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Dissertations / Theses on the topic 'DNA binding studies'

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Published: 10 December 2022
Last updated: 28 January 2023

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1

Umurtak, H. B. "Studies on DNA-binding peptides]." Thesis, University of Southampton, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235192.

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2

Rodríguez, Armando Chapin. "Structure-function studies of DNA-binding motors." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619565.

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3

Komori, Hirofumi. "Structural studies on DNA-binding proteins : DNA replication initiator and DNA photolyase." 京都大学 (Kyoto University), 2002. http://hdl.handle.net/2433/150005.

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4

Daly, Colette Lynn. "Binding studies using membrane electrodes." Thesis, University of Salford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252942.

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The research embodied within this thesis has contributed to the development and application of a novel electrode technique. The electrodes fabricated herein consist of a thin PVC/Poly (vinylchloride) membrane which is made sensitive to a particular organic cation, for example Acridine Orange. The only requirements necessary to make an electrode were that the substance to be incorporated into the membrane be cationic, water soluble and surface active. These membrane electrodes gave an emf directly proportional to the log of the ( concentration of organic cations present in solution.
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5

Menderin, Nathan. "Studies on the Human Sp1 DNA-Binding Domain." Thesis, University of Exeter, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507135.

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6

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

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HMG-D is a 112-residue, non-histone chromosomal protein from Drosophila melanogaster and is a member of the class of non-sequence specific HMGB proteins. The present project was based on the observation that other HMGB complexes that had been solved by NMR had a phenylalanine residue at a key interfacial location (corresponding to position 12 in HMG-D), whereas those like HMG-D that gave few intermolecular NOE cross peaks generally had a tyrosine at this location. This tyrosine was known to be involved in hydrogen-bonding to the DNA in a related complex that had been solved crystallographically. The Y12F mutant of full-length HMG-D was expressed and purified in isotope-labelled form suitable for NMR spectroscopy, and a set of multidimensional triple resonance experiments used to derive assignments for the backbond resonances of the protein both free and in complex with the dA2 bulge DNA. Sidechain assignments for the protein were obtained by a combination of “CCH”-transfer-based experiments and NOE spectra, while nearly complete assignments for the DNA in the complex were obtained from a combination of homonuclear 2D NOESY and TOCSY experiments together with filtered NOESY experiments where just cross peaks between protons both of which were not coupled to heteronuclei were selected. Filtered NOESY-based experiments were used to observe intermolecular NOE cross peaks in isolation, and, in contrast to the case of the wild-type complex, these experiments yielded around 50 intermolecular interactions. Together with an extensive set of assigned intramolecular NOE constraints, these formed the basis for a calculation of the structure of the complex starting from random conformations of both protein and DNA chains, which resulted in an NMR structure for the complex that had good precision over the structured region (residues 3-70 of the protein and stem 1 of the DNA).
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7

Maynard, Allister J. "NMR studies of protein folding and DNA binding." Thesis, University of Nottingham, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313244.

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8

Povey, Jane. "Structural studies of the DNA-binding protein GAL4." Thesis, University of Cambridge, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385462.

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9

Scarpantonio, Luca. "Studies of DNA binding of lanthanide platinum complexes." Thesis, University of Birmingham, 2011. http://etheses.bham.ac.uk//id/eprint/2860/.

