Dissertations / Theses: 'Protein-DNA'

1

Slayton, Mark D. "Protein-DNA Interactions of pUL34, an Essential Human Cytomegalovirus DNA-Binding Protein." Ohio University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1533638730703166.

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2

Moont, Gidon. "Computational modelling of protein/protein and protein/DNA docking." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1445703/.

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The docking problem is to start with unbound conformations for the components of a complex, and computationally model a near-native structure for the complex. This thesis describes work in developing computer programs to tackle both protein/protein and protein/DNA docking. Empirical pair potential functions are generated from datasets of residue/residue interactions. A scoring function was parameterised and then used to screen possible complexes, generated by the global search computer algorithm FTDOCK using shape complementarity and electrostatics, for 9 systems. A correct docking (RMSD < 2.5A) is placed within the top 12% of the pair potential score ranked complexes for all systems. The computer software FTDOCK is modified for the docking of proteins to DNA, starting from the unbound protein and DNA coordinates modelled computationally. Complexes are then ranked by protein/DNA pair potentials derived from a database of 20 protein/DNA complexes. A correct docking (at least 65% of correct contacts) was identified at rank < 4 for 3 of the 8 complexes. This improved to 4 out of 8 when the complexes were filtered using experimental data defining the DNA footprint. The FTDOCK program was rewritten, and improved pair potential functions were developed from a set of non-homologous protein/protein interfaces. The algorithms were tested on a non-homologous set of 18 protein/protein complexes, starting with unbound conformations. Us ing cross-validated pair potential functions and the energy rninimisation software MultiDock, a correct docking ( RMSD of CQ interface 25% correct contacts) is found in the top 10 ranks in 6 out of 18 systems. The current best computational docking algorithms are discussed, and strategies for improvement are suggested.

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Dikic, Jasmina, Georgij Kostiuk, Virginijus Siksnys, and Ralf Seidel. "Protein diffusion on DNA." Diffusion fundamentals 20 82013) 73, S. 1, 2013. https://ul.qucosa.de/id/qucosa%3A13660.

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Dikic, Jasmina, Georgij Kostiuk, Virginijus Siksnys, and Ralf Seidel. "Protein diffusion on DNA." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-183614.

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5

Cao, Zehui. "Designer oligonucleotides for probing dna-protein and protein-protein interactions." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0008333.

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6

Fekete, Richard Alfred. "Characterizing the protein and DNA interactions of the F plasmid DNA binding protein, TraM." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ60291.pdf.

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7

Seibert, Mark Marvin. "Protein Folding and DNA Origami." Doctoral thesis, Uppsala universitet, Molekylär biofysik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121549.

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In this thesis, the folding process of the de novo designed polypeptide chignolin was elucidated through atomic-scale Molecular Dynamics (MD) computer simulations. In a series of long timescale and replica exchange MD simulations, chignolin’s folding and unfolding was observed numerous times and the native state was identified from the computed Gibbs free-energy landscape. The rate of the self-assembly process was predicted from the replica exchange data through a novel algorithm and the structural fluctuations of an enzyme, lysozyme, were analyzed. DNA’s structural flexibility was investigated through experimental structure determination methods in the liquid and gas phase. DNA nanostructures could be maintained in a flat geometry when attached to an electrostatically charged, atomically flat surface and imaged in solution with an Atomic Force Microscope. Free in solution under otherwise identical conditions, the origami exhibited substantial compaction, as revealed by small angle X-ray scattering. This condensation was even more extensive in the gas phase. Protein folding is highly reproducible. It can rapidly lead to a stable state, which undergoes moderate fluctuations, at least for small structures. DNA maintains extensive structural flexibility, even when folded into large DNA origami. One may reflect upon the functional roles of proteins and DNA as a consequence of their atomic-level structural flexibility. DNA, biology’s information carrier, is very flexible and malleable, adopting to ever new conformations. Proteins, nature’s machines, faithfully adopt highly reproducible shapes to perform life’s functions robotically.

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Williams, Nicola Louise. "Protein gates in DNA gyrase." Thesis, University of Leicester, 1999. http://hdl.handle.net/2381/29641.

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DNA gyrase is a molecular machine comprising a series of protein gates. The opening and closing of these gates enables the passage of one segment of double-stranded DNA (the T segment) through a transient break in another (the G segment). We have blocked the passage of DNA through each of three dimer interfaces within gyrase and investigated the effects on gyrase mechanism. This has been achieved by cross-linking novel cysteine residues on either side of the dimer interface, or trapping the dimer interface in a closed conformation using a non-hydrolysable ATP analogue. Cross-linking a pair of novel cysteine residues on either side of the bottom dimer interface of DNA gyrase blocks catalytic supercoiling. Limited strand passage is allowed, but T-segment release is prevented. In contrast, ATP-independent relaxation of negatively supercoiled DNA is completely abolished, suggesting that T-segment entry via the bottom gate is blocked. These findings support a two-gate model for supercoiling in by DNA gyrase and suggest that relaxation by gyrase is the reversal of supercoiling. Cross-linking a truncated version of gyrase, (A642B2) that lacks the DNA wrapping domains, does not block ATP-dependent relaxation. This indicates that passage of DNA through the bottom dimer interface is not essential for this reaction. Using a similar approach, we have locked the DNA gate of gyrase using cysteine cross-linking. We show that this locked-gate mutant can bind quinolone drugs and perform DNA cleavage. However, locking the DNA gate prevents strand passage and the ability of DNA to stimulate ATP hydrolysis.

