The Tm vs. [Na+] results show that above 0.4M Na+, the structures adopt a conformation that suggests that the junctions are folded into stacked helix structures. The differences in thermal stabilities of the junctions JT1, JT2, JT3 and JT are due to the sequence composition of the arms and not the loops. JT1, JT2, JT3 and JT4 are thermally more stable than the underlying double-helical junction, Js. Similarly; the complete triple-helical four-way junctions JTIT3 and JT2T4 are thermally more stable than their substructures JT1, JT2, JT3 and JT4, The compiled transition enthalpies obtained for the individual arms of Js, JT1, JT2, JT3 and JT4 are less than the transition enthalpies associated with the melting of the complete junctions. The higher calorimetric enthalpies of the structures are due in part to the contribution from the single strands resulting from the partly unfolded arms. The overall results show that third strands have a stabilizing effect on the structure of the four-way junction.

26

Gerrard, Simon Richard. "Novel nucleotide analogues for forming stable DNA triple helices." Thesis, University of Southampton, 2009. https://eprints.soton.ac.uk/69835/.

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DNA triple helices are an important tool in a variety of medicinal and biotechnological applications, such as gene therapy and chemotherapeutics. DNA triple helices are formed by binding of a triplex-forming oligonucleotide (TFO) to a DNA duplex, via specific recognition of the individual base pairs in the target sequence. Mixed-sequence recognition of duplex DNA by TFOs is therefore an essential requirement for successful targeting. However, achieving strong, yet specific binding to the pyrimidine.purine (Py.Pu) base pairs CG and TA, by TFOs is a greater challenge than to the purine.pyrimidine (Pu.Py) base pairs (GC, AT), as fewer hydrogen bonds are presented for binding in the major groove of the double helix. Selective recognition of CG, could be achieved by utilising additional interactions across the CG base pair, via amino-modified nucleosides, to form more stable, selective triplets than those which can be formed by the natural base T. Four modified phosphoramidite monomers, meta-aminophenyl-modified analogues of the bicyclic nucleosides, (2,3H)-furano[2,3-d]pyrimidin-2(7H)-one and N-methyl-(2,3H)-pyrrolo- [2,3-d]pyrimidin-2(7H)-one, were synthesised to address this potential hydrogenbonding motif. Biophysical studies demonstrate selective recognition of the CG base pair. Results indicate selectivity for CG and binding affinity are much improved on previous modifications. Their fluorescence properties and general oligonucleotide deprotection conditions were also studied. In addition, the synthesis of a bis-amine modified 6-oxocytidine phosphoramidite monomer for GC recognition was re-investigated. This research shows significant advances in the field of triplexes for therapeutic use.

27

Hüsler, Paul L. "Thermodynamic characterization of DNA Triple-Helical three-way junctions." Doctoral thesis, University of Cape Town, 1995. http://hdl.handle.net/11427/18282.

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Watson-Crick CWC) and Hoogsteen (HG) triple-helical three-way junctions were constructed from three 33-mer oligonucleotides. The same sub-set of sequences have been used in the arms of the junctions. The junctions differ primary in the arrangement of the branch point and the ends of the arms. In the case of the HG triple-helical three-way junction, the three 33-mer oligonucleotides can fold into hairpin structures, linked by a four membered cytosine loop. Each of the hairpins contain a homo-pyrimidine 10-mer single strand extension which interacts with a neighboring hairpin to form a triple-helix on lowering the pH (between 6 and 4), via Hoogsteen (HG) hydrogen bonding. Collectively this process results in the formation of the branch point and the triple-helical arms. In the case of the WC triple-helical three-way junction, the three 33-mer oligonucleotides interact with a neighboring oligonucleotide to form a duplex. Collectively this process leads to the formation of a double-helical three-way junction with each arm containing a 9-mer homo-pyrimidine extension connected by four cytosines. Each of the single strand extensions can mutually fold back onto the duplex arms converting each arm into a triplex. The WC and HG triple-helical three-way junctions were characterized by gel electrophoresis, temperature gradient gel electrophoresis, circular dichroism (CD), uv melting, and differential scanning calorimetry (DSC). In both structures; arm A contained exclusively TAT triad bases, while arms B and C contained an increasing number of CGC+ triads, respectively. To counteract possible crowding at the branch point the 5' sequence was shortened by one base. The assembly of the completely folded structure was found to be spontaneous if an appropriate ionic strength and pH range was chosen. A separate set of isolated arms has been investigated to elucidate the role each arm plays in the complete structure. Comparing the summed-up properties of these arms with the data obtained for the integral three-way junctions, it is obvious that the we three-way junction is partly distorted at the branch point, in line with observation obtained from double-helical three-way junctions, while the HG threeway junction is completely ordered. A set of mathematical models has been developed to describe the thermal unfolding of the multi-strand DNA structure and to identify the intermediate states. Presented is a formalism, starting from the grand partition function, that describes the effects of pH on the thermal stability of triple-helices. The formalism can be used over a wide pH range. It covers nearest neighbor electrostatic effects of closely spaced cytosines in the Hoogsteen and Watson & Crick strands. A procedure is employed to predict enthalpy and entropy changes for triplex formation. The obtained values are in good agreement with the results obtained by differential scanning calorimetry. It is the first time that multistrand, branched DNA structures of this complexity were constructed, completely described, and characterized thermodynamically.

