subject:(DNA binding)

1. Aldridge, Matthew J. Functional analysis of a novel DNA binding protein of Streptomyces coelicolor.

Degree: PhD, 2012, Swansea University

URL: https://cronfa.swan.ac.uk/Record/cronfa42406 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678565

► 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… (more)

▼ 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.

Subjects/Keywords: 572.8; DNA binding protein; DNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Aldridge, M. J. (2012). Functional analysis of a novel DNA binding protein of Streptomyces coelicolor. (Doctoral Dissertation). Swansea University. Retrieved from https://cronfa.swan.ac.uk/Record/cronfa42406 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678565

Chicago Manual of Style (16^th Edition):

Aldridge, Matthew J. “Functional analysis of a novel DNA binding protein of Streptomyces coelicolor.” 2012. Doctoral Dissertation, Swansea University. Accessed March 04, 2021. https://cronfa.swan.ac.uk/Record/cronfa42406 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678565.

MLA Handbook (7^th Edition):

Aldridge, Matthew J. “Functional analysis of a novel DNA binding protein of Streptomyces coelicolor.” 2012. Web. 04 Mar 2021.

Vancouver:

Aldridge MJ. Functional analysis of a novel DNA binding protein of Streptomyces coelicolor. [Internet] [Doctoral dissertation]. Swansea University; 2012. [cited 2021 Mar 04]. Available from: https://cronfa.swan.ac.uk/Record/cronfa42406 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678565.

Council of Science Editors:

Aldridge MJ. Functional analysis of a novel DNA binding protein of Streptomyces coelicolor. [Doctoral Dissertation]. Swansea University; 2012. Available from: https://cronfa.swan.ac.uk/Record/cronfa42406 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678565

University of New South Wales

2. Konda, Shyam Kumar. INTERACTION OF ANTHRACENEDIONE COMPOUNDS WITH DNA.

Degree: Physical, Environmental & Mathematical Sciences, 2016, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/56836 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41600/SOURCE02?view=true

► Many mechanisms have been proposed for the anticancer activity of anthracenedione drugs. It has been suggested that the therapeutic activity of anthracenedione drugs is related… (more)

▼ Many mechanisms have been proposed for the anticancer activity of anthracenedione drugs. It has been suggested that the therapeutic activity of anthracenedione drugs is related to their ability to form covalent adducts with DNA. However, covalent adduct formation is governed by the initial reversible (intercalation) binding with DNA. This thesis aimed at exploring the various factors that control the rate and extent of covalent bond formation between anthracenediones and DNA. Initially, the reversible binding of the anticancer drug pixantrone to the oligonucleotide sequence d(TCATATGA)2 was studied by NMR spectroscopy and molecular modelling. The upfield shifts observed for the aromatic resonances of pixantrone upon addition of the drug to the oligonucleotide confirmed the drug bound by intercalation. For the duplex sequence d(TCATATGA)2, NOEs were observed from the pixantrone aromatic H7,8 and aliphatic Ha, Hb protons to the H6/H8 and H1' protons of the C2, A3, T6 and G7 nucleotides, demonstrating that pixantrone preferentially binds at the symmetric CpA sites. However, weaker NOEs observed to various protons from the T4 and A5 residues indicated alternative minor binding sites. NOEs from the H7,8 and Ha, Hb protons to both major (H6/H8) and minor groove (H1') protons indicated approximately equal proportions of intercalation from the major and minor groove at the CpA sites. The ability of the anthracenedione anticancer drug JEM-150 to form covalent adducts with DNA, after activation by formaldehyde, has been studied by electrospray ionisation mass spectrometry and HPLC. It was found that JEM-150 could form covalent adducts with d(ACGCGCGT)2 that contained one, two or even three covalent links to the octanucleotide; whereas the control anthracenedione drugs daunomycin, mitoxantrone and pixantrone only formed adducts with one covalent link to the octanucleotide. HPLC was used to examine the extent of covalent bond formation of JEM-150 with d(CGCGCG)2 and d(CG5MeCGCG)2. Incubation of JEM-150 with d(CG5MeCGCG)2 in the presence of formaldehyde resulted in the formation of significantly greater amounts of covalent adducts than was observed with d(CGCGCG)2. In order to understand the observed increase in the proportion of covalent adducts formed with d(CG5MeCGCG)2, an NMR study of the reversible interaction of JEM-150 at both CpG and 5MeCpG sites was undertaken. Intermolecular NOEs were observed in NOESY spectra of d(ACGGCCGT)2 with added JEM-150 that indicated that the drug selectively intercalated at the CpG sites and from the major groove. In particular, NOEs were observed from the JEM-150 H2,3 protons to the H1' protons of G3 and G7 and from the H6,7 protons to the H5 protons of C2 and C6. By contrast, intermolecular NOEs were observed between the JEM-150 H2,3 protons to the H2" proton of the 5MeC3 in d(CG5MeCGCG)2, and between the drug aliphatic protons and the H1' proton of G4. This demonstrated that JEM-150 preferentially intercalates at 5MeCpG sites, compared to CpG sequences, and predominantly via… Advisors/Committee Members: Collins, Grant, Physical, Environmental & Mathematical Sciences, UNSW Canberra, UNSW.

Subjects/Keywords: Anthracenediones; DNA binding

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APA (6^th Edition):

Konda, S. K. (2016). INTERACTION OF ANTHRACENEDIONE COMPOUNDS WITH DNA. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/56836 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41600/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Konda, Shyam Kumar. “INTERACTION OF ANTHRACENEDIONE COMPOUNDS WITH DNA.” 2016. Doctoral Dissertation, University of New South Wales. Accessed March 04, 2021. http://handle.unsw.edu.au/1959.4/56836 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41600/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Konda, Shyam Kumar. “INTERACTION OF ANTHRACENEDIONE COMPOUNDS WITH DNA.” 2016. Web. 04 Mar 2021.

Vancouver:

Konda SK. INTERACTION OF ANTHRACENEDIONE COMPOUNDS WITH DNA. [Internet] [Doctoral dissertation]. University of New South Wales; 2016. [cited 2021 Mar 04]. Available from: http://handle.unsw.edu.au/1959.4/56836 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41600/SOURCE02?view=true.

Council of Science Editors:

Konda SK. INTERACTION OF ANTHRACENEDIONE COMPOUNDS WITH DNA. [Doctoral Dissertation]. University of New South Wales; 2016. Available from: http://handle.unsw.edu.au/1959.4/56836 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:41600/SOURCE02?view=true

University of Manchester

3. Saeed, Sadia. Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228.

Degree: 2012, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:183543

► The multidrug resistance plasmid TP228 replicates at low copy number in Escherichia coli. Stable partitioning of this plasmid is mediated by three essential components: a… (more)

▼ The multidrug resistance plasmid TP228 replicates at low copy number in Escherichia coli. Stable partitioning of this plasmid is mediated by three essential components: a ParA homologue, ParF; a centromere binding protein, ParG; and a centromere site, parH. ParF and ParG jointly assemble on the parH centromere forming the segrosome complex, and thereby direct intracellular plasmid transport. ParG belongs to the ribbon-helix-helix (RHH) class of dimeric DNA binding proteins. ParG specifically binds the parH site and also is a transcriptional repressor of the parFG genes. Previous studies demonstrated that unstructured N-terminal tails in ParG are not important for dimerization. Instead the tails are implicated in assembly of higher order nucleoprotein complexes essential for transcriptional repression and segrosome assembly, and also influence ParF nucleotide hydrolysis and polymerization. In this study we defined the role of residues in the RHH folded domain that are crucial for ParG dimerization and function. To achieve our goal the two α-helices, the intervening loop, and two C-terminal residues were analyzed fully by alanine scanning mutagenesis. Initially, ParG mutants were constructed and assessed for effects on normal plasmid partition activity and on dimerization. In vivo segregation assays and bacterial two-hybrid studies revealed mutation of residues F49 in α-helix 1 and W71 and L72 in α-helix 2 of ParG each resulted in defective plasmid partition activity and impaired dimerization. In vitro chemical cross-linking of purified proteins ParG-F49A, ParG-W71A and ParG-L72A demonstrated predominant monomeric species whereas wild-type ParG formed dimeric species as noted previously. Multiangle light scattering and sedimentation equilibrium analysis of the mutant proteins showed shifts in molar mass towards monomeric species with increased Kd values for dimerization. Protein-DNA interactions studied by gel retardation assays showed impaired interactions of ParG-F49A, ParG-W71A and ParG-L72A with parH. Results of conserved substitutions at position 71 showed that aromatic substitutions of W71 to Y71 or F71 are tolerated and have no apparent effects on ParG mediated plasmid segregation, but the non-aromatic W71L mutation blocked the segregation. However, a ParG double mutant bearing the ‘reversed’ amino acid pair (W71L-A52Y) retained plasmid segregation activity and behaved like wild-type ParG in dimerization assays in vitro and in vivo. Thus, substitution of W71 by tyrosine or phenylalanine does not disturb the monomer-monomer interface interactions that pack α-helix 2 from one monomer against residues of α-helix 1 and α-helix 2 of the partner monomer. Moreover, the permissible amino acid combinations at interacting positions 52 and 71 in ParG show significant flexibility and reveal key roles for these residues in function and dimerization of ParG. Overall, our in vivo and in vitro interaction studies provide novel information about the role of hydrophobic residues F49, W71 and L72 in ParG dimerization and activity.… Advisors/Committee Members: Hayes, Finbarr.

Subjects/Keywords: ParG DNA binding protein

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saeed, S. (2012). Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:183543

Chicago Manual of Style (16^th Edition):

Saeed, Sadia. “Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228.” 2012. Doctoral Dissertation, University of Manchester. Accessed March 04, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:183543.

MLA Handbook (7^th Edition):

Saeed, Sadia. “Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228.” 2012. Web. 04 Mar 2021.

Vancouver:

Saeed S. Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228. [Internet] [Doctoral dissertation]. University of Manchester; 2012. [cited 2021 Mar 04]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:183543.