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Stafford, Ryan Leonard Grubbs Robert H. "Design of protein-DNA dimerizers /." Diss., Pasadena, Calif. : Caltech, 2008. http://resolver.caltech.edu/CaltechETD:etd-08232007-154048.

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Neaves, Kelly Jane. "Atomic force microscopy of DNA and DNA-protein constructs." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608615.

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Tuusa, J. (Jussi). "Human DNA polymerase ε:expression, phosphorylation and protein-protein interactions." Doctoral thesis, University of Oulu, 2001. http://urn.fi/urn:isbn:9514265815.

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Abstract DNA replication is a process in which a cell duplicates its genome before cell division, and must proceed accurately and in organized manner to guarantee maintenance of the integrity of the genetic information. DNA polymerases are enzymes that catalyse the synthesis of the new DNA strand by utilizing the parental strand as a template. In addition to chromosomal replication, DNA synthesis and therefore DNA polymerases are also needed in other processes like DNA repair and DNA recombination. The DNA polymerase is an essential DNA polymerase in eukaryotes and is required for chromosomal DNA replication. It has also been implicated in DNA repair, recombination, and in transcriptional and cell cycle control. The regulation of the human enzyme was explored by analysing its expression, phosphorylation and protein-protein interactions. Expression of both the A and B subunits of the human DNA polymerase ε was strongly growth-regulated. After serum-stimulation of quiescent fibroblasts, the steady-state mRNA levels were up-regulated at least 5-fold. In actively cycling cells, however, the steady-state mRNA and protein levels fluctuated less than 2-fold, being highest in G1/S phase. The promoter of the B subunit gene was analysed in detail. The 75 bp core promoter was essentially dependent on the Sp1 transcription factor. Furthermore, mitogenic control of the promoter required an intact E2F binding element, and binding of E2F2, E2F4 and p107 was demonstrated in vitro. A down-regulation element, located immediately downstream from the core promoter, bound E2F1, NF-1 and pRb transcription factors. A model of the promoter function is presented. Topoisomerase IIβ binding protein 1 (TopBP1) was found to be associated with human DNA polymerase ε. TopBP1 contains eight BRCT domains and is homologous to Saccharomyces cerevisiae Dpb11, Schizosaccharomyces pombe Cut5, Drosophila melanogaster Mus101 and the human Breast Cancer susceptibility protein 1 (BRCA1). TopBP1 is a phosphoprotein, whose expression is induced at the G1/S border and is required for chromosomal DNA replication. It co-localizes in S phase with BRCA1 into discrete foci, which do not represent sites of ongoing DNA replication. However, if DNA is damaged or replication is blocked in S phase cells, TopBP1 and BRCA1 re-localize into proliferating cell nuclear antigen (PCNA) containing foci that represent stalled replication forks. Finally, phosphorylation of DNA polymerase ε was described and at least three immunologically distinct and differentially phosphorylated forms were shown to exist. Phosphorylation is on serine and threonine residues and shows a cell cycle dependent fluctuation, but is not affected by DNA damage or by inhibition of DNA replication. BRCA1 co-immunoprecipitates with a hypophosphorylated form of DNA polymerase ε. In contrast, TopBP1 was shown to be associated with a hyperphosphorylated form.

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Kaliyaperumal, Saravanan. "hMSH6 Protein Phosphorylation: DNA Mismatch Repair or DNA Damage Signaling?" Connect to full text in OhioLINK ETD Center, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=mco1242933021.

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Dissertation (Ph.D.)--University of Toledo, 2009.
"In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Sciences." Title from title page of PDF document. Bibliography: p. 174-180, p. 201-238.

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Buck, Dorothy E. "The topology and geometry of DNA and DNA-protein interactions /." Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3008290.

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DiCapua, Elisabeth. "Complexes of recA protein with DNA /." [S.l.] : [s.n.], 1986. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=8212.

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Sauvé, Debra Marie. "Protein-DNA interactions and chromosome condensation." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ27237.pdf.

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Bisset, Louise Clair. "Fluorescence of a DNA-binding protein." Thesis, University of Newcastle Upon Tyne, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320129.

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Chen, Kai. "Use of green fluorescent protein for the analysis of protein-protein and protein-DNA interactions." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/4886.