28

Trkulja, Ivan. "Triple helical DNA containing non-nucleosidic polyaromatic building blocks /." Bern : [s.n.], 2007. http://www.zb.unibe.ch/download/eldiss/07trkulja_i.pdf.

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Tailor, Radha. "DNA triplexes in chemistry, biology and medicine." Thesis, University of Southampton, 2011. https://eprints.soton.ac.uk/192831/.

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The formation of DNA triple helices offers the possibility of selectively targeting specific genes to control their expression in vivo. This anti-gene strategy provides powerful tools for the development of therapeutics (anti-cancer drugs, drugs for viral infections) at the transcriptional level. DNA triplexes are formed when an oligonucleotide binds to the major groove of double helical DNA; the third strand can bind in either a parallel motif, or an anti-parallel motif. The requirement of low pH for the protonation of cytosine in the parallel binding motif makes the formation of triple helices difficult under physiological conditions. Described in this thesis is a novel method for the synthesis of the deoxycytidine analogue, 2-amino-3-methyl-5-(2’-deoxy-β-D-ribofuranosyl)pyridine (MeP). The phosphoramidite monomer of MeP was synthesised and incorporated as a “protonated” cytidine analogue into triplex forming oligonucleotides (TFOs). It was compared with other cytosine analogues, 5-methyl-(2’-deoxy-β-D-ribofuranosyl)cytosine (MeC), 2’-Omethyl MeP (MePOMe), and 2’-O-aminoethyl MeC (MeCAE). Triplex stability studies indicate that over the pH range 6.2-8.0, the general trend observed in terms of melting temperature (Tm) was as follows: MeP > MeC > MePOMe > MeCAE. DNase I footprinting studies indicate that at pH 7.5, MeP, when incorporated into the TFO, enhances the stability of the triplex by three-fold relative to MeC. In addition, UV melting, DNase I footprinting, and gel electrophoresis studies were carried out on a triplex formed by the binding of a TFO containing MeP and a 5’-Psoralen to a target duplex. This revealed the benefits of the combined modifications on the stability of the resultant triplex. “Soaking” experiments (in vivo) were also performed with this TFO on the organism C. elegans (the worms were soaked in solutions of the TFO for TFO delivery), to observe whether the TFO would induce loss-of-function phenotypes. Tm measurements indicated that in the pH range 6.6-8.0, photo-crosslinking of the TFO to the duplex created a shift in the triplex Tm of ~ + 26 °C when compared to the un-crosslinked triplex

30

Giesbertz, Anna [Verfasser], Elmar [Akademischer Betreuer] Weinhold, and Antal [Akademischer Betreuer] Kiss. "Triple helix-targeted DNA methylation with DNA methyltransferase-oligodeoxynucleotide conjugates / Anna Giesbertz ; Elmar Weinhold, Antal Kiss." Aachen : Universitätsbibliothek der RWTH Aachen, 2018. http://d-nb.info/1187346918/34.

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31

Gowers, Darren Matthew. "DNA triple helix formation at homopurine sites interrupted by pyrimidine residues." Thesis, University of Southampton, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264646.