Council of Science Editors:

Saeed S. Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228. [Doctoral Dissertation]. University of Manchester; 2012. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:183543

Colorado State University

4. Kramer, Michael A. Poly (ADP-ribose) polymerase 1 (PARP1) and its DNA-binding characteristics.

Degree: MS(M.S.), Biochemistry and Molecular Biology, 2011, Colorado State University

URL: http://hdl.handle.net/10217/47286

► The poly(ADP-ribose) polymerase (PARP) family is evolutionarily diverse, containing 18 different protein members. Roles played by PARP1 in the cell appear to be significant in… (more)

▼ The poly(ADP-ribose) polymerase (PARP) family is evolutionarily diverse, containing 18 different protein members. Roles played by PARP1 in the cell appear to be significant in establishing cellular complexity, as a correlation exists between higher eukaryotes and prevalence of PARP family members. Each member of the PARP family contains a conserved catalytic domain, which upon activation cleaves molecules of NAD+ to form polymers of ADP-ribose, with the release of nicotinamide. Poly(ADP-ribosyl)ation reactions carried out by PARP family members have been found to function in regulation of cellular systems including DNA-damage repair, transcription, mitotic spindle formation, telomere maintenance and cell-death signaling. The most well established member of the PARP family is poly(ADP-ribose) polymerase 1 or PARP1. PARP1 has been found to associate with an assortment of DNA structures within the cell. Despite being able to complex with any DNA present in the cell, PARP1 displays a propensity to interact with sites of DNA-damage. As such, PARP1 has been found to play a major role in initiation of DNA-damage repair. Through its catalytic activity PARP1 recruits additional DNA-damage repair machinery and promotes exposure of the site of damage through chromatin relaxation. Due to its ability to regulate chromatin structure, PARP1 has also been frequently connected with transcription regulation. Variable regulation of transcription by PARP1 has been observed. Catalytically inactive PARP1 can function in a similar fashion as the protein H1 to condense chromatin. Alternatively, active PARP1 functions to relax chromatin surrounding promoter regions and recruit transcription machinery. PARP1 activity appears to be primarily regulated through its association with DNA. Little is known regarding PARP1-DNA-binding affinity. Here I present a high-throughput in-solution FRET-based assay that I utilize to better characterize PARP1's interaction with sites of DNA-damage. In addition, the PARP1-nucleosome complex was analyzed utilizing the same FRET-based assay. Discrepancies found between PARP1 binding affinities to various DNA-damage and mononucleosome constructs provide insight into a potential variable mode of interaction exhibited by PARP1. Advisors/Committee Members: Luger, Karolin (advisor), Woody, Robert (committee member), Bailey, Susan M. (committee member).

Subjects/Keywords: DNA-binding; PARP1; PARP

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kramer, M. A. (2011). Poly (ADP-ribose) polymerase 1 (PARP1) and its DNA-binding characteristics. (Masters Thesis). Colorado State University. Retrieved from http://hdl.handle.net/10217/47286

Chicago Manual of Style (16^th Edition):

Kramer, Michael A. “Poly (ADP-ribose) polymerase 1 (PARP1) and its DNA-binding characteristics.” 2011. Masters Thesis, Colorado State University. Accessed March 04, 2021. http://hdl.handle.net/10217/47286.

MLA Handbook (7^th Edition):

Kramer, Michael A. “Poly (ADP-ribose) polymerase 1 (PARP1) and its DNA-binding characteristics.” 2011. Web. 04 Mar 2021.

Vancouver:

Kramer MA. Poly (ADP-ribose) polymerase 1 (PARP1) and its DNA-binding characteristics. [Internet] [Masters thesis]. Colorado State University; 2011. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10217/47286.

Council of Science Editors:

Kramer MA. Poly (ADP-ribose) polymerase 1 (PARP1) and its DNA-binding characteristics. [Masters Thesis]. Colorado State University; 2011. Available from: http://hdl.handle.net/10217/47286

University of Manchester

5. Saeed, Sadia. Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228.

Degree: PhD, 2012, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/uncovering-the-molecular-mechanism-of-parg-dimerization-and-its-role-in-segrosome-assembly-of-multidrug-resistance-plasmid-tp228(76dda7e1-a14c-4d85-9b10-6524e1fb9281).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647355

► The multidrug resistance plasmid TP228 replicates at low copy number in Escherichia coli. Stable partitioning of this plasmid is mediated by three essential components: a… (more)

▼ The multidrug resistance plasmid TP228 replicates at low copy number in Escherichia coli. Stable partitioning of this plasmid is mediated by three essential components: a ParA homologue, ParF; a centromere binding protein, ParG; and a centromere site, parH. ParF and ParG jointly assemble on the parH centromere forming the segrosome complex, and thereby direct intracellular plasmid transport. ParG belongs to the ribbon-helix-helix (RHH) class of dimeric DNA binding proteins. ParG specifically binds the parH site and also is a transcriptional repressor of the parFG genes. Previous studies demonstrated that unstructured N-terminal tails in ParG are not important for dimerization. Instead the tails are implicated in assembly of higher order nucleoprotein complexes essential for transcriptional repression and segrosome assembly, and also influence ParF nucleotide hydrolysis and polymerization. In this study we defined the role of residues in the RHH folded domain that are crucial for ParG dimerization and function. To achieve our goal the two α-helices, the intervening loop, and two C-terminal residues were analyzed fully by alanine scanning mutagenesis. Initially, ParG mutants were constructed and assessed for effects on normal plasmid partition activity and on dimerization. In vivo segregation assays and bacterial two-hybrid studies revealed mutation of residues F49 in α-helix 1 and W71 and L72 in α-helix 2 of ParG each resulted in defective plasmid partition activity and impaired dimerization. In vitro chemical cross-linking of purified proteins ParG-F49A, ParG-W71A and ParG-L72A demonstrated predominant monomeric species whereas wild-type ParG formed dimeric species as noted previously. Multiangle light scattering and sedimentation equilibrium analysis of the mutant proteins showed shifts in molar mass towards monomeric species with increased Kd values for dimerization. Protein-DNA interactions studied by gel retardation assays showed impaired interactions of ParG-F49A, ParG-W71A and ParG-L72A with parH. Results of conserved substitutions at position 71 showed that aromatic substitutions of W71 to Y71 or F71 are tolerated and have no apparent effects on ParG mediated plasmid segregation, but the non-aromatic W71L mutation blocked the segregation. However, a ParG double mutant bearing the ‘reversed’ amino acid pair (W71L-A52Y) retained plasmid segregation activity and behaved like wild-type ParG in dimerization assays in vitro and in vivo. Thus, substitution of W71 by tyrosine or phenylalanine does not disturb the monomer-monomer interface interactions that pack α-helix 2 from one monomer against residues of α-helix 1 and α-helix 2 of the partner monomer. Moreover, the permissible amino acid combinations at interacting positions 52 and 71 in ParG show significant flexibility and reveal key roles for these residues in function and dimerization of ParG. Overall, our in vivo and in vitro interaction studies provide novel information about the role of hydrophobic residues F49, W71 and L72 in ParG dimerization and activity.…

Subjects/Keywords: 572.8; ParG DNA binding protein

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saeed, S. (2012). Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/uncovering-the-molecular-mechanism-of-parg-dimerization-and-its-role-in-segrosome-assembly-of-multidrug-resistance-plasmid-tp228(76dda7e1-a14c-4d85-9b10-6524e1fb9281).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647355

Chicago Manual of Style (16^th Edition):

Saeed, Sadia. “Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228.” 2012. Doctoral Dissertation, University of Manchester. Accessed March 04, 2021. https://www.research.manchester.ac.uk/portal/en/theses/uncovering-the-molecular-mechanism-of-parg-dimerization-and-its-role-in-segrosome-assembly-of-multidrug-resistance-plasmid-tp228(76dda7e1-a14c-4d85-9b10-6524e1fb9281).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647355.

MLA Handbook (7^th Edition):

Saeed, Sadia. “Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228.” 2012. Web. 04 Mar 2021.

Vancouver:

Saeed S. Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228. [Internet] [Doctoral dissertation]. University of Manchester; 2012. [cited 2021 Mar 04]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/uncovering-the-molecular-mechanism-of-parg-dimerization-and-its-role-in-segrosome-assembly-of-multidrug-resistance-plasmid-tp228(76dda7e1-a14c-4d85-9b10-6524e1fb9281).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647355.

Council of Science Editors:

Saeed S. Uncovering the molecular mechanism of ParG dimerization and its role in segrosome assembly of multidrug resistance plasmid TP228. [Doctoral Dissertation]. University of Manchester; 2012. Available from: https://www.research.manchester.ac.uk/portal/en/theses/uncovering-the-molecular-mechanism-of-parg-dimerization-and-its-role-in-segrosome-assembly-of-multidrug-resistance-plasmid-tp228(76dda7e1-a14c-4d85-9b10-6524e1fb9281).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.647355

University of Victoria

6. Brick, David Joseph. Molecular characterization of poxviral RING finger proteins: virosome localization and identification of DNA binding and apoptosis inhibition activity.

Degree: Department of Biochemistry and Microbiology, 2018, University of Victoria

URL: https://dspace.library.uvic.ca//handle/1828/9400

► Shope fibroma virus (SFV) N1R is a member of a family of poxvirus proteins that is associated with virulence and largely defined by the presence… (more)

▼ Shope fibroma virus (SFV) N1R is a member of a family of poxvirus proteins that is associated with virulence and largely defined by the presence of a C-terminal RING finger motif and localization to virus factories within the cytoplasm of infected cells. Altered proteins, with deletions and site-specific mutations, were transiently expressed in vaccinia virus infected cells to discern regions of the protein that are required for localization. Deletion mutagenesis implicated a requirement of a small central region of the RING for localization, but the RING motif alone was not sufficient. A chimeric protein, however, in which the RING motif of the herpes simplex virus-1 ICP0 protein replaced the SFV N1R RING motif did localize to virus factories, indicating that the specificity for factory localization resided outside the RING motif of N1R. Critical evaluation of an alignment of poxviral N1R homologs identified a short, highly conserved N-terminal sequence 24-YINIT-28. When this sequence was deleted from N1R localization was abolished. Recombinant N1R protein isolated from vaccinia virus (VV) infected cells bound to calf-thymus DNA cellulose. Elution from this matrix required 0.5–0.75M NaCl, suggesting N1R localizes to the factory through an inherent DNA binding activity. Structural prediction analysis inferred that the conserved N-terminal region required for N1Rs factory localization forms a short β strand and subsequent alignment analysis with β sheet DNA binding proteins uncovered significant homology with the ribbon-helix-helix motif family which utilize a short β sheet for specific DNA interaction. Characterization of the factory localization of five N1R mutants, each having a single potential β strand residue replaced with Ala revealed that Asn 26 was the most important residue for factory localization. In contrast to N1R, which strongly binds DNA and rapidly sediments with the virus factories, SFV-N1RAsn26ΔAla mutant protein was found in the soluble fraction of infected cell lysates and failed to bind DNA cellulose. These results indicate that the N1R RING finger motif may not be central to DNA interactions and that N1R β strand residues particularly Asn 26 are involved in DNA binding and targeting N1R to the virus factories. Overexpression of N1R in vaccinia virus (VV) infected cells was found to inhibit virus induced apoptosis. To clarify the role of N1R protein with respect to apoptosis and to examine whether the related ectromelia virus virulence factor p28 (EVp28) might also play a role in apoptosis protection, a p28-mutant EV virus and the VV-N1R virus were tested for their ability to interfere with apoptosis induced by different signals. VV and EV infection were found to protect cells from Ultra Violet (UV) light, Tumor necrosis factor alpha (TNFα) and anti-Fas induced apoptosis. Expression of SFV N1R and EVp28 however, only protected infected HeLa cells from apoptosis induced by UV light, and did not protect from apoptosis induced by TNFα or anti-Fas antibody. Immunoblot analysis indicated… Advisors/Committee Members: Upton, Christopher (supervisor).