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Restriction modification (RM) systems play a crucial role in preventing the entry of foreign DNA into the bacterial cell. The best studied Type I RM system is EcoKI from Escherichia coli K12. Both bacteriophage and conjugative plasmids have developed a variety of strategies to circumvent the host RM system. One such strategy involves the production of antirestriction proteins that mimic a short segment of DNA and efficiently inhibit the RM system. The main aim of this project was to analyse the interaction of EcoKI and its cognate methylase (MTase) with the T7 antirestriction protein, known as overcome classical restriction (Ocr), and various ArdA antirestriction proteins. Currently, there is a paucity of structural data on the complex formed between the Type I system and the antirestriction proteins. The aim of this work was twofold; (i) compare the interaction of MTase with DNA and Ocr and (ii) quantify the strength of interaction between MTase and various ArdA proteins. The MTase was fused to the Green Fluorescent Protein (GFP) to facilitate determination of the orientation of interaction with DNA and Ocr. Time resolved fluorescence measurements were carried out using the GFP-MTase fusion to determine the fluorescence lifetime and anisotropy decay. These experiments were conducted using a time resolved fluorescence instrument fabricated in-house. The values determined in these experiments were then used to perform fluorescence resonance energy transfer (FRET) measurements with fluorescently labelled DNA or Ocr. These measurements gave information concerning the relative orientation of the MTase with either DNA or Ocr. The GFP-MTase fusion was also used to quantify the strength of interaction with various ArdA proteins. Previous attempts to determine the strength of interaction between MTase and ArdA proteins by employing conventional techniques have been unsuccessful. Therefore, a novel method was developed that exploits the interaction of MTase with a cation exchange medium, which can subsequently be displaced upon binding to ArdA. This method facilitated the determination, for the first time, of a set of binding affinities for the MTase and ArdA interaction.

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Barbeau, Olivier R. "Pyridopyrimidinone and quinolinone inhibitors of DNA-dependent protein kinase (DNA-PK)." Thesis, University of Newcastle Upon Tyne, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.512184.

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Cobb, Andrew Martin. "Resolving the flexibility and intricacy of DNA repair protein-DNA interactions." Thesis, University of East Anglia, 2010. https://ueaeprints.uea.ac.uk/10586/.

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Within all cells, complex molecular systems exist that are responsible for maintaining genome stability by detecting and repairing dangerous alterations in DNA. Ensuring the accurate and efficient functioning of such systems is necessary for the preservation of DNA integrity and avoidance of disease. The flexible and diverse modes of DNA-binding exhibited by human p53 permits this ‘guardian of the genome’ to elicit versatile cellular activities that are crucial in monitoring threats to genome dynamics and conducting appropriate responses. In conjunction with its sequence-specific DNA-binding activity that is essential to target gene transactivation, p53 can bind to unusual DNA structures independent of DNA sequence and it has been proposed this activity may allow p53 to interact with detrimental secondary structures that arise in unstable genomic regions. To provide further insight into p53-DNA interactions, an in vitro DNA binding assay was developed that was used to characterise binding properties towards several DNA molecules to allow comparison of non-specific, sequence-specific and structurespecific binding. It was determined that unusual structures in DNA significantly enhanced p53 binding in non-sequence specific DNA and that the presence of internal hairpin regions induced binding comparable to sequence-specific binding. In vivo p53-DNA interactions were also quantified using chromatin immunoprecipitation and variations in preference to different response element sequences was ascertained. DNA binding is also central to the ability of Ku proteins to function as essential components of non-homologous end joining and telomere maintenance in eukaryotes. Prokaryotic homologues of Ku proteins that function as homodimers in two-component repair systems have also been identified. Recently, 3 Ku homologues in Streptomyces coelicolor were reported, but very little is currently known regarding their biological activity. It was discovered that all 3 Ku proteins exhibited varied independent DNA-binding properties that were influenced by DNA topology, size and end-structure. Unusually for Ku, it was found 1 of these proteins exhibited strong binding to single-stranded DNA. Precipitation assays determined that these proteins may act as DNA end synapsis mediators during the DNA endjoining process and ligation experiments revealed Ku was responsible for rigidifying DNAs or completely inhibiting ligation activity, probably via DNA end-protection activity. Experimental evidence indicated that specific interactions could occur between S. coelicolor Ku suggesting these proteins form both homodimers and heterodimers.

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Dulic, Anna. "Studies on protein : protein interactions in mammalian DNA base-excision repair." Thesis, University College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.404820.

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Yang, Yi. "Ultrafast Hydration Dynamics on Protein Surface and at Protein-DNA Interface." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261450640.

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Wiener, Julius [Verfasser], and Matthias [Akademischer Betreuer] Meier. "On DNA-conjugated antibodies for protein detection and protein-interaction analysis." Freiburg : Universität, 2021. http://d-nb.info/123396626X/34.

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23

Fornés, Crespo Oriol 1983. "On the characterization of protein-DNA interactions using statistical potentials and protein-protein interactions." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/320192.