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Using supramolecular principles, we have been designing luminescent lanthanide complexes with a defined hairpin bis-interlacator in order to obtain luminescent probes able to recognise DNA. The complexes are comprised of Platinum(II) terpyridine, which acts as a DNA recognition site and is brought together with a "remote" luminescent lanthanide unit. All the synthetic approaches were based on the accessibility of the lanthanide-platinum complexes by the self-assembly of different components in a one pot reaction. Thus, we have been able to isolate a water soluble heterometallic complex based on thiophenal linkage named [LnPt\(_2\)]Cl\(_2\). The complex has a relatively weak lanthanide luminescence, which increases upon addition of DNA. Photophysical and DNA binding properties of the lanthanide-platinum complex were investigated by UV-vis absorption, luminescent studies and circular and linear dichroism. Oligonucleotides of twelve bases were also used to investigate the intercalation [LnPt\(_2\)]Cl\(_2\) and the mono-intercalator AATP used as control compound. Using bidimensional NMR techniques, we investigated the binding site for [LnPt\(_2\)]Cl\(_2\) and AATP upon interaction with Dickerson-Drew sequence. The sulphur lanthanide-platinum linkage in [LnPt\(_2\)]Cl\(_2\) was replaced with an acetylide one in order to introduce new photophysical features. Thus the self-assembly procedures based on DTPA-bis(amido-acetylide) and a platinum(II) terpyridine led us to isolate a new lanthanide-platinum complex named [LnC\(\equiv\)CPt\(_2\)] (CH\(_3\)SO\(_3\))\(_2\). The photophysical properties and the DNA binding properties toward interaction with CT-DNA were investigated. The complex named LnC\(\equiv\)CPt\(_2\)](CH\(_3\)S)\(_3\))\(_2\) exhibited a relatively strong lanthanide luminescence that increased upon addition of DNA. The bi-functional metal complex [EuLPt](PF\(_6\)) (where Pt=platinum-2,2':6'2"-terpyridine and L=assymmetric DTPA bisamide ligand with a thiopheno pendant arm and a quinoline moiety) was synthesised and the interaction of [EuLPt](PF\(_6\)) with CT-DNA was examined by luminescence spectroscopy, linear and circular dichroism studies and thermal denaturation studies. The [EuLPt](PF\(_6\)) retained the ability to increase its luminescence upon the addition of CT-DNA. The binding properties of the complexes were tested toward interaction with plasmid DNA by gel electrophoresis and properties such as the unwinding angle were measured. The bis-intercalators [LnPt\(_2\)]Cl\(_2\) and [LnC\(\equiv\)CPt\(_2\)](CH\(_3\)SO\(_3\))\(_2\) showed the ability to uncoil DNA almost as well as cisplatin and at low concentrations, while almost double the amount of mono-intercalators, such as [EuLPt](PF\(_6\)) is required to observe the same uncoiling effect.
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10

Mack, Lynsey A. "Studies of extremophilic single-stranded DNA-binding proteins." Thesis, University of Edinburgh, 2005. http://hdl.handle.net/1842/12512.

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In this study, 6 bacterial SSBs are investigated which have been obtained from 4 different Shewanella strains, from Aquifex aeolicus and from E. coli. The 4 Shewanella SSBs have been taken from strains isolated at different depths of the ocean, from sea-level down to 8600m. These organisms therefore differ in their growth pressure optima. By comparing the characteristics of each of these proteins, differences will lead to clues which relate to the pressure differences. In order to highlight the different adaptations of these proteins, the thermophilic SSB from Aquifex aeolicus and the mesophilic SSB from E. coli were used as benchmarks to the piezophilic Shewanella SSBs. Circular dichroism was used to determine proportions of secondary structure present in each SSB and these were compared to the values obtained from previous crystallography work on the E. coli, in order to get some preliminary details about each structure. Further biophysical work was carried out using ITC and DSC which provided thermodynamic data regarding the binding between ssDNA and SSB, and also probed the denaturation temperatures of each protein. Exhaustive crystallisation trials were carried out on each Shewanella SSB but unfortunately did not produce any crystals of sufficient quality. As AqSSB had previously been crystallised, the structure determination is described in this study. To complement the binding data, a crystal of AqSSB in complex with ssDNA was produced and its structure determined. The structure showed great similarities with the several previously published structures of EcoSSB. Therefore this study is focussed on SSB proteins from bacteria isolated form very different habitats. By comparing their various structural and biophysical properties, further clues as to how piezophilic proteins are able to survive extreme pressures may be gained.
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11

Mojally, Mariam. "DNA binding studies of fluorinated bioactive heterocyclic compounds." Thesis, Loughborough University, 2015. https://dspace.lboro.ac.uk/2134/16732.