Subjects/Keywords: Poxviruses; DNA-binding proteins

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Brick, D. J. (2018). Molecular characterization of poxviral RING finger proteins: virosome localization and identification of DNA binding and apoptosis inhibition activity. (Thesis). University of Victoria. Retrieved from https://dspace.library.uvic.ca//handle/1828/9400

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Brick, David Joseph. “Molecular characterization of poxviral RING finger proteins: virosome localization and identification of DNA binding and apoptosis inhibition activity.” 2018. Thesis, University of Victoria. Accessed March 04, 2021. https://dspace.library.uvic.ca//handle/1828/9400.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Brick, David Joseph. “Molecular characterization of poxviral RING finger proteins: virosome localization and identification of DNA binding and apoptosis inhibition activity.” 2018. Web. 04 Mar 2021.

Vancouver:

Brick DJ. Molecular characterization of poxviral RING finger proteins: virosome localization and identification of DNA binding and apoptosis inhibition activity. [Internet] [Thesis]. University of Victoria; 2018. [cited 2021 Mar 04]. Available from: https://dspace.library.uvic.ca//handle/1828/9400.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Brick DJ. Molecular characterization of poxviral RING finger proteins: virosome localization and identification of DNA binding and apoptosis inhibition activity. [Thesis]. University of Victoria; 2018. Available from: https://dspace.library.uvic.ca//handle/1828/9400

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

King Abdullah University of Science and Technology

7. Alharbi, Siba I. A Comparative DNA Binding Study of the Human MAPK ERK2 and the Plant MAPK MPK4.

Degree: Biological and Environmental Sciences and Engineering (BESE) Division, 2020, King Abdullah University of Science and Technology

URL: http://hdl.handle.net/10754/664480

► Mitogen-activated protein kinases (MAPKs) are an important subfamily of protein kinases that are well conserved in all eukaryotes. MAPKs are the final component of a… (more)

Subjects/Keywords: MAPK; MPK4; ERK2; DNA Binding

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APA (6^th Edition):

Alharbi, S. I. (2020). A Comparative DNA Binding Study of the Human MAPK ERK2 and the Plant MAPK MPK4. (Thesis). King Abdullah University of Science and Technology. Retrieved from http://hdl.handle.net/10754/664480

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Alharbi, Siba I. “A Comparative DNA Binding Study of the Human MAPK ERK2 and the Plant MAPK MPK4.” 2020. Thesis, King Abdullah University of Science and Technology. Accessed March 04, 2021. http://hdl.handle.net/10754/664480.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Alharbi, Siba I. “A Comparative DNA Binding Study of the Human MAPK ERK2 and the Plant MAPK MPK4.” 2020. Web. 04 Mar 2021.

Vancouver:

Alharbi SI. A Comparative DNA Binding Study of the Human MAPK ERK2 and the Plant MAPK MPK4. [Internet] [Thesis]. King Abdullah University of Science and Technology; 2020. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10754/664480.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Alharbi SI. A Comparative DNA Binding Study of the Human MAPK ERK2 and the Plant MAPK MPK4. [Thesis]. King Abdullah University of Science and Technology; 2020. Available from: http://hdl.handle.net/10754/664480

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rutgers University

8. Locke, George. Statistical mechanical modeling of protein-DNA binding.

Degree: PhD, Physics and Astronomy, 2014, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/45333/

►

Eukaryotes must pack their DNA into the nucleus tightly, yet accessibly. To accomplish this, the nucleus contains special proteins called histones. Histones bind together to… (more)

▼

Eukaryotes must pack their DNA into the nucleus tightly, yet accessibly. To accomplish this, the nucleus contains special proteins called histones. Histones bind together to form an octamer, and DNA will wrap around the octamer to form a DNA-protein complex called a nucleosome. Nuclesomes are the primary structure of chromatin, which is the assemblage of DNA and proteins that organizes and stores the genome. 75%-90% of the genome is wound into nucleosomes, yet nucleosomes in the wrong place can block the binding of critical proteins including RNA polymerase: nucleosomes must be kept in their proper locations if the cell is to thrive. Therefore, the cell must regulate the positions of its nucleosomes. How does it accomplish this? Experiments that map the locations of nucleosomes reveal that these locations have a variety of sequence signals in common. That is, nucleosomes are more likely to be form from some kinds of DNA sequences than others. This dissertation addresses the sequence specificity of nucleosome formation. We shall seek answers to questions such as the following: What is the causal role of DNA sequence composition in determining nucleosome positions in vivo? If histones prefer some sequences to others, can we predict which sequences are preferable? Can we quantify the degree of preference? How do intrinsic preferences stack up against the many forces operating in the crowded cell nucleus? To address these and related questions, we have investigated genome-wide nucleosome maps produced by the recently established technology known as Next Generation Sequencing – the first such maps became available less than a decade ago. We have developed a flexible model using the formalism of statistical mechanics on a 1-D lattice to model the binding of histones to DNA. Chapter 2 develops this formalism. In Chapter 3, we shall develop a biophysical model of sequence specificity, applying it to maps of nucleosomes in vitro and in vivo from baker’s yeast, otherwise known as S. cerevisiae. Chapter 4 investi- gates the role of in vivo factors in determining chromatin organization in the nematode C. elegans, where our model suggests that effects occurring on the scale of single nucleosomes are responsible for reorganization of chromatin on a length scale several orders of magnitude greater.

Advisors/Committee Members: Morozov, Alexandre V (chair), Olson, Wilma K (internal member), Sengupta, Anivan M (internal member), Mekjian, Aram Z (internal member), Case, David A (outside member).

Subjects/Keywords: DNA-binding proteins; Genomes

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Locke, G. (2014). Statistical mechanical modeling of protein-DNA binding. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/45333/

Chicago Manual of Style (16^th Edition):

Locke, George. “Statistical mechanical modeling of protein-DNA binding.” 2014. Doctoral Dissertation, Rutgers University. Accessed March 04, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/45333/.

MLA Handbook (7^th Edition):

Locke, George. “Statistical mechanical modeling of protein-DNA binding.” 2014. Web. 04 Mar 2021.

Vancouver:

Locke G. Statistical mechanical modeling of protein-DNA binding. [Internet] [Doctoral dissertation]. Rutgers University; 2014. [cited 2021 Mar 04]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45333/.

Council of Science Editors:

Locke G. Statistical mechanical modeling of protein-DNA binding. [Doctoral Dissertation]. Rutgers University; 2014. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45333/

University of Texas Southwestern Medical Center

9. Mak, Sin Man. Development of a T-Loop Assay to Investigate T-Loop Dynamics and Structure.

Degree: 2014, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/3320

► An attractive target in cancer therapy development has been the study of telomeres, which are repetitive sequences at the ends of chromosomes critical in maintaining… (more)

▼ An attractive target in cancer therapy development has been the study of telomeres, which are repetitive sequences at the ends of chromosomes critical in maintaining genomic stability. T-loops, formed by the 3’ overhang inserting into the double strand region of the telomere, are thought to protect the ends from being recognized as double-strand breaks. An almost universal marker for cancer, telomerase, is a promising therapeutic target since its inhibition results in critically short telomeres, compromising t-loop structures. The clinical application has yet to be fully realized due to the lag phase between the times in which telomerase is inhibited and the times that telomeres become sufficiently short that the tumor undergoes apoptosis. Thus, improvements are needed including a greater understanding in t-loop dynamics and the cooperative interaction with telomerase to provide the strategy in which the lag phase can be shortened. Unfortunately, the study of t-loops has been challenging due to the difficulty of isolating and visualizing DNA with intact loop structures. Thus, we have developed novel methods to isolate DNA such that biochemical assays and microscopic visualizations for authentic t-loops are now possible. Digestion of proteins that stabilize t-loop and significant melting at the ends of DNA allow the 3’overhang to migrate out of the double strand region, thus unfolding t-loop and exposing the overhang. DNA isolated with typical procedures (Proteinase K at 55°C for 4 hrs, phenol/chloroform extraction) are thus linear and telomeric overhangs are susceptible to digestion by a 3’-5’ exonuclease (ExoI). The “overhangs” in t-loop structures should be resistant to ExoI. If we lower the temperature of Proteinase K digestion to 4°C to reduce the amount of DNA melting that can occur, we find that the ends are in fact resistant to ExoI digestion. A consistent ~2 fold higher overhang signal in isolated t-loops compared to linear telomeres was observed to distinguish between the two samples. Heating these 4°C samples to 37°C and 55°C caused unfolding of t-loops, resulting in sensitivity of the overhangs to ExoI to the same extent as normal DNA preparations. To validate the t-loop assay, transmission electron microscopy (TEM), a method with powerful magnification and extremely high resolution, is used to visualize DNA isolated at 55°C (linear structures) and 4°C (t-loop structures). The assay was then used to investigate t-loop dynamics throughout cell cycle, and we found that t-loops remain in a folded conformation throughout S phase, confirming the hypothesis that t-loops would unfold a second time for late S/G2 C-strand fill in. We also found that an overhang size of ~30 nts is too short to maintain stabilized t-loops compared to ~90 nts in BJ cells. In summary, we have significant evidence that we are able to prepare and analyze t-loops. Using this assay to determine t-loop structure and timing of t-loop repackage following replication and telomerase action will exceedingly add to our… Advisors/Committee Members: Burma, Sandeep, Shay, Jerry W., Wright, Woodring E., Yu, Hongtao.

Subjects/Keywords: DNA, Single-Stranded; DNA-Binding Proteins; Telomere

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APA (6^th Edition):

Mak, S. M. (2014). Development of a T-Loop Assay to Investigate T-Loop Dynamics and Structure. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/3320

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Mak, Sin Man. “Development of a T-Loop Assay to Investigate T-Loop Dynamics and Structure.” 2014. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021. http://hdl.handle.net/2152.5/3320.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Mak, Sin Man. “Development of a T-Loop Assay to Investigate T-Loop Dynamics and Structure.” 2014. Web. 04 Mar 2021.

Vancouver:

Mak SM. Development of a T-Loop Assay to Investigate T-Loop Dynamics and Structure. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2014. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/2152.5/3320.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mak SM. Development of a T-Loop Assay to Investigate T-Loop Dynamics and Structure. [Thesis]. University of Texas Southwestern Medical Center; 2014. Available from: http://hdl.handle.net/2152.5/3320

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Texas State University – San Marcos

10. Schaub, Leasha J. Quantifying the Energetics of Binding Between p53 and DNA Using Electrophoretic Mobility Shift Assays.