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Protein-DNA interactions are indispensable players in the daily activities of cells. DNA-binding proteins regulate gene expression and are responsible of DNA replication, packaging, repair and recombination. Among them, transcription factors activate/repress gene transcription by binding to specific genomic sites. Hence, the characterization of transcription factor binding sites turns out to be crucial in order to understand gene regulation. In this context, the development of computational tools is foremost. Here, I show the prediction of redundant transcription factors in yeast using a combination of homology-based tools and protein-protein interactions. The approach was automated and incorporated into ModLink+, an online and user-friendly tool to infer the fold of remote homologs. Moreover, I describe split-statistical potentials for protein-DNA interactions. Finally, I present SHAITAN, a statistical/homology-based approach that can be used to both predict transcription factor binding sites and infer the more likely transcription factors to bind a DNA sequence of interest.
Les interaccions proteïna-ADN són indispensables en l’activitat diària de les cèl•lules. Les proteïnes que participen en aquestes interaccions s’encarreguen de la regulació de l'expressió gènica i són responsables de la replicació, l'empaquetament, la reparació i la recombinació de l’ADN. Entre aquestes proteïnes, els factors de transcripció activen/reprimeixen la transcripció de gens mitjançant la unió a llocs específics dins el genoma. Per tant, la caracterització dels llocs d'unió dels diferents factors de transcripció és crucial per tal d’entendre com funciona la regulació gènica. En aquest context, desenvolupar eines computacionals és importantíssim. En aquesta tesi predict redundància entre factors de transcripció de llevat eines fent servir eines basades en homologia i interaccions proteïna-proteïna. Aquesta aproximació va ser automatitzada i incorporada a ModLink+, una eina accessible des d’internet i fàcil d'usar per a inferir el plegament de proteïnes a partir d’homòlegs remots. D'altra banda, descric potencials estadístics fraccionats per a interaccions proteïna-ADN. Finalment presento SHAITAN, una aproximació basada en homologia i potencials estadistics que pot ser utilitzada per a predir els llocs d'unió de factors de transcripció així com per saber quins factors de transcripció són més probables que s’uneixin a una determinada seqüència d'ADN.

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Fancy, David A. "Site directed metal-catalyzed protein oxidation : a new method for investigating protein-protein interactions /." Digital version accessible at:, 1998. http://wwwlib.umi.com/cr/utexas/main.

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Fellinger, Karin. "Analysis of Protein Interactions Controlling DNA Methyltransferases." Diss., lmu, 2009. http://nbn-resolving.de/urn:nbn:de:bvb:19-98919.

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Mutalib, Abdul Rahim Bin Abdul. "DNA and protein characterisatiob of Mycoplasma hyopneumoniae." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339589.

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Tsai, Francis T. F. "Crystallographic studies of DNA gyrase B protein." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390473.

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28

Lisgo, Steven Newton. "Human TBX22 expression and protein-DNA interactions." Thesis, University of Newcastle Upon Tyne, 2010. http://hdl.handle.net/10443/1066.

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Cleft palate is one of the most common birth abnormalities. Figures published in 2006 by the American Centres for Disease Control and Prevention, report the incidence of those born in the United States with a cleft palate without the presence of a cleft lip (CPI) to be 6.39 for every 10000 in the three years between 1999 to 2001 and for cleft lip in association with a cleft palate (CLP) to be even greater - 10.48 per 10000 live births. In 2001, Braybrook and colleagues reported that mutations in the TBX22 gene cause X-linked cleft palate (CPX), a disease characterised by a cleft of the secondary palate and is often seen in association with ankyloglossia (tongue-tie) (Braybrook et al. 2001). A cleft of the secondary palate arises as a consequence of disturbance to correct development during palatogenesis: an anomaly in palatal shelf growth; delayed or failed shelf elevation; defective shelf fusion or a failure of medial edge epithelium cell death. This thesis reveals that the expression of TBX22 during these key developmental events in human embryos is consistent with the phenotype seen in CPX. To enable an investigation for TBX22 target genes, a DNA binding sequence is determined for the TBX22 protein. This sequence is used to generate a generic TBX22 DNA binding site, the presence of which is screened for in promoter regions, defined as 2kb upstream of transcription start sites. 132 genes were selected as candidate TBX22 targets on the basis that they underlie human disorders that include a cleft palate. The screen shows that 28 of these genes have at least one perfect or near perfect match to the generic TBX22 DNA binding site. Of these, only two both contained a perfect TBX22 generic DNA binding site and mouse mutants also had cleft palates: SUMO1 and MSX1. Interaction between SUMO1 and TBX22 has already been shown (Andreou et al. 2007). This study investigated MSX1 as a downstream target of TBX22 using a luciferase reporter gene construct in vitro. The results showed that in the presence of TBX22, the luciferase signal was reduced and support MSX1 being a downstream target gene of TBX22. These findings further the understanding of the molecular networks regulating craniofacial development. Unravelling these complex interactions is crucial to identifying the mechanisms of oro-facial clefting, important steps towards improved methods of counselling, treatment and prevention of these common birth disorders.

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Dezfouli, Mahya. "Barcoded DNA Sequencing for Parallel Protein Detection." Doctoral thesis, KTH, Genteknologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-159506.