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32

Moraru, Allen Ana-Ariana. "Studies on chemically modified oligonucleotides and on DNA triplexes." Thesis, University of Edinburgh, 1997. http://hdl.handle.net/1842/12683.

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The interactions between modified oligonucleotides and DNA binding proteins can provide important information on the mode of binding and the structure of the enzyme-substrate complex. Studies were carried out to determine the interaction of DNA with O⁶-methyl-G-transferase, a DNA repair enzyme which removes the alkyl group from guanine residues which are alkylated on the O⁶-position. A series of modified oligonucleotides have been synthesised containing O⁶-methylguanine, O⁶-ethylguanine and N⁶-methyl-2,6-diaminopurine. The oligonucleotides were obtained in high purity. UV melting (thermal denaturing) experiments have been carried out on duplexes containing the modified bases paired with cytosine and thymine respectively. These oligonucleotides were prepared in order to study their interactions with a mutant O⁶-methyl-G-transferase enzyme lacking DNA repair activity. Gel shift experiments suggest that the above oligonucleotides are recognised by the enzyme. Attempts were made to crystallise the enzyme-DNA complex. Triplex DNA is formed by the specific binding of a DNA strand in the major groove of a preformed DNA duplex. It has been suggested that such structures might have a biological role, especially in gene regulation, and that there is potential for therapeutic applications in which gene expression is repressed by triplex formation. One difficulty encountered in the studies of DNA triplexes is their low thermodynamic stability. In order to overcome this problem oligonucleotides with appropriate triplex forming sequences have been synthesised with the three strands linked by hexaethyleneglycol or 1,8-octanediol chains. These molecules are capable of folding back on themselves to give intramolecular triplexes with significantly increased stabilities compared to intermolecular triplexes. UV melting studies have been carried out to determine the thermal stability of these triplexes, in the presence and in the absence of the DNA triplex binding drug coralyne. Circular dichroism and NMR studies were carried out in collaboration with Dr A. Lane at the National Institute of Medical Research, London.

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Singleton, Scott F. Dervan Peter B. Dervan Peter B. "The thermodynamics of oligonucleotide-directed triple helix formation at single DNA sites /." Diss., Pasadena, Calif. : California Institute of Technology, 1995. http://resolver.caltech.edu/CaltechETD:etd-10242007-090557.

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34

Almeida, Carina Marisa dos Santos. "Gold nanoparticle-DNA conjugates for oligonucleotide vectorization towards gene silencing." Master's thesis, Faculdade de Ciências e Tecnologia, 2011. http://hdl.handle.net/10362/6212.

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Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina
The main objective of the work presented in this thesis was to develop a gene silencing system by taking advantage of the nanovectorization capability and optical properties of gold nanoparticles. The idea is based on the construction of a DNA structure containing a therapeutic oligonucleotide with the ability to form Hoogsteen hydrogen bonds with double-stranded DNA, producing a DNA triple helix, besides silencing the gene of interest. Hoogsteen bonds, more unstable than the conventional Watson-Crick bonds, permit the achievement of lower melting temperatures. This attribute, coupled with the ability to generate heat by laser irradiation of the gold nanoparticles used, will allow the release of the therapeutic oligonucleotide and subsequent gene silencing without significant increase in the medium’s temperature. Thus, the thesis comprises three major sections: structure design and formation, vectorization, and gene expression silencing; the tasks involved in each of these sections were conducted in parallel. The design of the obtained structure took into account the desired melting temperature, stability at physiological conditions of the sequence-forming nucleotides, the number of Hoogsteen bonds and ionic conditions. To evaluate the formation of this structure, spectroscopic techniques were mainly used: FRET analysis and ultraviolet melting curves. Both approaches allowed the identification of interactions in the presence of therapeutic oligonucleotide compared with its absence, which may indicate structure formation. In addition, melting curves allowed the determination of the temperature of release of this oligonucleotide – 40ºC. The double-stranded DNA functionalization to gold nanoparticles has been achieved, but there was no difference in electrophoretic migration when the three oligonucleotides were present. However, the therapeutic oligonucleotide was able to efficiently inhibit gene expression in in vitro transcription and translation assays with efficiency up to 95% and 60% respectively.

