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Tesis sobre el tema "DNA binding"

Autor: Grafiati

Publicado: 4 de junio de 2021

Última modificación: 25 de julio de 2025

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1

Pérez-Breva, Luis. "DNA binding economies." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42057.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Includes bibliographical references (p. 195-204).<br>This thesis develops a new scalable modeling framework at the interface of game theory and machine learning to recover economic structures from limited slices of data. Inference using economic models has broad applicability in machine learning. Economic structures underlie a su

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2

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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3

Pokhrel, Pujan. "Prediction of DNA-Binding Proteins and their Binding Sites." ScholarWorks@UNO, 2018. https://scholarworks.uno.edu/honors_theses/114.

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DNA-binding proteins play an important role in various essential biological processes such as DNA replication, recombination, repair, gene transcription, and expression. The identification of DNA-binding proteins and the residues involved in the contacts is important for understanding the DNA-binding mechanism in proteins. Moreover, it has been reported in the literature that the mutations of some DNA-binding residues on proteins are associated with some diseases. The identification of these proteins and their binding mechanism generally require experimental techniques, which makes large scale

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4

Sando, Shinsuke. "RATIONAL DESIGN OF DNA-BINDING MOLECULES AND DNA PHOTOCLEAVERS." 京都大学 (Kyoto University), 2001. http://hdl.handle.net/2433/150700.

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5

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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6

Geary, Joella Suzanne. "DNA binding proteins of archaeal viruses." Thesis, Montana State University, 2008. http://etd.lib.montana.edu/etd/2008/geary/GearyJ1208.pdf.

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Archaea are single-celled organisms comprising the third domain of life. The Achaeal species Sulfolobus are infected by the Fuselloviridae virus family: SSV1, SSV2, SSV-RH, and SSV-K. The genomes of these viruses have been annotated and contain putative DNA-binding proteins. The purpose of this work is to identify DNA sequences bound by the SSV1 putative DNA-binding protein C43. C43 protein was cloned, expressed, purified, and assayed at various temperatures for interaction with three SSV1 DNA sequences. C43 binds the T5-promoter, T6-promoter, and C43-promoter sequentially and consistently. Ad

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7

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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8

Bullen, Gemma Anne. "Anthracene tagged biomolecules for DNA binding." Thesis, University of Birmingham, 2015. http://etheses.bham.ac.uk//id/eprint/6369/.

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Within this thesis, the use of anthracene to perform various applications within biomolecules is assessed. Anthracene displays two interesting photo properties which make it an appealing molecule for incorporation; fluorescence and photodimerisation. The former is utilised to develop a single nucleotide polymorphism detection assay which is shown to allow for determination of the base present in a complementary strand of DNA. In addition to this, the photodimerisation properties of anthracene are used within a protein for the first time. This is utilised to develop a photoswitched binding prot

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9

Weinberg, Richard Lawrence. "The binding of p53 to DNA." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615988.

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10

Walavalkar, Ninad. "Structural basis of DNA binding complexes." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3162.

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The nucleosome remodeling and deacetylase (NuRD) complex is an abundant deacetylase complex, which couples histone deacetylation and chromatin remodeling ATPase activities, and has a broad cellular and tissue distribution. Although the working model of how this complex forms and functions is not well known, we have demonstrated that the coiled-coil interaction between two proteins (MBD2 and p66α) is critical for DNA methylation dependent gene silencing in vivo. Chapter one: ‘Unique features of the anti-parallel, heterodimeric coiled-coil interaction between methyl-cytosine binding domain 2 (MB

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11

Park, Frances E. "NF-kB DNA binding and transactivation /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3001261.

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12

Hlatshwayo, Nkosikhona Rejoyce. "Comparison of protein binding microarray derived and ChIP-seq derived transcription factor binding DNA motifs." Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1017907.

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Transcription factors (TFs) are biologically important proteins that interact with transcription machinery and bind DNA regulatory sequences to regulate gene expression by modulating the synthesis of the messenger RNA. The regulatory sequences comprise of short conserved regions of a specific length called motifs . TFs have very diverse roles in different cells and play a very significant role in development. TFs have been associated with carcinogenesis in various tissue types, as well as developmental and hormone response disorders. They may be responsible for the regulation of oncogenes and

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13

Goddard, C. "DNA and chromatin binding by the methyl-CpG-binding protein, MeCP2." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599452.