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The work presented in this thesis describes methodologies developed for integration and accurate interpretation of barcoded DNA, to empower large-scale-omics analysis. The objectives mainly aim at enabling multiplexed proteomic measurements in high-throughput format through DNA barcoding and massive parallel sequencing. The thesis is based on four scientific papers that focus on three main criteria; (i) to prepare reagents for large-scale affinity-proteomics, (ii) to present technical advances in barcoding systems for parallel protein detection, and (iii) address challenges in complex sequencing data analysis. In the first part, bio-conjugation of antibodies is assessed at significantly downscaled reagent quantities. This allows for selection of affinity binders without restrictions to accessibility in large amounts and purity from amine-containing buffers or stabilizer materials (Paper I). This is followed by DNA barcoding of antibodies using minimal reagent quantities. The procedure additionally enables efficient purification of barcoded antibodies from free remaining DNA residues to improve sensitivity and accuracy of the subsequent measurements (Paper II). By utilizing a solid-phase approach on magnetic beads, a high-throughput set-up is ready to be facilitated by automation. Subsequently, the applicability of prepared bio-conjugates for parallel protein detection is demonstrated in different types of standard immunoassays (Papers I and II). As the second part, the method immuno-sequencing (I-Seq) is presented for DNAmediated protein detection using barcoded antibodies. I-Seq achieved the detection of clinically relevant proteins in human blood plasma by parallel DNA readout (Paper II). The methodology is further developed to track antibody-antigen interaction events on suspension bead arrays, while being encapsulated in barcoded emulsion droplets (Paper III). The method, denoted compartmentalized immuno-sequencing (cI-Seq), is potent to perform specific detections with paired antibodies and can provide information on details of joint recognition events. Recent progress in technical developments of DNA sequencing has increased the interest in large-scale studies to analyze higher number of samples in parallel. The third part of this thesis focuses on addressing challenges of large-scale sequencing analysis. Decoding of a huge DNA-barcoded data is presented, aiming at phase-defined sequence investigation of canine MHC loci in over 3000 samples (Paper IV). The analysis revealed new single nucleotide variations and a notable number of novel haplotypes for the 2nd exon of DLA DRB1. Taken together, this thesis demonstrates emerging applications of barcoded sequencing in protein and DNA detection. Improvements through the barcoding systems for assay parallelization, de-convolution of antigen-antibody interactions, sequence variant analysis, as well as large-scale data interpretation would aid biomedical studies to achieve a deeper understanding of biological processes. The future perspectives of the developed methodologies may therefore stem for advancing large-scale omics investigations, particularly in the promising field of DNA-mediated proteomics, for highly multiplex studies of numerous samples at a notably improved molecular resolution.

QC 20150203

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Peacock, M. O. "UVA photosensitisers, protein oxidation and DNA repair." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1437625/.

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Pharmaceuticals can interact with sunlight to cause skin photosensitization and increase skin cancer risk. Interaction of drug molecules with solar UVA or visible radiation results in electronically excited states that damage biomolecules directly or indirectly via the formation of reactive species (RS). RS cause damage to DNA and its precursors, as well as to proteins and lipids. I have devised methods to examine the induction of oxidative protein damage in cultured human cells and used these to investigate the effects of UVA-activated photosensitizing drugs on the formation of protein carbonyls and the oxidation of protein thiol groups. I examined the effects of 6-thioguanine (6-TG) (a surrogate for azathioprine, an immunosuppressant), fluoroquinolone antibiotics, and the malignant melanoma therapeutic vemurafenib, each of which is associated with clinical skin photosensitivity and increased skin cancer risk in patients. All of these drugs are shown to be synergistically cytotoxic with UVA in cultured human cells and toxicity is concurrent with the generation of RS. I identify singlet oxygen as a major component of these photochemically-generated RS and show that widespread protein oxidation is caused. The Ku DNA repair heterodimer is identified as one of several targets for oxidation damage and I show using biochemical assays that damage to Ku compromises its function in the repair of DNA strand breaks. UVA irradiation of cells treated with the photosensitisers significantly compromises the removal of potentially mutagenic DNA lesions by the nucleotide excision repair pathway. Since this DNA repair pathway removes sunlight-induced DNA lesions and is the major protection against skin cancer, my findings have implications for the increased skin cancer risk associated with azathioprine. The ability of structurally dissimilar drugs to recapitulate the effects of 6-TG suggests that the observations may share a common mechanism.

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Mahmutovic, Anel. "Reaction-Diffusion kinetics of Protein DNA Interactions." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-263527.