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Fluorinated heterocyclic compounds have drug like properties and possess a valuable biological activity due to their rigid chemical structures and the high solubility profile. Novel fluorinated heteroarenes have been synthesised by SNAr reaction of a range of fluorinated arenes including pentafluoropyridine, hexafluorobenzene and pentafluorotoluene to introduce a range of groups specially nitriles, benzimidazole, carbazole and benzimidazole. A number of cyclization reactions have been investigated with the aim of forming polycyclic structures that could act as DNA intercalators. The synthesised compounds have been characterized by elemental analysis, IR, 1H and 19F NMR spectroscopy and single crystal analysis. These compounds have been screened for their biological activities including DNA thermal denaturation assay, UV-Visible spectroscopy, fluorescence spectroscopy, X-ray co-crystallization and antimicrobial activity study. Some of the compounds showed potential DNA bonding activity in particular the carbazole derivatives.
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12

Blomquist, Patrik. "Studies on nuclear factor 1 binding to nucleosomal DNA /." Stockholm, 1997. http://diss.kib.ki.se/1997/91-628-2633-6.

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13

Leonard, Philip Martin. "Structural studies on the LrpA protein from Pyrococcus furiosus." Thesis, University of Sheffield, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247186.

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14

Panjikar, Santosh. "Crystallographic studies of bacterial single stranded DNA-binding proteins." [S.l.] : [s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=964154366.

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15

Nkansah, Edwin. "In vitro studies of Stat3 dimerisation and DNA binding." Thesis, University of London, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540223.

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16

Isaac, Christian James. "Redox active metal complexes : synthesis and DNA binding studies." Thesis, University of Newcastle Upon Tyne, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.287813.

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17

Scott, Nerida Robyn. "Folding studies of the glucocorticoid receptor DNA-binding domain." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627279.

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18

Schmiedeskamp, Mia Ruth. "NMR studies of the DNA-binding domain of ADR1 /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/9208.

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19

Low, Lieh Yoon. "Thermodynamic studies of zinc binding and stability of nuclear hormone receptor DNA-binding domains." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620310.

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20

Massad, Tariq. "Structural Studies of Flexible Biomolecules and a DNA-binding Protein." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-42009.

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The knowledge of the three-dimensional structures of proteins and polypeptides is essential to understand their functions. The work shown in this thesis has two objectives. The first one is to develop a new analytical method based on maximum entropy (ME) theory to analyze NMR experimental data such as NOEs and J-couplings in order to reconstitute φ,ψ Ramachandran plots of flexible biomolecules. Two model systems have been used, the flexible polypeptide motilin and the disaccharide α-D-Mannosep-(1-2)-α-D-Mannosep-O-Me (M2M). The experimental data was defined as constraints that were combined with prior information (priors) which were the φ,ψ distributions obtained from either a coil library, the Protein DataBank or Molecular Dynamics Simulations. ME theory was utilized to formulate φ,ψ distributions (posteriors) that are least committed to the priors and in full agreement with the experimental data. Reparamerization of the Karplus relation was necessary to obtain realistic distributions for the M2M. Clear structural propensities were found in motilin with a nascent α-helix in the central part (residues Y7-E17), a left handed 31 helix in the C-terminus (R18-G21) and an extended conformation in the N-terminus. The contribution of each residue to the thermodynamic entropy (segmental entropy) was calculated from the posteriors and compared favorably to the segmental entropies estimated from 15N-relaxation data. For M2M the dominating conformation of the glycosidic linkage was found to be at φH=-40° ψH=33°, which is governed by the exo-anomeric effect. Another minor conformation with a negative ψH angle was discovered in M2M. The ratio between both populations is about 3:1. The second part of the thesis is a structural study of a DNA-binding protein, the C repressor of the P2 bacteriophage (P2 C). P2 C represses the lytic genes of the P2 bacteriophage, thereby directing the P2 lifecycle toward the lysogenic lifemode. The crystal and solution structures of P2 C have been solved by X-ray crystallography and NMR, respectively. Both structures revealed a homodimeric protein with five rigid α-helices made up by residues 5-66 and a β-strand conformation in residues 69-76 in each monomer. 15N-relaxation data showed that the C-terminus (residues 85-99) is highly flexible and fully unstructured. A model representing the P2 C-DNA complex was built based on the structure and available biochemical data. In the model, P2 C binds DNA cooperatively and two homodimeric P2 C molecules are close enough to interact and bind one direct DNA repeat each.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In press. Paper 5: Manuscript.
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21