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Mei, Ivy Yuhua. "Triple helix formation between a short DNA hairpin molecule and linear single stranded oligonucleotides." Thesis, Georgia Institute of Technology, 1995. http://hdl.handle.net/1853/25346.

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Bijapur, Jeevan. "Factors affecting the stability of nucleic acids." Thesis, University of Southampton, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299497.

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Weber, Zachary Thomas. "Applications of ctDNA Genomic Profiling to Metastatic Triple Negative Breast Cancer." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1586787923790178.

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Braich, Ravinderjit Singh. "Branched nucleic acids novel probes for studying pre mRNA processing and triple helical DNA." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape3/PQDD_0030/NQ64523.pdf.

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Völker, Jens. "The impact of global and local composition on the stability of Triple Helical DNA." Doctoral thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/21828.

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It is common practise in antisense technology to view third strand binding to be controlled by the same principles which are found to determine the stability of the double helix. In contrast to this view based on a general consideration of the various forces contributing to the binding energy of the third strand it was proposed that the dominant contributions will originate from electrostatic interactions. These electrostatic contributions can be subdivided into sequence independent repulsive forces between the negatively charged backbones and into sequence dependent attractive forces between the positively charged protonated Hoogsteen cytosines and the backbone phosphates. The observable changes in the stability of triple helices should be a reflection of the number (global composition) and distribution (local composition) of cytosines in the third strand. To this aim two families of 38-mer oligonucleotides were synthesized, which have as a common design feature a linear array of 10 homopurine bases followed by 10 homopyrimidine bases as Watson & Crick complementary strand to the homopurine region and ending in a 10 homopyrimidine residue stretch which binds to the W&C helix via Hoogsteen base-pairing. This arrangement of homopurine and homopyrimidine sections with connecting pyrimidine linkers allows the formation of intramolecular triple helices of predetermined stoichiometry and strand orientation. Physical (UV-spectroscopy, CD-spectroscopy and fluorimetry) and biochemical techniques (P1-nuclease digestion) have been used to show that the oligonucleotides undergo a stepwise folding process from a random coil into a hairpin with 3'dangling tail and then into a intramolecular triple helix. This folding occurs as a function of pH and/or ionic strength. The effect of local and global composition on the stability of the three conformational transitions has been evaluated from a comparison of the melting temperatures and the behavior of the phase boundaries of the different oligonucleotides. As the result of this thesis the following general rules emerge: The stability of the third strand depends on the particular combination of sequence, pH and ionic strength. At physiological conditions (pH 7.1, 150 mM Na⁺) thymines and cytosines contribute equally to the stability (global effect) provided that the cytosines are spaced by more than one thymine. (local effect). Below pH 7.1 (150 mM Na⁺) the stability increases linearly with the number of cytosines and at pH above pH 7.1 ( 150 mM Na⁺) it decreases. At ionic strength below 400 mM Na⁺ (pH 6. 75) the stability increases with the number of cytosine while above 400 mM Na⁺ (pH 6. 75) it decreases. Based on these results a rational approach for the design of oligonucleotide third strands and the choice of appropriate environmental conditions for the formation of a particular triple helix becomes feasible.

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Darian, Eva. "Triplex formation as monitored by EPR spectroscopy and molecular dynamics studies of spin-probe labeled DNAs." Morgantown, W. Va. : [West Virginia University Libraries], 2002. http://etd.wvu.edu/templates/showETD.cfm?recnum=2591.

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Abstract:

Thesis (Ph. D.)--West Virginia University, 2002.
Title from document title page. Document formatted into pages; contains xi, 121 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 113-115).

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Göckel, Anja [Verfasser]. "Bindungsmotive zur molekularen Erkennung von Nikotinamid-Cofaktoren auf der Basis von DNA-Triplexen / Anja Göckel." München : Verlag Dr. Hut, 2017. http://d-nb.info/1135596271/34.

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Buchini, Sabrina. "2'-O-Aminoethyl-oligoribonucleotides in DNA triple-helix formation : extending the sequence recognition code to three base pairs /." [S.l.] : [s.n.], 2004. http://www.zb.unibe.ch/download/eldiss/04buchini_s.pdf.