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Transcription factors need to rapidly find one specific binding site among millions of nonspecific sites on the chromosomal DNA. In this thesis I use various aspects of reaction-diffusion theory to investigate the interaction between proteins and DNA and to explain the searching, finding and binding to specific operator sites. Using molecular dynamics methods we calculate the free energy profile for the model protein LacI as it leaves a nonspecific stretch of DNA and as it slides along DNA. Based on the free energy profiles we estimate the microscopic dissociation rate constant, kdmicro ~1.45×104s-1, and the 1D diffusion coefficient, D1 ~ 0.05-0.29 μm2s-1 (2-40μs to slide 1 basepair (bp)). At a non-atomistic level of detail we estimate the number of microscopic rebindings before a macroscopic dissociation occurs which leads to the macroscopic residence time, τDmacro ~ 48±12ms resulting in a in vitro sliding length estimate of 135-345bp. When we fit the DNA interaction parameters for in vivo conditions to recent single molecule in vivo experiments we conclude that neither hopping nor intersegment transfer contribute to the target search for the LacI dimer, that it appears to bind the specific Osym operator site as soon as it slides into it, and that the sliding length is around 40bp in the cell. The estimated in vivo D1 ~ 0.025 μm2s-1 is higher than expected from estimates of D1 based on viscosity and the atomistic simulations. Surprisingly, we were also forced to conclude that the nonspecific association for the LacI dimer appeared reaction limited which is in conflict with the free energy profile. This inconsistency is resolved by allowing for steric effects. Using reaction-diffusion theory and simulations we show that an apparent reaction limited association can be diffusion limited if geometry and steric effects are taken into account. Furthermore, the simulations show that a protein binds ~2 times faster to a DNA molecule with a helical reactive patch than to a stripe patch running along the length of the DNA. This facilitated binding has a direct impact on the search time especially in the presence of other DNA binding proteins.

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Cselik, Frank. "DNA and protein interactions in filamentous bacteriophages." Thesis, University of Cambridge, 1986. https://www.repository.cam.ac.uk/handle/1810/270397.

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Plaxco, Kevin W. Goddard William A. "Protein-DNA interactions molecular modeling and energetics /." Diss., Pasadena, Calif. : California Institute of Technology, 1994. http://resolver.caltech.edu/CaltechTHESIS:11112009-144801757.

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Thesis (Ph. D.)--California Institute of Technology, 1994. UM #94-06,216.
Advisor names found in the Acknowledgements pages of the thesis. Title from home page. Viewed 01/15/2010. Includes bibliographical references.

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Pond, Sergei L. "Modeling evolution of protein coding DNA sequences." Diss., The University of Arizona, 2003. http://hdl.handle.net/10150/289906.

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We develop a new class of computationally feasible stochastic models for statistical analysis of genetic sequence evolution and inference of properties of the underlying substitution processes in the context of maximum likelihood framework. Existing models for evolution of protein coding sequences allow site to site variation in non-synonymous substitution rates, but assume that the rate of synonymous substitutions is constant for all sites. New models provide a rigorous statistical framework for testing the hypothesis of synonymous rate constancy, and enable a host of data exploration and analysis tools. For several indicative data sets, the constancy assumption is shown to be violated, and some possible explanations are given. We also present an algorithm for improving efficiency of maximum likelihood evaluations, and discuss HyPhy--a user friendly and publicly distributed software implementation of our methods.

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Drew, Gail L. "DNA-Protein Cross-Linking by Pyrrolizidine Alkaloids." DigitalCommons@USU, 1997. https://digitalcommons.usu.edu/etd/3919.

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Pyrrolizidine alkaloids (PAs) are natural plant compounds found in hundreds of plant species worldwide and are reported to have cytotoxic, carcinogenic, antimitotic, and gentotoxic activity. PAs are metabolized by the cytochrome P450 (CYP) sytem to the pyrrole or the N-oxide form. They pyrroles are bifunctional electrophillic alkylators that bind cellular nucleophiles such as DNA and proteins and disrupt normal cell processes, including DNA replication and gene transcription, and can cause megalocytosis. The pyrroles dehyrosenecionine (DHSN) and dehydromoncrotaline (DHMO) are among the most potent PA cross-linkers and inducers of megalocytosis. DHSN and DHMO-induced cross-links in cultured normal (MDBK) and neoplastic (MCF7) cells were nalyzed by SDS-PAGE and Western blot and both were found to contain the protein actin. Actin is crucial to DNA replication and is known to be involved in cross-links induced by cis-dichlorodiammine platinum II (cistplatin), a well known cross-linking drug used for the treatment of cancer. Actin cross-linking may explain the antimitotic, megalocytotic, and anticarcinogenic effects of PAs. Since protein cross-linking is an important mode of action for PAs, we were interested in what characteristics of the protein might make it a good nucleophilic target. Thus, further research was undertaken based on the hypothesis that cysteine residues, and specifically free sulfhydryl groups, are attractive targets for the bifunctional electrophilic alkylators DHSN and DHMO. Nucleophiles were selected for their abundance in the cell, their cysteine content, and their relationship to the documented side effects of PAs. Actin, glutathione (GSH), metallothionein, topoisomerase II, and cysteine were all found to cross-link with DHSN and DHMO in vitro while methionine, with no free sulfhydryl groups, did not cross-link. Our results support the hypothesis that cysteine residues are a key characteristic of proteins that are cross-linked by PAs. The cross-links could have negative effects to the cell as in the case of binding actin or topoisomerase II to alter normal DNA processes and replication, or beneficial effects such as binding to electrophillic scavengers like GSH or metallothionine as a detoxifying mechanism. the nucleophiles we tested in vitro and found to form cross-links with DHSN and DHMO may help to explain the antimitotic carcinogenic, and anticarcinogenic effects of PAs.