Novac, Olivia. "Studies on origin binding proteins involved in mammalian DNA replication." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=83084.

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The objective of this thesis is to investigate the proteins interacting with specific DNA sequences, termed origins of DNA replication in vivo. Two previously described origin binding proteins, OBA/Ku and CBP/14-3-3 were analyzed. Previously, Ku was shown to bind to A3/4, a 36-bp origin sequence, in vitro, and 14-3-3 isoforms were identified as cruciform binding proteins (CBP) which interact with cruciform structures present in mammalian replication origins.
Here, the in vivo association of Ku and 14-3-3 with mammalian origins of DNA replication was analyzed by studying its association with the monkey (CV-1) replication origins ors8 and ors12, by formaldehyde cross-linking, followed by chromatin immunoprecipitation (Chip) and quantitative PCR analysis. The involvement of 14-3-3 in mammalian DNA replication was also analyzed by studying the effect of anti-14-3-3beta, epsilon, gamma, and zeta antibodies in the in vitro replication of p186, a plasmid containing the minimal replication origin of ors8.
Ku and 14-3-3beta, epsilon, gamma, zeta and sigma isoforms were found to be associated with mammalian origins of DNA replication and their association was the highest in cells synchronized at the G1/S phase of the cell cycle. In addition, Anti-14-3-3epsilon, gamma and zeta antibodies inhibited p186 replication by approximately 30--80%.
The Ku80 mutant (xrs-5) and deficient (Ku80-/- MEFs) cell lines were also tested for their ability to replicate p186, in vitro. Whole cell (WCE) and cytoplasmic cell extracts from the xrs-5 cells replicated p186 with the same efficiency as are wild-type (wt) CHO K1 cells. In contrast, xrs-5 nuclear extracts did not possess any detectable replication activity, while the Ku80 -/- WCE had a decrease of ~70% in their ability to support p186 replication, by comparison to the wt Ku80-/- extracts. Furthermore, in vivo, the p186 episomal DNA replication in transfected xrs-5 cells was reduced by 45% by comparison to CHO K1 cells.
The in vivo association of Ku with the Chinese hamster DHFR oribeta or the mouse Adenosine deaminase (ADA) origins of DNA replication was examined in both the Ku80 mutant (xrs-5) and deficient (Ku80-/-) cell lines, and in their respective wild-type counterparts. Anti-Ku antibodies failed to immunoprecipitate a detectable amount of Ku from the either xrs-5 or Ku80-/- cells in the origin-containing-sequence, in contrast to the wild type cells, wherein Ku was found to be associated with the oribeta and ADA origins, respectively.
The data implicate Ku antigen in DNA replication and suggest the existence of another protein in rodent cells that is able to substitute for Ku function. They also indicate a novel function for Ku and the 14-3-3 isoforms beta, epsilon, gamma, zeta and sigma, as origin-binding-proteins in vivo, which provides a better understanding of the chromosomal association and DNA binding sequences of mammalian initiator proteins with origins of replication in their natural chromosomal environment.
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22

Phillips, Tim. "DNA Binding and Photophysical Studies on Organic Derivatives of Dipyridophenazine." Thesis, University of Sheffield, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.489744.

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23

Munnur, Deeksha Ganesh. "Structural studies of DNA complexes with minor groove-binding drugs." Thesis, University College London (University of London), 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.550498.