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In eukaryotes, methylation at CpG dinucleotides causes transcriptional repression. MeCP2 is a good candidate for a transducer of this methylation signal as it is capable of binding to methylated DNA and can repress transcription <i>in vitro</i>. This thesis describes experiments to further investigate the DNA and chromatin binding properties of MeCP2. Chapter 2 describes the subcloning, overexpression and purification of recombinant rat MeCP2 and also the purification of native MeCP2 from rat brain. The similarity in purification protocols indicates that the recombinant protein is a good model

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14

Sheldon, Deuser Shelby Diane. "Two-site DNA Minor Groove Binding Compounds." Digital Archive @ GSU, 2012. http://digitalarchive.gsu.edu/chemistry_theses/51.

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DNA minor groove binding compounds have had limited therapeutic uses, in part due to problems with sequence specificity. A two-site model has been developed to enhance specificity, in which compounds bind to two short AT sites separated by one or two GC base pairs. Using thermal melting, heterocyclic dications with this capability were tested with various oligonucleotides for binding affinity and specificity. Compounds of interest were further probed using circular dichroism, mass spectrometry, biosensor-SPR, and molecular modeling. Several compounds were found to “jump” a GC base pair, bindin

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15

Moon, Nam Sung 1972. "Modes and regulations of CDPCux DNA binding." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=38244.

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The CDP/Cux transcription factor contains four DNA binding domains: three Cut repeats (CR1, CR2 and CR3) and the Cut homeodomain (HD). The CCAAT-displacement protein (CDP) was first identified as it represses transcription of certain promoters by competing for the occupancy of the CCAAT sequence. CDP was then found to be the ortholog of the Drosophila Cut protein (Cux: Cu t homeobox&barbelow;). The goal of my project was to define the modes of interactions of CDP/Cux with DNA. I demonstrated that high affinity DNA binding requires the cooperation between at least two of the CDP/Cux DNA binding

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16

Choo, Yen. "Design of site-specific DNA-binding proteins." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363127.

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17

Broome, Mark John. "Interaction of DNA with groove binding ligands." Thesis, University of Warwick, 2008. http://wrap.warwick.ac.uk/1933/.

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Synthetic molecules that target the major groove in a sequence-selective way are a major goal in molecular medicine. Recently a major step has been taken toward achieving this goal: a novel cylinder has been developed that binds strongly into the major groove of DNA. Experimental techniques have provided some information regarding the binding strength and preferred binding sites of the cylinder on DNA. From all the experimental data it is clear that the parent cylinder binds in the major groove and is able to induce dramatic conformational changes in the DNA; these are unprecedented effects wi

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18

Simanis, V. "T antigen binding sequences in cellular DNA." Thesis, Imperial College London, 1985. http://hdl.handle.net/10044/1/37854.

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19

Leczkowska, Anna. "Non-covalent DNA-binding ruthenium anticancer drugs." Thesis, University of Birmingham, 2011. http://etheses.bham.ac.uk//id/eprint/1695/.

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The research work described in this thesis concerns metal-based anticancer drugs with an emphasis on non-covalent DNA-binding supramolecular assemblies. The project involves the preparation of a series of mono- and bi-metallic ruthenium complexes with a primary focus on fluorescent dinuclear triple-stranded helicates with different structural topographies. Emphasis is then directed towards an investigation of the DNA binding characteristics of these molecules and an evaluation of their anticancer properties in human cancer cell lines. Attention is brought to the significance that the cylinder-

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20

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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21

Nickols, Nicholas George Mayo Stephen L. Dervan Peter B. "Endogenous gene regulation by DNA binding polyamides /." Diss., Pasadena, Calif. : California Institute of Technology, 2008. http://resolver.caltech.edu/CaltechETD:etd-06212007-155330.