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Nilsson, Mikael. "Protein-DNA recognition : in vitro evolution and characterization of DNA-binding proteins /." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4269.

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Aristegui, Sonsoles Rodriguez. "Substituted chromenones and isocoumarins as DNA-dependent protein kinase (DNA-PK)inhibitors." Thesis, University of Newcastle Upon Tyne, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.533701.

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Turner, David Paul. "Recognition of DNA by the E.coli DNA G:T mismatch endonuclease (VSR protein)." Thesis, University of Newcastle Upon Tyne, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.364797.

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Stockley, Martin Lee. "Design and synthesis of selective DNA-dependent protein kinase (DNA-PK) inhibitors." Thesis, University of Newcastle Upon Tyne, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369816.

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Berge, Torunn. "Structural analysis of DNA and DNA-protein complexes using atomic force microscopy." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621339.

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Sun, Qing. "Mining Structure Patterns Based on 3D Features in the Protein-DNA and Protein-protein Complex." Diss., North Dakota State University, 2018. https://hdl.handle.net/10365/28967.

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For a long time, researchers have been searching for the ?recognition codes? of protein complexes, which determine what DNA sequence or other protein a protein can bind to. The binding part prediction of protein complexes have important applications in many biological research fields, such as cleavage enzyme design and drug design and so on. Most sequence-based and PWM methods only capture sequence features on the protein interfaces and ignore the crucial spatial attributes of the features. This study investigates the recognition codes from a new angle, in which the preferred binding modes are captured using local structural motifs spanning the protein-DNA, protein-protein and protein-ligand interfaces. Using product graph, we transformed the structural motif discovery problem into a search for maximal cliques. These motifs include more information than the traditional amino acid-base contacting pairs. For example, in the protein-DNA interfaces research, we studied two domains, Zinc-finger and Helix-Turn-Helix (HTH), that both used a recognition helix to interact with DNA. In each domain, we found a few frequent structural motifs spanning the protein-DNA interfaces. Each motif includes at least 2 amino acids and 1 nucleotide from both sides of the interfaces. The motifs specify not only the types of amino acids and nucleotides involved in the interaction, but also the distances between them and their relative orientation. The same method has been implemented in protein-protein and protein-ligand complexes. These motifs reveal preferred binding modes at the interfaces that involve more entities than the traditional contacting pairs. The biological and statistical significance of the motifs were confirmed using evolutionary conservation analysis and bootstrapping We also performed many other tests to evaluate our motifs? critical roles in the interactions. For example, we compared our motifs with experimentally verified hotspots. We also compared our method with other computational prediction methods to assess the effectiveness of the method. Our results confirmed that the graph motifs discovered in this study play important roles in protein-DNA, protein-protein and protein-ligand interactions. We believe that the proposed graph method will be a very helpful tool for studying protein complexes interaction and other types of molecular interactions.

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42

Smith, Ngaio Charlotte. "Investigating the role of protein-protein and protein-DNA interactions in the function of Isl1." Thesis, The University of Sydney, 2019. http://hdl.handle.net/2123/20655.

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LIM-homeodomain (LIM-HD) transcription factors act as key developmental regulators, through their ability to both bind DNA through homeodomain-DNA interactions, and to form larger complexes through protein-protein interactions. Many interactions that have been characterised are formed using their LIM domains, but likely also involve other regions, which have not yet been described for many LIM-HD proteins. The LIM-HD protein Isl1 has been implicated in the development of many tissues. However, relatively little detail is known about how Isl1 functions in these systems and the pathways in which it acts. The first part of this thesis aimed to identify and characterise novel binding partners for Isl1. An earlier project isolated ~180 potential binding partners through use of yeast two-hybrid mating screens; throughout this thesis further methodology was developed to identify additional proteins in a medium throughput manner. Validation protocols were then applied to determine which interactors were likely to represent biologically relevant interaction partners for Isl1. The second part of this thesis focussed on the mechanisms by which Isl1 and Lhx3 direct cell fate determination in the developing central nervous system. These proteins, along with Ldb1, interact via LIM:LID interactions to form cell-specific transcriptional complexes that target genes different to those targeted by either LIM-HD protein alone. It was not known if the homeodomains target these different sites solely because of the LIM:LID interactions or if the homeodomains themselves bind cooperatively to DNA. The DNA-binding behaviour of various iterations of the Lhx3/Isl1/Ldb1 complex are described, and structural characterisation of the Isl1/Lhx3 DNA-binding unit has been pursued. These data provide new insights into the mechanisms by which Isl1 and Lhx3 work together in regulating gene expression.

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Cridland, Peter James. "An investigation of the protein-protein interactions of human DNA topoisomerase II." Thesis, University of Newcastle Upon Tyne, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.364796.

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Wentzell, Lois Marie. "DNA communications by the SfiI restriction endonuclease." Thesis, University of Bristol, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388002.

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El, Hassan M. "The geometry and structure of DNA and its role in DNA/protein recognition." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361765.