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Targeting the minor groove of DNA with small molecules is an important recognition strategy in biology. A wide range of minor groove binding ligands (MGBLs) with good sequence discrimination ability are of interest as potential therapeutic agents in a variety of human diseases such as cancer, along with anti-bacterial and/or anti-parasitic activities. Whilst the detailed mechanism of action of some of these MGBLs is still unproven, they are known to be effective inhibitors of a number of minor and major groove binding protein-DNA interactions. This thesis reports on crystallographic studies to determine the molecular structure of MGBLs bound to DNA sequences, in order to better understand the details of their molecular recognition by DNA. Several interesting MGBLs differing in their structural features were crystallised with AT rich oligonucleotides for neutron and high-resolution X-ray data collection. Phases for the X-ray crystal structures were determined using molecular replacement, with diffraction data up to 1.2 A resolution. The crystal structure revealed the MGBLs bound in the central AATT or AAA TTT rich region of the minor groove of the DNA. The ligands form hydrogen bonds with the bases of the DNA at the floor of the minor groove directly or mediated via water molecules depending on the shape of the ligand. Several oligonucleotide-MGBL complexes were crystallised in the presence of deuterium oxide (heavy water) with the aim of studying the water network around the minor groove in the presence of ligand using neutron crystallography. In order to further our understanding of the biological mechanism of action ofMGBLs, biophysical studies were undertaken with the DNA major groove binding transcription factor, NF-KB. This transcription factor binds to the continuous guanine and cytosine bases of the major groove leaving the minor groove exposed to other molecules. Surface plasmon resonance (SPR) and small angle X-ray scattering (SAXS) studies were undertaken to study the effects on MGBLs on NF-KB - DNA binding. It was revealed that MGBLs had significant effect on the protein-DNA interactions which was further dependent on the shape of the MGBLs.
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24

Jones, Gareth. "NMR studies of the DNA-binding domain of B-Myb." Thesis, University of Kent, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270703.

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25

Hobbs, Jeanette Roseanna. "Structural studies on the DNA binding modes of topoisomerase poisons." Thesis, University of Reading, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342117.

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26

Vitorino, Susana Ricardo. "Rhodium(III) supramolecular complexes : synthesis, DNA binding and biological studies." Thesis, University of Birmingham, 2011. http://etheses.bham.ac.uk//id/eprint/2814/.

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The work described in this thesis concerns the synthesis, DNA binding and cytotoxicity studies of new Rh(III) supramolecular complexes. Chapter 1 reviews DNA molecular recognition by synthetic agents; exploring the different DNA binding modes and their importance in the anticancer properties of several metallodrugs. Special attention is given to the exciting cylinder agents, which underpin the work in this thesis and to the work with rhodium complexes and their studies with DNA and as anticancer drugs. Chapter 2 describes the synthesis, purification and characterization of Rh(III) mononuclear, dinuclear single, double and triple stranded complexes. NMR, MS, UV‐Vis, elemental analyses and in some cases X‐ray crystallography are discussed in detail. In Chapter 3, DNA binding properties of the Rh(III) complexes are explored by CD and LD spectroscopy. Gel Electrophoresis experiments are also carried out using plasmid DNA (pBR322). The dinuclear complexes are found to bind to ct‐DNA and to have more dramatic effects than the mononuclear analogues. In addition they were found to cleave plasmid DNA. Chapter 4 presents cytotoxicity studies for some of the complexes synthesized against breast and ovarian cancer cell lines. A PCR study with the Rh(III) double stranded isomers is also carried out demonstrating that these complexes are able to inhibit and block DNA transactions as represented by PCR DNA replication.
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27

Schechner-Resom, Martina Gabriele. "Ligand binding and molecular flexibility : Studies on DNA gyrase B." Université Louis Pasteur (Strasbourg) (1971-2008), 2005. http://www.theses.fr/2005STR1A001.