Degree: MS, Biochemistry, 2012, Texas State University – San Marcos

URL: https://digital.library.txstate.edu/handle/10877/4371

► A new class of proteins has been termed “intrinsically disordered” or “ID” for short. The proteins within this class appear to lack tertiary stability, though… (more)

Subjects/Keywords: p53; Intrinsically disordered protein; Binding; p53 protein; DNA; DNA-protein interactions; DNA-binding proteins; Electrophoresis

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APA (6^th Edition):

Schaub, L. J. (2012). Quantifying the Energetics of Binding Between p53 and DNA Using Electrophoretic Mobility Shift Assays. (Masters Thesis). Texas State University – San Marcos. Retrieved from https://digital.library.txstate.edu/handle/10877/4371

Chicago Manual of Style (16^th Edition):

Schaub, Leasha J. “Quantifying the Energetics of Binding Between p53 and DNA Using Electrophoretic Mobility Shift Assays.” 2012. Masters Thesis, Texas State University – San Marcos. Accessed March 04, 2021. https://digital.library.txstate.edu/handle/10877/4371.

MLA Handbook (7^th Edition):

Schaub, Leasha J. “Quantifying the Energetics of Binding Between p53 and DNA Using Electrophoretic Mobility Shift Assays.” 2012. Web. 04 Mar 2021.

Vancouver:

Schaub LJ. Quantifying the Energetics of Binding Between p53 and DNA Using Electrophoretic Mobility Shift Assays. [Internet] [Masters thesis]. Texas State University – San Marcos; 2012. [cited 2021 Mar 04]. Available from: https://digital.library.txstate.edu/handle/10877/4371.

Council of Science Editors:

Schaub LJ. Quantifying the Energetics of Binding Between p53 and DNA Using Electrophoretic Mobility Shift Assays. [Masters Thesis]. Texas State University – San Marcos; 2012. Available from: https://digital.library.txstate.edu/handle/10877/4371

University of Edinburgh

11. Syed, Shahida Nina. Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification.

Degree: PhD, 2014, University of Edinburgh

URL: http://hdl.handle.net/1842/9617

► Denaturation and renaturation is indispensable for the biological function of nucleic acids in many cellular processes, such as for example transcription for the synthesis of… (more)

▼ Denaturation and renaturation is indispensable for the biological function of nucleic acids in many cellular processes, such as for example transcription for the synthesis of RNA and DNA replication during cell division. However, the reversible hybridisation of complementary nucleic acids is equally crucial in nearly all molecular biology technologies, ranging from nucleic acid amplification technologies, such as the polymerase chain reaction, and DNA biosensors to next generation sequencing. For nucleic acid amplification technologies, controlled DNA denaturation and renaturation is particularly essential and achieved by cycling elevated temperatures. Although this is by far the most commonly used method, the management of rapid temperature changes requires bulky instrumentation and intense power supply. These factors so far precluded the development of true point-of-care tests for molecular diagnostics. This Thesis explored the possibility of using electrochemical means to control reversible DNA hybridisation by using electroactive intercalators. First, fluorescence-based melting curve analysis was employed to gain an in depth understanding of the reversible process of DNA hybridisation. Fundamental properties, such as stability of the double helix, were investigated by studying the effect of common denaturing agents, such as formamide and urea, pH and monovalent salt concentration. Thereafter, four different electroactive intercalators and their effect on the thermodynamic stability of duplex DNA were screened. The intercalators investigated were methylene blue, thionine, daunomycin and adriamycin. Absorbance-based melting curve analysis revealed a significant increase of the melting temperature of duplex DNA in the presence of oxidised daunomycin. This was not observed in the presence of chemically reduced daunomycin, which confirmed the hypothesis that switching of the redox-state of daunomycin altered its properties from DNA binding to non-binding. Accordingly this altered the thermodynamic stability of duplex DNA. The difference in the stability of duplex DNA, as a direct result of the redox-state of daunomycin, was exploited to drive cyclic electrochemically controlled DNA denaturation and renaturation under isothermal conditions. This proof-of-principle was demonstrated using complementary synthetic 20mer and 40mer DNA oligonucleotides. Analysis with in situ UV–vis and circular dichroism spectroelectrochemistry, as two independent techniques, indicated that up to 80 % of the duplex DNA was reversibly hybridised. Five cycles of DNA denaturation and renaturation were achieved and gel electrophoresis as well as NMR showed no degradation of DNA or daunomycin. As no extreme conditions were implicated, no covalent modification of DNA was required and isothermal conditions were kept, this finding has great potential to simplify future developments of miniaturised and portable bioanalytical systems for nucleic acid-based molecular diagnostics.

Subjects/Keywords: 572.8; DNA denaturation; DNA hybridisation; DNA binding molecules; electrochemical control; spectroelectrochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Syed, S. N. (2014). Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/9617

Chicago Manual of Style (16^th Edition):

Syed, Shahida Nina. “Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification.” 2014. Doctoral Dissertation, University of Edinburgh. Accessed March 04, 2021. http://hdl.handle.net/1842/9617.

MLA Handbook (7^th Edition):

Syed, Shahida Nina. “Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification.” 2014. Web. 04 Mar 2021.

Vancouver:

Syed SN. Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification. [Internet] [Doctoral dissertation]. University of Edinburgh; 2014. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/1842/9617.

Council of Science Editors:

Syed SN. Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification. [Doctoral Dissertation]. University of Edinburgh; 2014. Available from: http://hdl.handle.net/1842/9617

12. Priya Rajan, S. “Curcumin and its derivatives as Antioxidants and DNA Intercalators.

Degree: Applied Chemistry, 2013, Cochin University of Science and Technology

URL: http://dyuthi.cusat.ac.in/purl/3754

►

The scope of the work was to synthesis few biologically active derivatives of curcumin. The derivatives were prepared by altering the keto-enol centre of curcumin… (more)

Subjects/Keywords: natural curcuminoids; Antioxidant-prooxidant; DNA binding modes

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APA (6^th Edition):

Priya Rajan, S. (2013). “Curcumin and its derivatives as Antioxidants and DNA Intercalators. (Thesis). Cochin University of Science and Technology. Retrieved from http://dyuthi.cusat.ac.in/purl/3754

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Priya Rajan, S. ““Curcumin and its derivatives as Antioxidants and DNA Intercalators.” 2013. Thesis, Cochin University of Science and Technology. Accessed March 04, 2021. http://dyuthi.cusat.ac.in/purl/3754.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Priya Rajan, S. ““Curcumin and its derivatives as Antioxidants and DNA Intercalators.” 2013. Web. 04 Mar 2021.

Vancouver:

Priya Rajan S. “Curcumin and its derivatives as Antioxidants and DNA Intercalators. [Internet] [Thesis]. Cochin University of Science and Technology; 2013. [cited 2021 Mar 04]. Available from: http://dyuthi.cusat.ac.in/purl/3754.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Priya Rajan S. “Curcumin and its derivatives as Antioxidants and DNA Intercalators. [Thesis]. Cochin University of Science and Technology; 2013. Available from: http://dyuthi.cusat.ac.in/purl/3754

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Mississippi State University

13. Tata, Sri Ramya. Using NMR spectroscopy to investigate the binding of DNA to the globular domain of histone H1.0.

Degree: MS, Chemistry, 2016, Mississippi State University

URL: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03162016-124953/ ;

► Linker histones (H1) are a family of lysine-rich proteins that bind to or near the point at which DNA enters and exits the nucleosomal… (more)

Subjects/Keywords: Binding; DNA; NMR; Histone1.0; Globular Domain; Spectroscopy

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APA (6^th Edition):

Tata, S. R. (2016). Using NMR spectroscopy to investigate the binding of DNA to the globular domain of histone H1.0. (Masters Thesis). Mississippi State University. Retrieved from http://sun.library.msstate.edu/ETD-db/theses/available/etd-03162016-124953/ ;

Chicago Manual of Style (16^th Edition):

Tata, Sri Ramya. “Using NMR spectroscopy to investigate the binding of DNA to the globular domain of histone H1.0.” 2016. Masters Thesis, Mississippi State University. Accessed March 04, 2021. http://sun.library.msstate.edu/ETD-db/theses/available/etd-03162016-124953/ ;.

MLA Handbook (7^th Edition):

Tata, Sri Ramya. “Using NMR spectroscopy to investigate the binding of DNA to the globular domain of histone H1.0.” 2016. Web. 04 Mar 2021.

Vancouver:

Tata SR. Using NMR spectroscopy to investigate the binding of DNA to the globular domain of histone H1.0. [Internet] [Masters thesis]. Mississippi State University; 2016. [cited 2021 Mar 04]. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03162016-124953/ ;.

Council of Science Editors:

Tata SR. Using NMR spectroscopy to investigate the binding of DNA to the globular domain of histone H1.0. [Masters Thesis]. Mississippi State University; 2016. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03162016-124953/ ;

University of Texas Southwestern Medical Center

14. Rommel, Amy Ann. KU70 Binding Protein 5 (KUB5), A Novel Factor in DNA Double Strand Break Repair and Radio-Resistance in Human Breast Cancer.

Degree: 2011, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/865

► DNA double strand breaks (DSBs) are considered both mutagenic and carcinogenic if left un-repaired resulting in genomic instability and ultimately cancer. There are two main… (more)

Subjects/Keywords: Carrier Proteins; DNA-Binding Proteins; Breast Neoplasms

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APA (6^th Edition):

Rommel, A. A. (2011). KU70 Binding Protein 5 (KUB5), A Novel Factor in DNA Double Strand Break Repair and Radio-Resistance in Human Breast Cancer. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/865

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Rommel, Amy Ann. “KU70 Binding Protein 5 (KUB5), A Novel Factor in DNA Double Strand Break Repair and Radio-Resistance in Human Breast Cancer.” 2011. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021. http://hdl.handle.net/2152.5/865.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Rommel, Amy Ann. “KU70 Binding Protein 5 (KUB5), A Novel Factor in DNA Double Strand Break Repair and Radio-Resistance in Human Breast Cancer.” 2011. Web. 04 Mar 2021.

Vancouver:

Rommel AA. KU70 Binding Protein 5 (KUB5), A Novel Factor in DNA Double Strand Break Repair and Radio-Resistance in Human Breast Cancer. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2011. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/2152.5/865.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Rommel AA. KU70 Binding Protein 5 (KUB5), A Novel Factor in DNA Double Strand Break Repair and Radio-Resistance in Human Breast Cancer. [Thesis]. University of Texas Southwestern Medical Center; 2011. Available from: http://hdl.handle.net/2152.5/865

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas Southwestern Medical Center

15. Nash, Abigail I. Structural Basis for Signal Transduction in LOV Blue Light Photoreceptors.

Degree: 2011, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/871

► This research focused on studying the mechanisms of signal transduction within Light-Oxygen-Voltage domains, a subset of the PAS domain family. The first of two projects… (more)

Subjects/Keywords: Light; DNA-Binding Proteins; Bacterial Proteins

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APA (6^th Edition):

Nash, A. I. (2011). Structural Basis for Signal Transduction in LOV Blue Light Photoreceptors. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/871

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nash, Abigail I. “Structural Basis for Signal Transduction in LOV Blue Light Photoreceptors.” 2011. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021. http://hdl.handle.net/2152.5/871.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nash, Abigail I. “Structural Basis for Signal Transduction in LOV Blue Light Photoreceptors.” 2011. Web. 04 Mar 2021.