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Puchrík, Matej. "Simulace Triple play služeb v pasivních optických sítích v prostředí OMNeT++." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2015. http://www.nusl.cz/ntk/nusl-220390.

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The thesis deals with dynamic bandwidth allocation in passive optical networks of NG- PON2 standard. The paper also describes the so-called. triple play services and the practical part is a simulation of these services in passive optical networks NG-PON2 in the simulation environment OMNeT ++. As part of this work modules for passive optical network NG-PON2 were created as an expansion of project INET. Namely ONU, OLT and splitter modules were created. The first four chapters are theoretical and descibe older standards PON networks, further NG-PON2 networks and DBA algorithm then describes triple play services and explains their current status respectively. In another part a description of the programm OMNeT++ a description of the structure of simulation models. The practical part contains a description of modules, implementation of DBA algorithm and its modification, design simulated topology and detailed description of the configuration simulation. At the end of the practical part presents the results of simulations with the corresponding explanations.

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PERI, SEBASTIANO. "METFORMIN AND GLUCOSE STARVATION ATTENUATE THE DNA-DAMAGE RESPONSE THROUGH THE ACTIVATION OF PROTEIN PHOSPHATASE 2A." Doctoral thesis, Università degli Studi di Milano, 2022. https://hdl.handle.net/2434/946012.

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The DNA-Damage Response (DDR) mediates DNA-damage sensing and repair. Protein Phosphatase 2A (PP2A) is a major phosphatase in eukaryotes and plays a critical role in countless cellular processes. Among them, PP2A has been shown to modulate the DDR, although many aspects of this regulation remain to be better characterized. PP2A integrates metabolic sensing with the DDR in yeast. Through a pharmacological and genetic approach, our group found that the combination of metformin (the most commonly used drug for type 2 diabetes) with glucose starvation increased PP2A activity. In Triple Negative Breast Cancer (TNBC) cell lines and patient-derived tumors, metformin and glucose starvation enhanced the efficacy of low-dose, DNA-damaging chemotherapy. We demonstrated that PP2A, over-activated by metformin and glucose starvation, attenuated the DDR triggered by chemotherapy, thus preventing the cell cycle arrest necessary for DNA repair and increasing genomic fragmentation, which finally led to cell death. We showed that metformin and glucose starvation increased PP2A recruitment on the chromatin; this could stabilize PP2A catalytic subunit and increase its phosphatase activity. In mouse models of TNBC, metformin and cycles of intermittent fasting (which lowered blood glucose) increased the efficacy of low-dose chemotherapy and induced tumor regression. Targeting the DDR is considered an attractive therapeutic opportunity, based on the intrinsic genomic instability of tumor cells. Here we provide a metabolic strategy to mitigate the DDR at multiple levels, which is safe, tolerable and immediate.

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Bakalara, Norbert. "Caracterisation dans le genome d'un annelide polychete : owenia fusiformis, d'une region comprenant la repetition du triplet nucleotidique ccx." Aix-Marseille 2, 1987. http://www.theses.fr/1987AIX22121.

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Granzhan, Anton. "Synthesis and studies of annelated quinolizinium derivatives as versatile constructs for fluorescent probes and ligands for triple helical and abasic DNA structures." [S.l.] : [s.n.], 2006. http://www.ub.uni-siegen.de/epub/diss/granzhan.htm.

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Chen, Xiaomi. "Aberrant DNA Replication at an Ectopic Chromosomal Site in Human Cells." Wright State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=wright1302884072.

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Chen, Yen-Shan. "MAMMALIAN TESTIS-DETERMINING FACTOR SRY HAS EVOLVED TO THE EDGE OF AMBIGUITY." Case Western Reserve University School of Graduate Studies / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=case1372888881.

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Sugita, Bruna Mayumi. "Análise integrada do padrão de expressão de microRNAS e alteração do número de cópias de DNA em tumores de mama triplo-negativos." reponame:Repositório Institucional da UFPR, 2014. http://hdl.handle.net/1884/37077.