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L’ADN gyrase est une enzyme vitale pour la bactérie grâce à sa capacité de manipuler les molécules d’ADN dans la cellule vivante. Cette capacité fait de l’ADN gyrase une cible idéale pour des composés anti-infectieux. Dans ce travail, l’ADN gyrase a été étudié par des méthodes de modélisatoin moléculaire. Une approche de conception de ligands basée sur la structure a été entreprise sur le sous-domaine N-terminal de 24 kDa de l’ADN gyrase B (domaine GHKL). La flexibilité de deux boucles du site actif du domaine GHKL a été étudiée par des simulations de dynamiques moléculaires en présence de différents ligands. Dans une dernière partie, une analyse des modes normaux du dimère du domaine N-terminal de 43 kDa a été entreprise
DNA gyrase is a vital bacterial enzyme necessary for the handling of the large DNA molecules in the living cell. Therefore DNA gyrase is an ideal target enzyme for anti-infectious compounds. In this work DNA gyrase has been studied by molecular modelling methods. A computational structure-based ligand design approach has been carried out on the N-terminal 24 kDa subdomain of DNA gyrase B (GHKL domain). To further examine the flexibility of two active site loops, molecular dynamics simulations have been carried out on the GHKL domain in different ligand binding conditions. In a final part, normal mode analysis has been carried out on the dimer of the 43 kDa domain of DNA gyrase B
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28

Stracy, Mathew. "Single-molecule studies of DNA-binding proteins in live bacteria." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:d2b6ad0a-0fd4-4742-9ca2-dc13ba95f267.

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Protein-DNA interactions are critical to many important biological functions, from transcription to DNA replication. To better understand these processes we need to look at molecular details, such as the stoichiometries and binding kinetics of these proteins. However, focusing on the molecular level can miss the bigger picture; we also need to understand how protein-DNA interactions shape the organisation of chromosomes and cause phenotypical changes over the whole cell. In this thesis I describe the construction of a super-resolution fluorescence microscope to image single molecules in live bacteria, and show how analysis with tools like single-particle tracking allow individual proteins specifically bound to DNA to be distinguished from mobile molecules, offering a new perspective on protein-DNA interactions, from the molecular level to the length scale of whole bacterial cells. I detail how I have applied these techniques to answer key questions in transcription, chromosome organisation, and DNA segregation in Escherichia coli. Firstly, I looked at RNA polymerase (RNAP) to study how transcription affects the organisation of the nucleoid. Discriminating specifically bound RNAPs showed that low levels of transcription can occur throughout the nucleoid, but clustering analysis and 3D Structured Illumination Microscopy (SIM) showed that dense clusters of transcribing RNAPs format the nucleoid periphery, indicating a movement of gene loci out of the bulk of DNA as levels of transcription increase. Furthermore, I developed an assay to characterise the search process and non-specific DNA interactions of RNAP, which I also apply to a diverse selection of other DNA-binding proteins. I also characterized the in vivo behaviour of the type II topoisomerase, TopoIV. Imaging both subunits of TopoIV, combined with over-expression of unlabelled subunits, allowed the fraction of functional enzymes to be determined. Measuring the duration of catalytic events indicated that the majority of active TopoIV molecules catalyse decatenation. Finally, I studied MukBEF, an SMC (Structural Maintenance of Chromosomes) complex that acts in chromosome segregation, to show that TopoIV and MukB interact directly in vivo and determine the dissociation constant and turnover of this TopoIV-MukB complex.
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29

Zhong, Shan. "Studies on the human homolog of the yeast Noc3p in human cells /." View abstract or full-text, 2004. http://library.ust.hk/cgi/db/thesis.pl?BICH%202004%20ZHONG.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004.
Includes bibliographical references (leaves 83-100). Also available in electronic version. Access restricted to campus users.
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30

Deegan, Brian J. "Biophysical Studies of the Binding of ERα Nuclear Receptor to DNA." Scholarly Repository, 2011. http://scholarlyrepository.miami.edu/oa_dissertations/579.