Vancouver:

Nash AI. Structural Basis for Signal Transduction in LOV Blue Light Photoreceptors. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2011. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/2152.5/871.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nash AI. Structural Basis for Signal Transduction in LOV Blue Light Photoreceptors. [Thesis]. University of Texas Southwestern Medical Center; 2011. Available from: http://hdl.handle.net/2152.5/871

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas Southwestern Medical Center

16. Dewey, Colleen Marie. TDP-43 Is Directed to Stress Granules by Sorbitol, a Novel Physiological Osmotic and Oxidative Stressor.

Degree: 2012, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/1021

► TDP-43, or TAR DNA-binding protein 43, is a pathological marker of a spectrum of neurodegenerative disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration… (more)

Subjects/Keywords: Cytoplasmic Granules; DNA-Binding Proteins; Sorbitol

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APA (6^th Edition):

Dewey, C. M. (2012). TDP-43 Is Directed to Stress Granules by Sorbitol, a Novel Physiological Osmotic and Oxidative Stressor. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/1021

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Dewey, Colleen Marie. “TDP-43 Is Directed to Stress Granules by Sorbitol, a Novel Physiological Osmotic and Oxidative Stressor.” 2012. Thesis, University of Texas Southwestern Medical Center. Accessed March 04, 2021. http://hdl.handle.net/2152.5/1021.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Dewey, Colleen Marie. “TDP-43 Is Directed to Stress Granules by Sorbitol, a Novel Physiological Osmotic and Oxidative Stressor.” 2012. Web. 04 Mar 2021.

Vancouver:

Dewey CM. TDP-43 Is Directed to Stress Granules by Sorbitol, a Novel Physiological Osmotic and Oxidative Stressor. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2012. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/2152.5/1021.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Dewey CM. TDP-43 Is Directed to Stress Granules by Sorbitol, a Novel Physiological Osmotic and Oxidative Stressor. [Thesis]. University of Texas Southwestern Medical Center; 2012. Available from: http://hdl.handle.net/2152.5/1021

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Connecticut

17. Quader, Saad A. Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites.

Degree: MS, Computer Science and Engineering, 2013, University of Connecticut

URL: https://opencommons.uconn.edu/gs_theses/448

► Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites are not well suited to the variability in the lengths… (more)

▼ Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC) and the positional dependence of nucleotides within an aligned set of TFBSs has not been well researched for modeling variable-length binding sites. In this paper, we propose ML-Consensus, a consensus model for variable-length binding sites which does not exclude any input binding sites. We consider Pairwise Score (PS) as a measure of positional dependence of nucleotides within an alignment of binding sites. We investigate how the prediction accuracy of ML-Consensus is affected by using IC, PS, and any particular binding site alignment strategy. We perform leave-one-out cross-validations on datasets of six species from the TRANSFAC public database, and analyze the results using ROC curves and Wilcoxon matched-pair signed-ranks test. Results: We observed that the incorporation of IC and PS in ML-Consensus results in statistically significant improvement in the prediction accuracy. Moreover, any two positions in the multiple sequence alignment of the binding sites were found to be interdependent only when they the distance between them was below a certain value. Lastly, configurations with state-of-the-art alignment strategies did not perform significantly better than configurations with a naive alignment strategy. Conclusions: There exists a core region within a set of known binding sites, ix and positions in that core region are interdependent. Additionally, it is possible to improve the existing state-of-the-art multiple sequence alignment algorithms by using such information as mentioned above about the core region among the binding sites. Availability: All source codes (C#), results, supporting evidence, supplementary data and figures are available from <a href="http://biogrid.engr.uconn.edu/mlconsensus/">http://biogrid.engr.uconn.edu/mlconsensus/</a> . Advisors/Committee Members: Sanguthevar Rajasekaran, Daniel Schwartz, Chun-Hsi Huang.

Subjects/Keywords: Transcription Factor Binding Sites; DNA motif

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APA (6^th Edition):

Quader, S. A. (2013). Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites. (Masters Thesis). University of Connecticut. Retrieved from https://opencommons.uconn.edu/gs_theses/448

Chicago Manual of Style (16^th Edition):

Quader, Saad A. “Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites.” 2013. Masters Thesis, University of Connecticut. Accessed March 04, 2021. https://opencommons.uconn.edu/gs_theses/448.

MLA Handbook (7^th Edition):

Quader, Saad A. “Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites.” 2013. Web. 04 Mar 2021.

Vancouver:

Quader SA. Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites. [Internet] [Masters thesis]. University of Connecticut; 2013. [cited 2021 Mar 04]. Available from: https://opencommons.uconn.edu/gs_theses/448.

Council of Science Editors:

Quader SA. Effect of Positional Dependence in Recognizing Transcription Factor Binding Sites. [Masters Thesis]. University of Connecticut; 2013. Available from: https://opencommons.uconn.edu/gs_theses/448

Durham University

18. Bobba, Gabriella. Interaction of chiral lanthanide complexes with nucleic acids.

Degree: PhD, 2002, Durham University

URL: http://etheses.dur.ac.uk/4131/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251134

► Enantiopure A and A lanthanide complexes, bearing a phenanthridinium or a dipyridoquinoxaline chromophore as a sensidser, have been designed with the aim of developing structural… (more)

Subjects/Keywords: 546; DNA binding

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APA (6^th Edition):

Bobba, G. (2002). Interaction of chiral lanthanide complexes with nucleic acids. (Doctoral Dissertation). Durham University. Retrieved from http://etheses.dur.ac.uk/4131/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251134

Chicago Manual of Style (16^th Edition):

Bobba, Gabriella. “Interaction of chiral lanthanide complexes with nucleic acids.” 2002. Doctoral Dissertation, Durham University. Accessed March 04, 2021. http://etheses.dur.ac.uk/4131/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251134.

MLA Handbook (7^th Edition):

Bobba, Gabriella. “Interaction of chiral lanthanide complexes with nucleic acids.” 2002. Web. 04 Mar 2021.

Vancouver:

Bobba G. Interaction of chiral lanthanide complexes with nucleic acids. [Internet] [Doctoral dissertation]. Durham University; 2002. [cited 2021 Mar 04]. Available from: http://etheses.dur.ac.uk/4131/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251134.

Council of Science Editors:

Bobba G. Interaction of chiral lanthanide complexes with nucleic acids. [Doctoral Dissertation]. Durham University; 2002. Available from: http://etheses.dur.ac.uk/4131/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251134

University of Oregon

19. McKeown, Alesia. Molecular Mechanisms for the Evolution of DNA Specificity in a Transcription Factor Family.

Degree: PhD, Department of Chemistry and Biochemistry, 2015, University of Oregon

URL: http://hdl.handle.net/1794/18723

► Transcription factors (TFs) bind to specific DNA sequences near target genes to precisely coordinate their regulation. Despite the central role of transcription factors in development… (more)

Subjects/Keywords: DNA-binding specificity; Molecular evolution; Transcription factors

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APA (6^th Edition):

McKeown, A. (2015). Molecular Mechanisms for the Evolution of DNA Specificity in a Transcription Factor Family. (Doctoral Dissertation). University of Oregon. Retrieved from http://hdl.handle.net/1794/18723

Chicago Manual of Style (16^th Edition):

McKeown, Alesia. “Molecular Mechanisms for the Evolution of DNA Specificity in a Transcription Factor Family.” 2015. Doctoral Dissertation, University of Oregon. Accessed March 04, 2021. http://hdl.handle.net/1794/18723.

MLA Handbook (7^th Edition):

McKeown, Alesia. “Molecular Mechanisms for the Evolution of DNA Specificity in a Transcription Factor Family.” 2015. Web. 04 Mar 2021.

Vancouver:

McKeown A. Molecular Mechanisms for the Evolution of DNA Specificity in a Transcription Factor Family. [Internet] [Doctoral dissertation]. University of Oregon; 2015. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/1794/18723.

Council of Science Editors:

McKeown A. Molecular Mechanisms for the Evolution of DNA Specificity in a Transcription Factor Family. [Doctoral Dissertation]. University of Oregon; 2015. Available from: http://hdl.handle.net/1794/18723

University of Waikato

20. Summers, Emma Louise. The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis .

Degree: 2012, University of Waikato

URL: http://hdl.handle.net/10289/6628

► Lsr2 is a small, basic DNA binding protein that is highly conserved in mycobacteria and related actinomycetes. Lsr2 is essential for growth in Mycobacterium tuberculosis… (more)

▼ Lsr2 is a small, basic DNA binding protein that is highly conserved in mycobacteria and related actinomycetes. Lsr2 is essential for growth in Mycobacterium tuberculosis and previous studies have shown that Lsr2 is involved in down-regulating a wide range of genes involved in cell wall synthesis and metabolic functions. This regulatory function is likely to influence bacterial growth and survival. This research investigated the biochemistry and 3D structure of Lsr2 from M. tuberculosis. Transmission electron microscopy (TEM) analysis of Lsr2 in complex with DNA revealed a regular fibril-like arrangement of protein coating double-stranded DNA. In addition, it was shown that Lsr2 physically protected DNA from DNase activity. The structure of the C-terminal DNA binding domain of Lsr2, determined by others part way through this research, prompted site directed mutagenesis of residues proposed to interact with DNA. Modification of arginine residues significantly reduced the binding of Lsr2 to DNA and fibril-like structures were not observed using TEM, for arginine mutants. The first crystal structure of the N-terminal domain of Lsr2 is reported here. Two high resolution structures in monoclinic and hexagonal space groups were solved using X-ray crystallography and ab initio phasing. Proteolytic processing of the N-terminus of Lsr2 was revealed by the structure in P2₁ and this process was recreated using the protease trypsin which resulted in crystal formation in a P3₁21 space group. Both structures show linear chains of dimeric N-terminal Lsr2, as shown by crystallographic symmetry, linked by overlapping anti-parallel β-sheets, revealing a mechanism of protein oligomerisation. Oligomerisation only occurs after the removal of the first three residues M1, A2 and K3. In solution, protein oligomerisation was recreated with trypsin, resulting in the formation of large protein complexes. A change in DNA topology after the addition of trypsin to full-length Lsr2/DNA complexes was observed using TEM. This mechanism is likely to be important to M. tuberculosis under “stress” conditions where proteases are known to be upregulated and where cross-linking and condensation of DNA is critical. Advisors/Committee Members: Arcus, Vickery L (advisor), Cursons, Raymond T (advisor).

Subjects/Keywords: DNA binding protein; Mycobacterium tuberculosis; Tuberculosis; Lsr2

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APA (6^th Edition):

Summers, E. L. (2012). The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis . (Doctoral Dissertation). University of Waikato. Retrieved from http://hdl.handle.net/10289/6628

Chicago Manual of Style (16^th Edition):

Summers, Emma Louise. “The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis .” 2012. Doctoral Dissertation, University of Waikato. Accessed March 04, 2021. http://hdl.handle.net/10289/6628.

MLA Handbook (7^th Edition):

Summers, Emma Louise. “The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis .” 2012. Web. 04 Mar 2021.