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Amato, Nicholas J. "Impact of DNA Structure and Aeropyrum pernix Single-Strand DNA Binding Protein on Oxidative Damage to DNA." University of Toledo / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1372296254.

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47

Luo, Dan. "Novel crosslinking technologies to assess protein-DNA binding and DNA-DNA complexes for gene delivery and expression." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1114436532.

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Luo, Dan. "Novel crosslinking technologies to assess protein-DNA binding and DNA-DNA complexes for gene delivery and expression /." Connect to resource, 1998. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1114436532.

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Aldridge, Matthew J. "Functional analysis of a novel DNA binding protein of Streptomyces coelicolor." Thesis, Swansea University, 2012. https://cronfa.swan.ac.uk/Record/cronfa42406.

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Secondary metabolism occurs after the main growth phase in Streptomyces. A 'transition phase' occurs to remodel global patterns of gene expression at the onset of physiological and developmental differentiation. Many different signals influence this transition phase, integrating, for example, information on nutritional status, growth rate, and stress responses. Several pleiotropic transcription factors that regulate the transition phase have been identified, but aspects of epigenetic control of gene expression are not well understood. This study focused on the characterisation of a novel gene sco2075 in S. coelicolor encoding a protein that combines a histone-like domain with a conserved DksA-like domain, the latter considered a ppGpp cofactor. The protein is important for integrating responses to both oxidative and osmotic stresses. The sco2075- mutant strain is sensitive to oxidative stress at least in part due to reduced induction of the alternative sigma factor sigmaR. SCO2075, similarly to E. coli DksA, may play a possible role in the liberation of core RNA polymerase to bind alternative sigma factors such as sigmaR. In addition DSCO2075 has an altered topological profile of a reporter plasmid under osmotic stress, showing little alteration in negative supercoiling when compared to the significant increase in wildtype. DSCO2075 also has a reduction in aerial hyphae and a possible reduction in actinorhodin production when grown with osmolyte. The histone-like domain of SCO2075 binds DNA non-specifically. SCO2075 expression appears to coincide with diffused FtsZ expression prior to Z-ring formation when SCO2075 appears to become nucleoid associated. Analysis of pre-spore compartment lengths showed SCO2075 is one of several nucleoid associated proteins involved in nucleoid compaction during aerial hyphal erection and sporulation. Absence of sco2075, however, does not affect the production of unigenomic spore chains. Finally, over-expression of SCO2075 suppresses defects in secondary metabolism of a relA mutant affected in ppGpp synthesis. SCO2075 could potentially be a new type of regulator, likely acting as a node to integrate stress and physiological cues by modulating DNA topology/compaction and RNA polymerase activity.

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Petzold, Herman E. III. "Discovery of New Protein-DNA and Protein-Protein Interactions Associated With Wood Development in Populus trichocarpa." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/89363.

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The negative effects from rising carbon levels have created the need to find alternative energy sources that are more carbon neutral. One such alternative energy source is to use the biomass derived from forest trees to fulfill the need for a renewable alternative fuel. Through increased understanding and optimization of regulatory mechanisms that control wood development the potential exists to increase biomass yield. Transcription factors (TFs) are DNA-binding regulatory proteins capable of either activation or repression by binding to a specific region of DNA, normally located in the 5-prime upstream promoter region of the gene. In the first section of this work, six DNA promoters from wood formation-related genes were screened by the Yeast One-Hybrid (Y1H) assay in efforts to identify novel interacting TFs involved in wood formation. The promoters tested belong to genes involved in lignin biosynthesis, programmed cell death, and cambial zone associated TFs. The promoters were screened against a mini-library composed of TFs expressed 4-fold or higher in differentiating xylem vs phloem-cambium. The Y1H results identified PtrRAD1 with interactions involving several of the promoters screened. Further testing of PtrRAD1 by Yeast Two-Hybrid (Y2H) assay identified a protein-protein interaction (PPI) with poplar DIVARACATA RADIALIS INTERACTING FACTOR (DRIF1). PtrDRIF1 was then used in the Y2H assay and formed PPIs with MYB/SANT domain proteins, homeodomain family (HD) TFs, and cytoskeletal-related proteins. In the second section of this work, PPIs involving PtrDRIF1s' interaction partners were further characterized. PtrDRIF1 is composed of two separate domains, an N-terminal MYB/SANT domain that interacted with the MYB/SANT domain containing PtrRAD1 and PtrDIVARICATA-like proteins, and a C-terminal region containing a Domain of Unknown Function 3755 (DUF3755). The DUF3755 domain interacted with HD family members belonging to the ancient WOX clade and Class II KNOX domain TFs. In addition, PtrDRIF1 was able to form a complex between PtrRAD1 and PtrWOX13c in a Y2H bridge assay. PtrDRIF1 may function as a regulatory module linking cambial cell proliferation, lignification, and cell expansion during growth. Combined, these findings support a role for PtrDRIF1 in regulating aspects of wood formation that may contribute to altering biomass yield.
Ph. D.

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Dissertations / Theses on the topic 'Protein-DNA'

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