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Estrogen receptor α (ERα) is a member of a family of ligand-modulated transcription factors that have come to be known as nuclear receptors. ERα mediates the action of estrogens and plays an integral role in a wide range of physiological processes ranging from embryonic development and morphogenesis to reproduction to cardiovascular health. Not surprisingly, malfunction of the estrogen system is associated with a host of pathological conditions such as osteoporosis, heart disease and most notably breast cancer. Essential to its functioning as a transcription factor are specific protein-DNA interactions which are mediated by the binding of the DNA-binding (DB) domain of ERα to particular DNA sequences located within target gene promoters called estrogen response elements (EREs). Here, using a diverse array of biophysical techniques, including in particular isothermal titration calorimetry coupled with molecular modeling and semi-empirical analysis, I provide new insights into the ERα-DNA interaction in thermodynamic and structural terms. My data show that the binding of the DB domain of ERα to DNA is coupled to protonation at two specific amino acids, H196 and E203. Protonation of these residues is non-trivial and is required for high affinity binding. Amino acid sequence alignment of the DB domains of the NR family suggests that this may be a hallmark feature common to the functioning of all nuclear receptors. Furthermore, I demonstrate that the DB domain can tolerate all single nucleotide substitutions within the ERE and bind in the physiologically relevant nanomolar to micromolar range. Comparative thermodynamic analysis reveals that the DB domain binds to these ERE sequences utilizing a considerable range of energetic signatures such that any one thermodynamic component of binding is not predictive of associated affinity. In addition, it is shown that nucleotide substitution results in significant changes in secondary and three-dimensional features of the oligonucleotides and may impact binding affinity. Finally, I demonstrate that the zinc-finger of the DB domain of ERα is relatively promiscuous and can accommodate several heavy-metal divalent cations. Other than zinc, only DB domains reconstituted with cobalt, cadmium and mercury were capable of binding DNA. Incorporation of the metals resulted in a wide range of CD spectroscopic features which were found not to be predictive of DNA binding capacity. Thus, isostructure does not equate to isofunction in the case of metal reconstituted DB domain of ERα. This analysis suggests that metal coordination is not likely to be required for domain folding, but rather is required to bind DNA. Taken together, this thesis provides novel insights into the physicochemical basis of a key protein-DNA interaction essential to human health and disease. My studies bear the potential to impact the development of novel therapies harboring greater efficacy coupled with lower toxicity for the treatment of disease.
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31

Dutnall, Robert Nicholas. "Structural and functional studies of a zinc finger DNA-binding domain." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360030.

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32

Rajput, Chatna. "Synthesis and binding studies of DNA duplex and quadruplex interactive ligands." Thesis, University of Sheffield, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.425171.

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33

McIntosh, Pauline Bernadette. "NMR based studies of the DNA-binding domain from B-Myb." Thesis, Open University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388299.

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34

Norman, Jenna Anne. "Functionalised iron(II) supramolecular helicates : design, synthesis and DNA binding studies." Thesis, University of Birmingham, 2013. http://etheses.bham.ac.uk//id/eprint/4088/.

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The work described in this thesis concerns the design, synthesis and DNA binding activity of functionalised iron(II) supramolecular helicates. DNA and the ways that organic and metallo-molecules recognise and bind to it are reviewed. The field of supramolecular chemistry and particularly supramolecular helicates is considered, including those developed as anticancer agents. The design of a novel functionalisation route for the development of functionalised helicates is presented. The synthesis and characterisation of several metallo-helicates functionalised with simple chemical groups, such as hydroxyl and phenyl moieties, is described. Studies reveal that this functionalisation does not inhibit the inherent DNA binding activity of these types of cylinders. The development of steroid-hormone functionalised iron(II) helicates for targeted delivery to cancerous tissues is also detailed, including their synthesis and characterisation. These steroid functionalised complexes bind to DNA, inducing changes in the DNA conformation. The design, synthesis and characterisation of several metallo-helicates functionalised with targeting sugar vectors, is also presented. These sugar-conjugates can bind to DNA, causing intramolecular coiling and unwinding of the DNA helix.
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35

Alonso, Natalia Calle. "Tetra-stranded metallo-supramolecular cylinders : design, synthesis and DNA binding studies." Thesis, University of Birmingham, 2013. http://etheses.bham.ac.uk//id/eprint/4053/.