Vancouver:

Summers EL. The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis . [Internet] [Doctoral dissertation]. University of Waikato; 2012. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10289/6628.

Council of Science Editors:

Summers EL. The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis . [Doctoral Dissertation]. University of Waikato; 2012. Available from: http://hdl.handle.net/10289/6628

Louisiana State University

21. Jain, Teesta. DNA topoisomerases I from Pseudomonas aeruginosa and vaccinia virus and their use as drug targets.

Degree: PhD, 2008, Louisiana State University

URL: etd-01202009-104542 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3244

► Pseudomonas aeruginosa encodes a putative topoisomerase with sequence similarity to the type IB topoisomerase enzyme from vaccinia virus. Residues in the active site are conserved,… (more)

▼ Pseudomonas aeruginosa encodes a putative topoisomerase with sequence similarity to the type IB topoisomerase enzyme from vaccinia virus. Residues in the active site are conserved, notably Tyr292 which would be predicted to form the transient covalent bond to DNA. The gene encoding the P. aeruginosa topoisomerase I (PAT) was cloned and expressed in E. coli. The enzyme relaxes supercoiled DNA, while a mutant of P. aeruginosa containing a Tyr292 to Phe substitution at the active site was found to be catalytically inert. This is consistent with the role of Tyr in forming the covalent intermediate. Like vaccinia topoisomerase (VT), PAT relaxes DNA in the absence of ATP. Unlike VT, PAT does not relax supercoiled DNA without MgCl2 (or MnCl2) present. In addition, high concentration of NaCl is not able to substitute for MgCl2 as seen for VT. A truncated derivative of the topoisomerase lacking residues 1-98 relaxes DNA in the absence of the N-terminal domain, with both full length and truncated enzyme exhibiting equivalent requirements for divalent cations. Data shows that P. aeruginosa encodes a functional topoisomerase with significant similarity to the type IB enzyme encoded by poxviruses. Fluoroquinolones are antibacterial agents in clinical use with activity against DNA gyrase and DNA topoisomerase IV. P. aeruginosa is an opportunistic pathogen causing life-threatening diseases. Sparfloxacin, enrofloxacin and norfloxacin fluoroquinolones, are able to inhibit the PAT at high concentrations but other drugs belonging to this family are unable to do so. VT is ¡Ö32 KDa and one-third the size of the human topoisomerase ¡Ö 100 KDa. It shares sequence and biochemical similarities with the human topoisomerase. The VT binds duplex DNA with stringent specificity for transesterification at 5`-(C/T) CCTT site, where the 3` phosphate of the incised strand is linked to the Tyr274 of the enzyme to form a covalent cleavage complex. The fluoroquinolone enrofloxacin inhibits relaxation of supercoiled DNA by VT in a Mg2+-dependent fashion. Further results indicate that the mechanism by which enrofloxacin inhibits VT is by preventing formation of the covalent complex which suggest that fluoroquinolones may be structurally optimized to target type IB topoisomerases.

Subjects/Keywords: DNA binding; Topoisomerases

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APA (6^th Edition):

Jain, T. (2008). DNA topoisomerases I from Pseudomonas aeruginosa and vaccinia virus and their use as drug targets. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-01202009-104542 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3244

Chicago Manual of Style (16^th Edition):

Jain, Teesta. “DNA topoisomerases I from Pseudomonas aeruginosa and vaccinia virus and their use as drug targets.” 2008. Doctoral Dissertation, Louisiana State University. Accessed March 04, 2021. etd-01202009-104542 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3244.

MLA Handbook (7^th Edition):

Jain, Teesta. “DNA topoisomerases I from Pseudomonas aeruginosa and vaccinia virus and their use as drug targets.” 2008. Web. 04 Mar 2021.

Vancouver:

Jain T. DNA topoisomerases I from Pseudomonas aeruginosa and vaccinia virus and their use as drug targets. [Internet] [Doctoral dissertation]. Louisiana State University; 2008. [cited 2021 Mar 04]. Available from: etd-01202009-104542 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3244.

Council of Science Editors:

Jain T. DNA topoisomerases I from Pseudomonas aeruginosa and vaccinia virus and their use as drug targets. [Doctoral Dissertation]. Louisiana State University; 2008. Available from: etd-01202009-104542 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3244

Louisiana State University

22. Huang, Hao. MarR Family Transcriptional Regulators from Streptomyces coelicolor.

Degree: PhD, 2013, Louisiana State University

URL: etd-10022013-163614 ; https://digitalcommons.lsu.edu/gradschool_dissertations/64

► A family of transcriptional regulators that ubiquitously exists in prokaryotes is the multiple antibiotic resistance regulator (MarR) family. These transcriptional regulators participate in many cellular… (more)

▼ A family of transcriptional regulators that ubiquitously exists in prokaryotes is the multiple antibiotic resistance regulator (MarR) family. These transcriptional regulators participate in many cellular processes and can provide valuable knowledge about transcriptional regulation in response to specific conditions. The closely related MarR homologs TamR (trans-aconitate methyltransferase regulator) and PecS in Streptomyces coelicolor were studied to investigate their potential role in this bacterium. In Streptomyces coelicolor, the gene (SCO3133), which encodes TamR, is oriented divergently from the tam gene, which encodes trans-aconitate methyltransferase. TamR was found to regulate several target genes, which encode several enzymes closely related to the citric acid cycle, by binding to their promoter regions. TamR can regulate the transcription of tamR (encoding TamR), tam (encoding trans-aconitate methyltransferase), sacA (encoding aconitase), aceB1 (encoding malate synthase), mdh (encoding malate dehydrogenase) and idh (encoding isocitrate dehydrogenase). Moreover, the divergent tam-tamR gene pairs and the predicted TamR binding sites are highly conserved in the promoter regions of its target genes in different Streptomyces species. Trans-aconitate can attenuate DNA-binding by TamR, as can citrate, cis-aconitate and isocitrate, which are the substrate, intermediate and product of aconitase, respectively. In vivo results also showed that citrate and hydrogen peroxide can induce upregulation of these target genes. The collected information in this study suggests that TamR plays an important and conserved role in promoting metabolic flux through the citric acid cycle under some stress conditions. S. coelicolor also encodes a PecS homolog (SCO2647) that regulates a pecM gene (SCO2646). S. coelicolor PecS, which exists as a homodimer, binds the intergenic region between pecS and pecM genes with high affinity. The binding of PecS to its target DNA can be efficiently attenuated by the ligand urate, which also quenches the intrinsic fluorescence of PecS, indicating a direct interaction between urate and PecS. In vivo measurement of gene expression showed that activity of pecS and pecM genes is significantly elevated after exposure of S. coelicolor cultures to urate. These results indicate that S. coelicolor PecS responds to the ligand urate by attenuated DNA binding in vitro and upregulation of gene activity in vivo.

Subjects/Keywords: DNA binding protein; transcriptional regulator; bacteria; MarR

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APA (6^th Edition):

Huang, H. (2013). MarR Family Transcriptional Regulators from Streptomyces coelicolor. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-10022013-163614 ; https://digitalcommons.lsu.edu/gradschool_dissertations/64

Chicago Manual of Style (16^th Edition):

Huang, Hao. “MarR Family Transcriptional Regulators from Streptomyces coelicolor.” 2013. Doctoral Dissertation, Louisiana State University. Accessed March 04, 2021. etd-10022013-163614 ; https://digitalcommons.lsu.edu/gradschool_dissertations/64.

MLA Handbook (7^th Edition):

Huang, Hao. “MarR Family Transcriptional Regulators from Streptomyces coelicolor.” 2013. Web. 04 Mar 2021.

Vancouver:

Huang H. MarR Family Transcriptional Regulators from Streptomyces coelicolor. [Internet] [Doctoral dissertation]. Louisiana State University; 2013. [cited 2021 Mar 04]. Available from: etd-10022013-163614 ; https://digitalcommons.lsu.edu/gradschool_dissertations/64.

Council of Science Editors:

Huang H. MarR Family Transcriptional Regulators from Streptomyces coelicolor. [Doctoral Dissertation]. Louisiana State University; 2013. Available from: etd-10022013-163614 ; https://digitalcommons.lsu.edu/gradschool_dissertations/64

University of Louisville

23. Kruer, Traci L., 1979-. Characterization of DNA-binding proteins as clinically relevant biomarkers of breast cancer behavior.

Degree: PhD, 2011, University of Louisville

URL: 10.18297/etd/778 ; https://ir.library.louisville.edu/etd/778

► While investigating estrogen response element (ERE) binding properties of Era in de-identified human breast cancer extracts, additional proteins were observed that recognized ERE sequences (ERE-BP).… (more)

▼ While investigating estrogen response element (ERE) binding properties of Era in de-identified human breast cancer extracts, additional proteins were observed that recognized ERE sequences (ERE-BP). In order to unravel the apparent role of these proteins, our goal was to compare properties of these novel ERE-BP with those of ERa, determine their identity and evaluate their clinical relevance in breast cancer behavior. ERE-BP were present in various tissue types including breast, ovarian, uterine and colon cancers and normal tissues. These proteins were present in both cytoplasm and nuclei although higher binding activities were detected in nuclear extracts. ERE-BP did not supershift with numerous anti-ERa or ERß antibodies recognizing different ER epitopes suggesting that they are not fragments of either ERa or ERß. ERE-BP competed with rhERa for binding to the VitA2-ERE yet overall exhibited significantly different sequence specificity compared to that of human ERa. The ERE-BP we observed in breast cancer extracts were not specific for ERE sequences. To further support this conclusion, various estrogens had no effect on the ERE-binding of these proteins in contrast to rhERa. Furthermore, ERE-BP activities were not correlated with levels of expression of in either ERa- or ERE-mediated transcription. An immune-based method was established for purifying ERE-BP from tissue extracts and proteins were identified by mass spectrometry. Ku70 (XRCC6) and Ku80 (XRCC5) were determined to be the most likely candidates for the identity of ERE-BP. Supershift assays confirmed that ERE-BP/ERE complexes observed by EMSA were specifically recognized by antibodies to the Ku70/Ku80 heterodimer (Ku). Western blotting with Ku70/Ku80 antibodies confirmed their presence in breast cancer extracts. Increased Ku DNA-binding activities in cytosols of breast biopsies correlated with higher grade tumors, positive lymph node status and decreased patient survival. Also increased Ku DNA-binding activities in cancers from patients receiving adjuvant chemotherapy correlated with decreased survival, suggesting Ku DNA-binding activities may be used to predict response to treatment. Collectively, our results suggest that Ku DNA-binding activities in cytosols prepared from carcinoma biopsies are useful biomarkers for assessing breast cancer recurrence and response to therapy. Advisors/Committee Members: Wittliff, James L..