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22

Gapian, Bianké Jean-Paul. "DNA mimics containing artificial metal-binding sites /." [S.l.] : [s.n.], 2006. http://www.zb.unibe.ch/download/eldiss/06bianke_g.pdf.

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23

Schilter, David. "Synthesis and DNA-binding of Metallocyclic Architectures." Thesis, The University of Sydney, 2009. http://hdl.handle.net/2123/5317.

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A new family of cationic N-heterocyclic ligand derivatives was prepared and characterised. Among these compounds are halide salts of the dications [Y(spacer)Y]2+, each of which comprise two N heterocyclic donor groups (Y = 4,4′-bipy, pyz, apyz, apym) linked by a conformationally flexible spacer such as (CH2)n, α,α′-xylylene, 2,6-lutidylene or thiabicyclo[3.3.1]nonane-2,6 diyl. The diquaternary halide salts were converted to NO3- and PF6- salts, and interaction of these bridging ligands with labile palladium(II) and platinum(II) precursors afforded several multinuclear complexes. Bis(4,4′-bipyr

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24

Schilter, David. "Synthesis and DNA-binding of Metallocyclic Architectures." University of Sydney, 2009. http://hdl.handle.net/2123/5317.

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PhD<br>A new family of cationic N-heterocyclic ligand derivatives was prepared and characterised. Among these compounds are halide salts of the dications [Y(spacer)Y]2+, each of which comprise two N heterocyclic donor groups (Y = 4,4′-bipy, pyz, apyz, apym) linked by a conformationally flexible spacer such as (CH2)n, α,α′-xylylene, 2,6-lutidylene or thiabicyclo[3.3.1]nonane-2,6 diyl. The diquaternary halide salts were converted to NO3- and PF6- salts, and interaction of these bridging ligands with labile palladium(II) and platinum(II) precursors afforded several multinuclear complexes. Bis(4,4

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25

Preston, Nicola Susan. "Structure and DNA binding of HMG boxes." Thesis, University of Portsmouth, 1996. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310386.

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26

Cruickshank, Jennifer. "The DNA binding mechanism of the Epstein-Barr origin binding protein, EBNA1." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0006/MQ46091.pdf.

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27

Phillips, Christine M. (Christine Marie). "Relating metal binding to DNA binding in the nickel regulatory protein NikR." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/57569.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Vita. Cataloged from student-submitted PDF version of thesis.<br>Includes bibliographical references.<br>The concentration of transition metals within the cell must be tightly regulated. If the concentration of a given transition metal is too low the cell may not be able to perform life-sustaining processes, while high levels of metals are poisonous to the cell a

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28

Roberts, Jennifer Nicole. "Investigating the DNA binding properties of the Telomere End-Binding Protein Cdc13." Connect to online resource, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3337145.

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29

Luo, Dan. "Novel cross-linking 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=osu1487946776022443.

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30

Watts, Richard A. "Relationship between a fetal DNA-binding antibody and the DNA-binding antibodies produced by patients with systemic lupus erythematosus." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.291603.

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31

Andrade, Helena. "DNA Oligomers - From Protein Binding to Probabilistic Modelling." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-218709.

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This dissertation focuses on rationalised DNA design as a tool for the discovery and development of new therapeutic entities, as well as understanding the biological function of DNA beyond the storage of genetic information. The study is comprised of two main areas of study: (i) the use of DNA as a coding unit to illustrate the relationship between code-diversity and dynamics of self-assembly; and (ii) the use of DNA as an active unit that interacts and regulates a target protein. In the study of DNA as a coding unit in code-diversity and dynamics of self-assembly, we developed the DNA-Based

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32

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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33

Burton, Sara Katherine. "DNA-binding proteins associated with DNA polymerase alpha in pea (Pisum sativum)." Thesis, University of Exeter, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.357961.

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34

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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35

James, Daniel Peter. "Computational methods for the measurement of protein-DNA interactions." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/277257.