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The work described in this thesis concerns the design, synthesis, DNA binding and biological activity of palladium(II) supramolecular cylinders that might be capable of recognizing a DNA four-way junction. An introduction to DNA structure will be presented, as well as the different binding modes of natural and synthetic agents that can recognise and bind to DNA. Since this work is focused on the design of large metallo-structures, the general principles of supramolecular chemistry will be summarised with particular emphasis on metallo-supramolecular structures. Palladium(II) supramolecular cylinders have already been reported and these show promising cytotoxicity against different cancer cell lines. However, these complexes present poor solubility in aqueous solutions. It is therefore the aim of this thesis to improve the water solubility of palladium(II) supramolecular cylinders without significantly changing their structure or quenching their cytotoxic activity. The DNA binding properties of the newly synthesised palladium(II) complexes will be presented. Several spectroscopic techniques, such as circular and linear dichroism and ethidium bromide displacement assays, as well as electrophoresis experiments were carried out and these will be discussed. Initial DNA four-way junction experiments and cytotoxicity studies will also be discussed.
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36

Nordzell, Mariette. "Functional studies on the nuclear receptor Nurr1 /." Stockholm : Karolinska institutet, 2004. http://diss.kib.ki.se/2004/91-7349-867-X/.

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37

Vaughan, P. J. "Studies on a component of the herpes simplex virus DNA polymerase." Thesis, University of Leeds, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.379648.

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38

Parkinson, John Andrew. "NMR studies on the Met J operator from Escherichia coli." Thesis, University of Leeds, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328964.

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39

Johnson, Vinu. "Structural and Biophysical Studies of Single-Stranded DNA Binding Proteins and dnaB Helicases, Proteins Involved in DNA Replication and Repair." University of Toledo / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1198939056.

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40

Wilson, Dale F. "Synthesis, Characterization, DNA Binding and Photocleavage Studies of a Di-Ruthenated Porphyrin." University of Dayton / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1398882510.

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41

Lee, Myung Soo. "Studies on the DNA helicase activities of the Escherichia coli primosome : involved in DNA replication fork movement /." Access full-text from WCMC, 1989. http://proquest.umi.com/pqdweb?did=744115351&sid=1&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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42

Siu, Kit-man Phyllis. "Luminescent cyclometalated platinum(II) complexes : protein binding studies and biological applications /." View the Table of Contents & Abstract, 2005. http://sunzi.lib.hku.hk/hkuto/record/B30575357.

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43

Kantola, Angeline R. "Nuclear magnetic resonance studies of the xUBF Box 1 DNA binding domain /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/9228.

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44

Hermanson, Elisabet. "Studies on the nuclear receptor Nurr1 : identification of Nurr1-regulated genes /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-833-5/.

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45

Raber, Johan. "Quantum Chemical Studies of Chemotherapeutic Drug Cisplatin : Activation and Binding to DNA." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7824.

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46

Mok, Yu-Keung. "Studies on the DNA binding domain human papillomavirus strain 16 E2 protein." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264157.

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47

Swanson, Gary Robert. "Expression, characterisation and n.m.r. studies of the DNA-binding domain of SW15." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240054.

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48

Williamson, Josephine. "Studies of the DNA mismatch binding proteins MutS, VSR and CEL I." Thesis, University of Southampton, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.403846.

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49

Koorsen, Gerrit. "Studies of the binding of linker histone H5 to DNA and chromatin." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613656.

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50

Zhang, Jinjin. "Structural Studies of Escherichia coli RecE Exonuclease." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1254972783.

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