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Abstract:

Orientadora : Profª Drª Enilze M. S. F. Ribeiro
Co-orientadores : Profª Drª Luciane R. Cavalli, Prof. Dr. Iglenir J. Cavalli
Dissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências Biológicas, Programa de Pós-Graduação em Genética. Defesa: Curitiba, 28/03/2014
Inclui referências
Área de concentração: Genética
Resumo: Os microRNAs (miRNAs) são uma classe de moléculas de RNA não codificadoras que apresentam um papel na tumorigênese mamária, regulando genes envolvidos no ciclo celular, proliferação celular, invasão e metástase. Os diferentes subtipos de câncer de mama apresentam diferentes padrões de expressão de miRNAs, dessa forma essas moléculas podem ser potenciais marcadores terapêuticos para subtipos agressivos, como os tumores mamários triplo negativos (TN). Os tumores TN são clinicamente agressivos e possuem baixa ou nenhuma expressão dos receptores de estrogênio (ER), progesterona (PR) e HER2, dessa forma não respondem efetivamente a terapias alvos disponíveis atualmente. No presente trabalho, foi analisado o padrão de expressão de miRNAs de 83 tumores TN e 12 não-TN, juntamente com dados de alterações de números de cópias de DNA por array-CGH obtidos das mesmas amostras, a fim de identificar os miRNAs mais relevantes e seus respectivos genes alvos que podem estar envolvidos na patogênese dos tumores de mama TN. 117 miRNAs foram encontrados com expressão diferencial em tumores TN, quando comparados com os não-TN. A análise combinada de miRNA/aCGH resultou em 17 miRNAs que apresentaram dados concordantes de expressão de miRNA e alterações de números de cópias (ganho/perda de aCGH com alta/baixa expressão de miRNA, respectivamente). Análises de sistemas biológicos downstream de alvos conhecidos e possíveis alvos dos miRNAs selecionados indicaram as vias de sinalização do TGF-beta, PI3K-Akt e HER2, assim como vias envolvidas na adesão celular e outros processos relacionados ao câncer. Estes resultados sugerem que os 17 miRNAs e seus respetivos genes alvos podem ser futuramente estudados como marcadores moleculares específicos para tumores TN, sugerindo a necessidade de estudos de análise funcional e biológica que comprovem suas participações na tumorigênese mamária de tumores do tipo TN.
Abstract: MicroRNAs (miRNAs) are a class of non-coding endogenous RNA molecules that play a role in breast tumorigenesis regulating genes involved in cell cycle, proliferation, invasion and metastasis. Different subtypes of breast cancer presents different expression of miRNAs, and they can be potential therapeutic markers for aggressive subtypes as triple negative breast cancers (TNBC). TNBC are clinically aggressive tumors that lack the expression of ER, PR and HER2 receptors, therefore they do not respond effectively to the available target therapies. In the present study, we investigated miRNA expression pattern of 83 TNBC and 12 non-TNBC tumors and integrated the data with DNA copy number alterations data by array-CGH from the same samples, to obtain the most relevant miRNAs and their respective target genes that may be involved in the pathogenesis of TNBC. 117 miRNAs were found as differentially expressed in TNBC, when compared to non-TNBC. The combined analysis (miRNA/aCGH) resulted in 17 miRNAs that presented miRNA concomitant genomic gains and losses by aCGH and miRNA increase or decrease expression, respectively. KEGG pathway enrichment analysis of the selected 17 miRNAs revealed that their main pathways involved in TGF-beta signaling pathway, PI3K-Akt and HER2 signaling pathways as well as the ones involved in adherence junction and other cancer related processes. Our results suggest that the 17 miRNAs and their target genes may be studied as specific molecular markers for TNBC, suggesting the need for functional and biological analysis that proves their roles in TN tumorigenesis.

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Sirivolu, Venkata Ramana. "DNA containing side chains with terminal triple bonds: Synthesis, base pairing and functionalization of nucleosides and oligonucleotides by the azide-alkyne cycloaddition = DNA mit Terminalen Dreifachbindungen in Seitenketten: Synthese, Basenpaarung und Funktionalisierung von Nucleosiden und Oligonucleotiden durch die Azid-Alkin Cycloaddition /." Osnabrück, 2008. http://opac.nebis.ch/cgi-bin/showAbstract.pl?sys=000254558.

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Dissertations / Theses on the topic 'Triplex DNA'

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