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It is of interest to know where in the genome DNA binding proteins act in order to effect their gene regulatory function. For many sequence specific DNA binding proteins we plan to predict the location of their action by having a model of their affinity to short DNA sequences. Existing and new models of protein sequence specificty are investigated and their ability to predict genomic locations is evaluated. Public data from a micro-fluidic experiment is used to fit a matrix model of binding specificity for a single transcription factor. Physical association and disassociation constants from th

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36

Rehmani, Imran J. "Studying the DNA Binding and Conformation of Metal-Binding Site Mutations in Pirin." Digital Archive @ GSU, 2012. http://digitalarchive.gsu.edu/chemistry_theses/53.

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The transcription factor NF-κB interacts with many other co-regulator proteins that modulate its binding and transcriptional activity. One of these co-regulators, Pirin, is an iron-dependent metalloprotein that has been shown to enhance the DNA binding of NF-κB homodimers. Here, we characterize the interactions between Pirin and its known NF-κB binding partners and examined the role of Bcl-3, a protein that is required for Pirin’s interaction with p50. In addition, we use site-directed mutagenesis to alter conserved residues within Pirin’s metal binding environment and observed how it affected

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37

Goytisolo, Fermin Alejandro. "DNA and chromatin binding sites on histone H5." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262871.

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38

Fouquier, d'Herouel Aymeric. "Statistical models of TF/DNA interaction." Licentiate thesis, Stockholm : Numerisk analys och datalogi, Numerical Analysis and Computer Science, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4633.

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39

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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40

Miao, Yi. "Shape-Dependent Molecular Recognition of Specific Sequences of DNA by Heterocyclic Cations." Digital Archive @ GSU, 2006. http://digitalarchive.gsu.edu/chemistry_diss/4.

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SHAPE-DEPENDENT MOLECULAR RECOGNITION OF SPECIFIC SEQUENCES OF DNA BY HETEROCYCLIC CATIONS by YI MIAO Under the Direction of Dr. W. David Wilson ABSTRACT DB921 and DB911 are biphenyl-benzimidazole-diamidine isomers with a central para- and meta-substituted phenyl group, respectively. Unexpectedly, linear DB921 has much stronger binding affinity with DNA than its curved isomer, DB911. This is quite surprising and intriguing since DB911 has the classical curved shape generally required for strong minor groove binding while DB921 clearly does not match the groove shape. Several biophysical tech

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41

Sunstrom, Noëlle-Ann. "Specific DNA binding by polyomavirus large T antigen." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=70257.

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To define the DNA binding domain of polyomavirus large T antigen, systematic deletion mutagenesis was carried out on large T antigen. A set of plasmids coding for unidirectional carboxy- or amino-terminal deletion mutations in large T antigen were constructed. Deleted proteins were expressed by plasmid transfection of Cos-1 cells. Analysis of origin-specific DNA binding by mutant proteins revealed that the C-terminal boundary of the DNA-binding domain is at or near Glu 398. Fusion proteins of large T antigen lacking the first 200 N-terminal amino acids bound specifically to polyomavirus origin

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42

Jacobs, Grant H. "Computer analysis of motifs in DNA binding proteins." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259565.

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43

Gill, Martin. "DNA-binding ruthenium complexes : cellular imaging and cytotoxicity." Thesis, University of Sheffield, 2010. http://etheses.whiterose.ac.uk/1161/.

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44

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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45

Fairweather, Victoria S. S. "Biophysical characterisation of DNA-binding proteins and oxidoreductases." Thesis, University of Bristol, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.508074.

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46

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 <i>Drosophila melanogaster </i>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 crystallogra

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47

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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48

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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49

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 o

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50

White, Jenifer Christine. "Novel functionalised, nanoarrays of DNA binding supramolecular helicates." Thesis, University of Birmingham, 2016. http://etheses.bham.ac.uk//id/eprint/6625/.

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Work described in this thesis shows the design, synthesis, DNA binding activity and gold nanoparticle interaction of functionalised triple stranded supramolecular helicates. DNA structures and the way molecules recognise and bind to them are reviewed, with specific emphasis on supramolecular compounds. Supramolecular helicates are discussed in detail with consideration of how they may be used as anticancer agents. Nanoparticles, specifically gold nanoparticles are studied, with specific reference to how they are able to enhance anticancer properties of drug molecules and how they may be used t

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