Subjects/Keywords: Breast cancer; Ku; DNA-binding proteins

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APA (6^th Edition):

Kruer, Traci L., 1. (2011). Characterization of DNA-binding proteins as clinically relevant biomarkers of breast cancer behavior. (Doctoral Dissertation). University of Louisville. Retrieved from 10.18297/etd/778 ; https://ir.library.louisville.edu/etd/778

Chicago Manual of Style (16^th Edition):

Kruer, Traci L., 1979-. “Characterization of DNA-binding proteins as clinically relevant biomarkers of breast cancer behavior.” 2011. Doctoral Dissertation, University of Louisville. Accessed March 04, 2021. 10.18297/etd/778 ; https://ir.library.louisville.edu/etd/778.

MLA Handbook (7^th Edition):

Kruer, Traci L., 1979-. “Characterization of DNA-binding proteins as clinically relevant biomarkers of breast cancer behavior.” 2011. Web. 04 Mar 2021.

Vancouver:

Kruer, Traci L. 1. Characterization of DNA-binding proteins as clinically relevant biomarkers of breast cancer behavior. [Internet] [Doctoral dissertation]. University of Louisville; 2011. [cited 2021 Mar 04]. Available from: 10.18297/etd/778 ; https://ir.library.louisville.edu/etd/778.

Council of Science Editors:

Kruer, Traci L. 1. Characterization of DNA-binding proteins as clinically relevant biomarkers of breast cancer behavior. [Doctoral Dissertation]. University of Louisville; 2011. Available from: 10.18297/etd/778 ; https://ir.library.louisville.edu/etd/778

University of New South Wales

24. Dewi, Vitri Aryani. Phosphorylation of KLF3 affects its DNA binding activity and biological function.

Degree: Biotechnology & Biomolecular Sciences, 2012, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/52940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:11618/SOURCE01?view=true

► Krüppel-Like Factor 3 (KLF3) is a broadly expressed zinc-finger transcriptional repressor, which binds to CACCC-boxes and GC-rich regions in the promoters and enhancers of its… (more)

▼ Krüppel-Like Factor 3 (KLF3) is a broadly expressed zinc-finger transcriptional repressor, which binds to CACCC-boxes and GC-rich regions in the promoters and enhancers of its target genes. Studies using knock-out mice have revealed functional roles for KLF3 in diverse tissues. Klf3-/- mice have a reduced life-span, leaner body composition, disturbed B-cell maturation and mild anaemia.This thesis explores the regulation of KLF3 function via post-translational modifications. We show that KLF3 exists as a phospho-protein in vivo and that post-translational modifications change in response to physiological stimuli. We have found that phosphorylation by Homeodomain Interacting Protein Kinase 2 (HIPK2) enhances KLF3’s DNA binding affinity. A mutant form of KLF3, in which serine 249 has been mutated to alanine has significantly reduced affinity for DNA, suggesting that phosphorylation at this site contributes to DNA binding capacity. Given that HIPK2 has been implicated in the cellular response to UV DNA damage, we investigated a potential role for KLF3 in this pathway. We found that cells lacking KLF3 have an altered response to UV stress, showing a complex phenotype indicative of a deregulated apoptotic pathway. Rescue of KLF3 null cells with wild-type KLF3, restored a normal response, while expression of a mutant version of KLF3, in which serine 249 has been mutated to alanine, showed only a partial rescue of the wild-type phenotype. Finally, we investigated the possibility of self-interaction within KLF3 using yeast two-hybrid assays and identified a putative self-association domain within the first 150 amino acids of KLF3.In conclusion, this study has identified post-translational modification of KLF3 as an important regulator of its activity. In particular, phosphorylation of serine 249 enhances KLF3’s DNA binding and plays a role in controlling its activity in biological pathways, such as the cellular response to UV stress and DNA damage. It also provides the first evidence of self-association within the KLF family. Advisors/Committee Members: Crossley, Merlin, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW, Pearson, Richard, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW.

Subjects/Keywords: DNA binding; Kruppel-Like Factor; KLF

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APA (6^th Edition):

Dewi, V. A. (2012). Phosphorylation of KLF3 affects its DNA binding activity and biological function. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/52940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:11618/SOURCE01?view=true

Chicago Manual of Style (16^th Edition):

Dewi, Vitri Aryani. “Phosphorylation of KLF3 affects its DNA binding activity and biological function.” 2012. Doctoral Dissertation, University of New South Wales. Accessed March 04, 2021. http://handle.unsw.edu.au/1959.4/52940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:11618/SOURCE01?view=true.

MLA Handbook (7^th Edition):

Dewi, Vitri Aryani. “Phosphorylation of KLF3 affects its DNA binding activity and biological function.” 2012. Web. 04 Mar 2021.

Vancouver:

Dewi VA. Phosphorylation of KLF3 affects its DNA binding activity and biological function. [Internet] [Doctoral dissertation]. University of New South Wales; 2012. [cited 2021 Mar 04]. Available from: http://handle.unsw.edu.au/1959.4/52940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:11618/SOURCE01?view=true.

Council of Science Editors:

Dewi VA. Phosphorylation of KLF3 affects its DNA binding activity and biological function. [Doctoral Dissertation]. University of New South Wales; 2012. Available from: http://handle.unsw.edu.au/1959.4/52940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:11618/SOURCE01?view=true

University of New South Wales

25. Artuz, Crisbel Marie. DNA binding proteins and cell fate.

Degree: Biotechnology & Biomolecular Sciences, 2015, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/54400 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:34914/SOURCE02?view=true

► Sequence-specific DNA binding proteins, known as transcription factors, play a central role in the control of eukaryotic gene regulation. Understanding the mechanisms through which DNA… (more)

▼ Sequence-specific DNA binding proteins, known as transcription factors, play a central role in the control of eukaryotic gene regulation. Understanding the mechanisms through which DNA binding domains recognise their target sequences will greatly improve our understanding of genetic diseases that result from mutations in DNA binding domains and gene promoters. Such information will also assist in the design of factors capable of artificially controlling gene expression. The zinc finger motif, commonly present in tandem arrays of three or more fingers, is the most prevalent DNA recognition structure found in eukaryotic transcription factors. The first project in this thesis aimed to better understand how zinc finger domains bind DNA by examining the two-zinc finger motif of the transcriptional regulator and oncogene ZNF217. By performing a comprehensive mutagenesis analysis, we were able to identify the amino acid residues that are essential for DNA recognition. Our findings indicate that ZNF217 binds to its preferred consensus site by a novel mechanism, an understanding of which may lead to a better appreciation of diseases that result from dysregulation of ZNF217 oncogenic function, and ultimately to the design of novel therapeutic strategies. In the second project, we examined the potential of DNA binding proteins to alter gene expression networks and hence cell fate, in the context of reprogramming fibroblasts towards the megakaryocytic lineage. Megakaryocytes are required for the production of platelets, which are essential for blood coagulation. Reduction in their numbers causes a life-threatening condition termed thrombocytopenia, which is currently treated by platelet transfusions. However, this treatment is restricted by the short storage life and limited supply of platelet concentrates. To investigate alternative approaches, we examined the potential of ectopic expression of combinations of transcription factors to direct fibroblasts towards the megakaryocyte lineage. We have discovered that over-expression of a combination of GATA1 or its mutant isoform, GATA1 short (GATA1s), FLI1 and TAL1 can drive phenotypic changes consistent with partial reprogramming of fibroblasts towards the megakaryocyte lineage, laying the foundation for follow up studies. Advisors/Committee Members: Crossley, Merlin, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW.

Subjects/Keywords: Megakaryopoiesis; ZNF217; DNA binding; Reprogramming; Transdifferentiation

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APA (6^th Edition):

Artuz, C. M. (2015). DNA binding proteins and cell fate. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/54400 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:34914/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Artuz, Crisbel Marie. “DNA binding proteins and cell fate.” 2015. Doctoral Dissertation, University of New South Wales. Accessed March 04, 2021. http://handle.unsw.edu.au/1959.4/54400 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:34914/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Artuz, Crisbel Marie. “DNA binding proteins and cell fate.” 2015. Web. 04 Mar 2021.

Vancouver:

Artuz CM. DNA binding proteins and cell fate. [Internet] [Doctoral dissertation]. University of New South Wales; 2015. [cited 2021 Mar 04]. Available from: http://handle.unsw.edu.au/1959.4/54400 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:34914/SOURCE02?view=true.

Council of Science Editors:

Artuz CM. DNA binding proteins and cell fate. [Doctoral Dissertation]. University of New South Wales; 2015. Available from: http://handle.unsw.edu.au/1959.4/54400 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:34914/SOURCE02?view=true

University of Oklahoma

26. She, Weifeng. Mutational Analysis of Bacterial Condensins.

Degree: PhD, 2011, University of Oklahoma

URL: http://hdl.handle.net/11244/318609

► A new member of the bacterial condensins is discussed in the end. In bacteria, two families of condensins were identified before this study, MukBEF and… (more)

Subjects/Keywords: Escherichia coli; DNA-binding proteins; Chromosomes

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APA (6^th Edition):

She, W. (2011). Mutational Analysis of Bacterial Condensins. (Doctoral Dissertation). University of Oklahoma. Retrieved from http://hdl.handle.net/11244/318609

Chicago Manual of Style (16^th Edition):

She, Weifeng. “Mutational Analysis of Bacterial Condensins.” 2011. Doctoral Dissertation, University of Oklahoma. Accessed March 04, 2021. http://hdl.handle.net/11244/318609.

MLA Handbook (7^th Edition):

She, Weifeng. “Mutational Analysis of Bacterial Condensins.” 2011. Web. 04 Mar 2021.

Vancouver:

She W. Mutational Analysis of Bacterial Condensins. [Internet] [Doctoral dissertation]. University of Oklahoma; 2011. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/11244/318609.

Council of Science Editors:

She W. Mutational Analysis of Bacterial Condensins. [Doctoral Dissertation]. University of Oklahoma; 2011. Available from: http://hdl.handle.net/11244/318609

University of Alberta

27. Peng, Zhenling. Large-scale Characterization Of Intrinsic Disorder And High-throughput Prediction Of RNA, DNA and Protein Binding Mediated By Intrinsic Disorder.

