Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 108 for “"DNA-Binding Proteins"”.
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Calling Cards For DNA-Binding Proteins
… by transcription factors, which bind to specific DNA sequences near genes. In order to understand the regulatory networks that control transcription, the genomic targets of all transcription factors under various conditions and in different cell types must be identified. This remains a distant …
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Analysis of DNA-binding Proteins in Yeast Saccharomyces Cerevisiae
… involving the regulated interactions of multiple proteins with promoter and enhancer elements. A variety of approaches are currently used to study these interactions in vivo, in vitro as well as in silico. With the genome sequences of many organisms now readily available, a plethora of DNA …
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Mechanical Manipulation of Eukaryotic Chromatin by DNA-Binding Proteins
… serves to exert spatiotemporal control of many DNA-transacting processes such as gene expression. Despite emerging progress, the biophysical mechanism underpinning eukaryotic genome organization remains an outstanding question in the field. In this thesis, I describe mechanistic insights on …
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Structural Studies of Two Sequence-General DNA -Binding Proteins
On the other hand, ssDNA-protein interaction is far less well understood than dsDNA-protein interactions. Gene V proteins from the filamentous phages are excellent systems for studying the interactions between protein and ssDNA. Some high resolution crystal structures were determined already. The …
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Designing Novel DNA-Binding Proteins with Generative Deep Learning
Protein-DNA interactions play a critical role in various biological processes, such as gene regulation and genome maintenance. Designing protein backbones specifically tailored for DNA binding remains a challenging task, requiring the exploration of novel computational approaches. This thesis …
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NMR Studies on Kinetics of Processes Involving DNA-Binding Proteins
… function. In response to external stimuli, DNA binding proteins very efficiently carry out their cognate tasks by making use of different kinetic mechanisms. Here we quantitatively analyze the kinetics of various processes involving DNA binding proteins. Chapter I provides an introduction to …
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DNA -Binding Proteins That Facilitate Integration of Transmissible DNA Elements in Bacteroides Thetaiotaomicron
… utilizing heparin column, size-exclusion and DNA-affinity chromatography, 2-D gel electrophoresis and mass fingerprinting to identify proteins that bound the attachment sites of CTnDOT (attDOT ) and NBU1 (attNI), and stimulated integration in vitro for both DNA elements. The proteins isolated …
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Intact and Damaged DNA and their Interaction with DNA-Binding Proteins: a Single Molecule Approach
… we study the architecture of intact and damaged DNA and their interaction with DNA-binding proteins using a combination of atomic force microscopy (AFM) and fluorescence correlation spectroscopy (FCS). In the beginning of this scientific work we therefore focus our efforts on the development of a …
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Molecular, Biochemical, and Evolutionary Analysis of Single-Stranded Dna-Binding Proteins From the Mesophilic Archaeon Methanosarcina Acetivorans
"One of the critical proteins involved in DNA replication across the three domains of life is single-stranded DNA-binding protein. At the replication fork, these proteins bind to stabilize and protect transiently exposed ssDNA from nucleases during DNA transactions. The ssDNA-binding protein is …
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A two-color bacterial two-hybrid system for selecting sequence-specific DNA-binding proteins via fluorescence activated cell sorting
Proteins that recognize specific DNA sequences play a major role in many biological processes, and the ability to select or design novel DNA binding proteins could have a major impact on many areas of biotechnology and medicine. This thesis begins with background information on zinc finger …
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Functional Analysis of Novel Replication Protein a Homologs in the Euryarchaeota: Implications in the Evolution of Single -Stranded DNA Binding Proteins Across the Three Domains of Life
Single-stranded DNA binding proteins (SSB) play an essential role in all cellular DNA transactions including DNA replication, repair, and recombination. At the replication fork, SSBs serve to stabilize and protect the transient intermediate ssDNA, which is generated by a replicative helicase. …
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Computational Identification and Functional Characterisation of Candidate DNA Binding Effectors in <i>Phytophthora</i>
… host nuclei during infection, where they bind DNA and modify gene expression. Computational methods for predicting DNA-binding proteins can provide a high-throughput means of candidate selection. However, current prediction algorithms are limited in plants and pathogens. <br/>Here we have …
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Computational Methods for the Measurement of Protein-DNA Interactions
It is of interest to know where in the genome DNA binding proteins act in order to effect their gene regulatory function. For many sequence specific DNA binding proteins we plan to predict the location of their action by having a model of their affinity to short DNA sequences. Existing and new …
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Complexity of transcription factor target search: effect of DNA natural decoys and DNA methylation through interplay with methyl-CpG-binding proteins on transcription factor DNA association
… elements of genes. However, chromosomal DNA contains numerous sites that are similar to the target sequences recognized by transcription factors. These sequences potentially serve as natural decoys that sequester transcription factors. The impact that these decoys have on transcription …
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Single -Molecule and Ensemble Fluorescence Studies of Single -Stranded DNA and Replication Proteins
DNA replication is a complex process involving many proteins that must be performed for a cell to proliferate. In this work, we will study three members of the replication system: single-stranded DNA, single-stranded DNA binding proteins, and the sliding clamp and clamp loader proteins. …
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Molecular analysis of glycogen phosphorylase-1 gene expression during the development of dictyostelium discoideum
… (Rutherford, et. aI., 1991). A complementary DNA (cDNA) encoding glycogen phosphorylase-}, gp-l, was isolated from a λgtll expression library made from amoebae stage mRNA. The 5' upstream region of the gp-l gene was cloned by inverted polymerase chain reaction (IPCR) and partial genomic DNA …
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Elucidating Pseudomonas aeruginosa virulence gene regulation by the ribbon-helix-helix transcription factor AmrZ
… a member of the ribbon-helix-helix family of DNA binding proteins, regulates several virulence factors, including alginate biosynthesis, flagellum expression, and type IV pili localization and twitching motility. AmrZ also acts as an autorepressor by binding two sites on its own promoter.
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Structure and Function Analysis of a Plant Transcription Activator
… TGACG, that is crucial for as-1 function and binding of a tobacco nuclear factor, activation sequence factor (ASF)-1. Two other TGACG-containing cis-elements from plant promoters were identified by a computer assisted search of a gene bank. These cis-elements, hex-1 from the wheat histone H3 …
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