Degree: PhD, Department of Electrical and Computer Engineering, 2014, University of Alberta

URL: https://era.library.ualberta.ca/files/dv13zt305

► Intrinsically disordered proteins lack stable 3D structures in vivo, are functionally important, and are very common in nature. In the past three decades, many studies… (more)

▼ Intrinsically disordered proteins lack stable 3D structures in vivo, are functionally important, and are very common in nature. In the past three decades, many studies focused on prediction of intrinsic disorder from protein sequence, estimation of its abundance, and analyses of its functional roles. However, these studies were limited in their scope; for example, they focused only on one of many functional and structural aspects. We performed first-of-its-kind comprehensive and detailed analysis of abundance, functional roles, and cellular localizations of intrinsic disorder in complete proteomes. We show that intrinsic disorder is abundant across all kingdoms of life including viruses, is involved in crucial cellular processes, such as translation, transcription, metabolism, regulation, signaling, and so on, and is preferentially located in the ribosome and nucleus. We also mapped intrinsic disorder into eukaryotic, bacterial and archaean cells. These observations motivated us to further analyze two protein families  ribosomal proteins and proteins involved in the programmed cell death. We performed analysis across multiple species, which shows that intrinsic disorder is enriched and performs a variety of important cellular functions in ribosomal and cell death proteins. These two studies reveal that intrinsic disorder is involved in the interactions between proteins, RNAs, and DNAs. The prediction and characterization of these interactions for ordered proteins (i.e., proteins with stable 3D structures in vivo) recently attracted significant attention. However, there are no methods that target these functions/interactions mediated by the intrinsic disorder. Development of such methods is now possible by using the curated functional annotations of intrinsic disorder from the DisProt database. Utilizing these data we developed the first computational prediction method, DisoRDPbind, that predicts protein-protein, -RNA and -DNA interactions mediated by the intrinsic disorder. Our method utilizes logistic regression algorithm and a custom-designed and empirically selected set of descriptors of the input protein sequence. Empirical assessment using two benchmark datasets and large-scale predictions on four eukaryotic proteomes suggests that DisoRDPbind provides good predictive quality, differs from the methods focused on the predictions for the ordered proteins, and its computational efficiency allows for annotation of these interactions in whole proteomes.

Subjects/Keywords: protein-DNA binding; protein-RNA binding; protein-protein interaction; Intrinsic disorder

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Peng, Z. (2014). Large-scale Characterization Of Intrinsic Disorder And High-throughput Prediction Of RNA, DNA and Protein Binding Mediated By Intrinsic Disorder. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/dv13zt305

Chicago Manual of Style (16^th Edition):

Peng, Zhenling. “Large-scale Characterization Of Intrinsic Disorder And High-throughput Prediction Of RNA, DNA and Protein Binding Mediated By Intrinsic Disorder.” 2014. Doctoral Dissertation, University of Alberta. Accessed March 04, 2021. https://era.library.ualberta.ca/files/dv13zt305.

MLA Handbook (7^th Edition):

Peng, Zhenling. “Large-scale Characterization Of Intrinsic Disorder And High-throughput Prediction Of RNA, DNA and Protein Binding Mediated By Intrinsic Disorder.” 2014. Web. 04 Mar 2021.

Vancouver:

Peng Z. Large-scale Characterization Of Intrinsic Disorder And High-throughput Prediction Of RNA, DNA and Protein Binding Mediated By Intrinsic Disorder. [Internet] [Doctoral dissertation]. University of Alberta; 2014. [cited 2021 Mar 04]. Available from: https://era.library.ualberta.ca/files/dv13zt305.

Council of Science Editors:

Peng Z. Large-scale Characterization Of Intrinsic Disorder And High-throughput Prediction Of RNA, DNA and Protein Binding Mediated By Intrinsic Disorder. [Doctoral Dissertation]. University of Alberta; 2014. Available from: https://era.library.ualberta.ca/files/dv13zt305

Rhodes University

28. Matereke, Lavious Tapiwa. Analysis of predictive power of binding affinity of PBM-derived sequences.

Degree: Faculty of Science, Biochemistry and Microbiology, 2015, Rhodes University

URL: http://hdl.handle.net/10962/d1018666

► A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding… (more)

▼ A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding these transcription factor binding sites (TFBS) have been developed. In vivo technologies analyze DNA binding regions known to have bound to a TF in a living cell. Most widely used in vivo methods at the moment are chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing. In vitro methods derive TFBS based on experiments with TFs and DNA usually in artificial settings or computationally. An example is the Protein Binding Microarray which uses artificially constructed DNA sequences to determine the short sequences that are most likely to bind to a TF. The major drawback of this approach is that binding of TFs in vivo is also dependent on other factors such as chromatin accessibility and the presence of cofactors. Therefore TFBS derived from the PBM technique might not resemble the true DNA binding sequences. In this work, we use PBM data from the UniPROBE motif database, ChIP-seq data and DNase I hypersensitive sites data. Using the Spearman’s rank correlation and area under receiver operating characteristic curve, we compare the enrichment scores which the PBM approach assigns to its identified sequences and the frequency of these sequences in likely binding regions and the human genome as a whole. We also use central motif enrichment analysis (CentriMo) to compare the enrichment of UniPROBE motifs with in vivo derived motifs (from the JASPAR CORE database) in their respective TF ChIP-seq peak region. CentriMo is applied to 14 TF ChIP-seq peak regions from different cell lines. We aim to establish if there is a relationship between the occurrences of UniPROBE 8-mer patterns in likely binding regions and their enrichment score and how well the in vitro derived motifs match in vivo binding specificity. We did not come out with a particular trend showing failure of the PBM approach to predict in vivo binding specificity. Our results show Ets1, Hnf4a and Tcf3 show prediction failure by the PBM technique in terms of our Spearman’s rank correlation for ChIP-seq data and central motif enrichment analysis. However, the PBM technique also matched the in vivo binding specificities of FoxA2, Pou2f2 and Mafk. Failure of the PBM approach was found to be a result of variability in the TF’s binding specificity, the presence of cofactors, narrow binding specificity and the presence ubiquitous binding patterns.

Subjects/Keywords: Transcription factors; Protein binding; DNA-binding proteins; Chromatin; Protein microarrays

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Matereke, L. T. (2015). Analysis of predictive power of binding affinity of PBM-derived sequences. (Thesis). Rhodes University. Retrieved from http://hdl.handle.net/10962/d1018666

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Matereke, Lavious Tapiwa. “Analysis of predictive power of binding affinity of PBM-derived sequences.” 2015. Thesis, Rhodes University. Accessed March 04, 2021. http://hdl.handle.net/10962/d1018666.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Matereke, Lavious Tapiwa. “Analysis of predictive power of binding affinity of PBM-derived sequences.” 2015. Web. 04 Mar 2021.

Vancouver:

Matereke LT. Analysis of predictive power of binding affinity of PBM-derived sequences. [Internet] [Thesis]. Rhodes University; 2015. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10962/d1018666.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Matereke LT. Analysis of predictive power of binding affinity of PBM-derived sequences. [Thesis]. Rhodes University; 2015. Available from: http://hdl.handle.net/10962/d1018666

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Washington

29. Zhou, Wei. High-throughput methods to analyze protein-DNA and protein-RNA interactions.

Degree: PhD, 2020, University of Washington

URL: http://hdl.handle.net/1773/45502

► The genome of a cell contains the information to make thousands of RNA and protein molecules. However, a cell typically expresses only a fraction of… (more)

▼ The genome of a cell contains the information to make thousands of RNA and protein molecules. However, a cell typically expresses only a fraction of its genes, with different phenotypes arising because of differentially expressed genes. A cell controls its gene expression at different levels. For example, it can control when and how often a gene is transcribed, or it can selectively destabilize mRNA molecules. These biological processes are controlled by DNA- and RNAbinding proteins. In this dissertation, I first discuss the current state of the field of transcription factor (TF) variation, and I describe in vitro and in vivo technologies for mapping TF-DNA interactions. I then describe studies that apply the “calling card” assay to analyze interactions between chromatin and TF variants. In Chapter 2, I use this assay to characterize the interactions with chromatin of six single amino acid variants of Ste12, a yeast transcription factor regulating mating and invasion. My study showed that while subtle changes in the coding region of this transcription factor can result in large regulatory rewiring, the major determinants of organismal phenotype are the changes in the expression of a small, related set of genes. In Chapter 3, I use next generation sequencing technology to score the RNA-binding activity of variants in each of eight repeats present within a PUF domain. In this assay, in addition to the PUF variants, I generated a library of RNA variants in which each possible RNA base was present at the cognate position recognized by one of the PUF domain repeats. I identified many PUF domain variants with highly specific interactions by comparing their binding across the four RNA bases. This approach allows us to propose a complete code for RNA recognition by this PUF domain. In Chapter 4, I discuss a new method to concurrently profile the whole and newly synthesized transcriptome in each of many single cells, and use the data to quantify the dynamics of the cell cycle and glucocorticoid receptor activation. Finally, in Chapter 5, I discuss some of the 2 outstanding questions for mapping protein-DNA and protein-RNA interactions, including research directions that I believe will be important in the future. Advisors/Committee Members: Fields, Stanley (advisor).

Subjects/Keywords: DNA binding proteins; genetics; high throughput; RNA binding proteins; Genetics; Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhou, W. (2020). High-throughput methods to analyze protein-DNA and protein-RNA interactions. (Doctoral Dissertation). University of Washington. Retrieved from http://hdl.handle.net/1773/45502

Chicago Manual of Style (16^th Edition):

Zhou, Wei. “High-throughput methods to analyze protein-DNA and protein-RNA interactions.” 2020. Doctoral Dissertation, University of Washington. Accessed March 04, 2021. http://hdl.handle.net/1773/45502.

MLA Handbook (7^th Edition):

Zhou, Wei. “High-throughput methods to analyze protein-DNA and protein-RNA interactions.” 2020. Web. 04 Mar 2021.

Vancouver:

Zhou W. High-throughput methods to analyze protein-DNA and protein-RNA interactions. [Internet] [Doctoral dissertation]. University of Washington; 2020. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/1773/45502.

Council of Science Editors:

Zhou W. High-throughput methods to analyze protein-DNA and protein-RNA interactions. [Doctoral Dissertation]. University of Washington; 2020. Available from: http://hdl.handle.net/1773/45502

30. Pokhrel, Nilisha. Establishing the Roles of the DNA Binding Domains of Replication Protein A (RPA).

Degree: 2020, Marquette University

URL: https://epublications.marquette.edu/dissertations_mu/899

► During DNA metabolic processes such as replication and repair, double-stranded DNA is transiently unwound to expose single-stranded DNA (ssDNA). Such ssDNA intermediates are immediately coated… (more)

Subjects/Keywords: DNA Binding Domains; Dynamic Binding; Homologous Recombination; Non Canonical Amino Acids; RPA; Single Stranded DNA binding Proteins; Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pokhrel, N. (2020). Establishing the Roles of the DNA Binding Domains of Replication Protein A (RPA). (Thesis). Marquette University. Retrieved from https://epublications.marquette.edu/dissertations_mu/899

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Pokhrel, Nilisha. “Establishing the Roles of the DNA Binding Domains of Replication Protein A (RPA).” 2020. Thesis, Marquette University. Accessed March 04, 2021. https://epublications.marquette.edu/dissertations_mu/899.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Pokhrel, Nilisha. “Establishing the Roles of the DNA Binding Domains of Replication Protein A (RPA).” 2020. Web. 04 Mar 2021.

Vancouver:

Pokhrel N. Establishing the Roles of the DNA Binding Domains of Replication Protein A (RPA). [Internet] [Thesis]. Marquette University; 2020. [cited 2021 Mar 04]. Available from: https://epublications.marquette.edu/dissertations_mu/899.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Pokhrel N. Establishing the Roles of the DNA Binding Domains of Replication Protein A (RPA). [Thesis]. Marquette University; 2020. Available from: https://epublications.marquette.edu/dissertations_mu/899

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Open Access Theses and Dissertations