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 38 for “"recognition site"”.
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Using mutagenesis and molecular cloning techniques to identify key residues within the molecular recognition site of the Glucuronide Membrane Transporter (GusB).
… GusB must be structurally relevant for molecular recognition of glucuronide molecules; however information relating this is not yet available. Therefore, identifying key residues within the molecular recognition site of GusB became the focus of this research project. Using E. coli as a model …
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Assay for Rifampicin Resistant M13 RF Synthesis
… in the bacterium Escherichia coli. The recognition site for n' on the ØXl74 viral strand DNA constitutes the origin of replication for the ØX174 complementary strand.</p> <p>On ØX174 viral single-stranded DNA, synthesis of the complementary strand is initiated by the primosome. RNA …
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Analysis of FokI Cleavage Resistance Observed in DNA Sequences Generated via the Combinatorial Selection Method, REPSA
… 5’-GGATG-3’, and cleaves outside of this site 9 and 13 base-pairs downstream. The shifted cleavage function possessed by this kind of endonuclease is utilized in many applications including the combinatorial selection method, REPSA. FokI employment in the REPSA procedure has demonstrated …
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A study of protein-DNA interactions using atomic force microscopy and DNA origami
… of the detail of how proteins find their target sites and how they cleave at the sites remains unclear. Despite much progress in lab environments, where the tolerance for imprecise cutting is relatively high, in vivo treatment remains difficult. Most genome editing tools are derived from …
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Development of High Pressure Surface Plasmon Resonance for the Study of Biosystems
… of the BamH1 restriction enzyme to its DNA recognition site.
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Studies of sequence recognition by the EcoRI restriction/modification system of Escherichia coli
Sequence recognition by the EcoRI restriction/modification system of Escherichia coli is currently the subject of intense study as a model of the general phenomenon of target location by nucleotide sequence-specific enzymes and binding proteins. Models have proposed a variety of means for site …
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Accurate Estimation of Isoform and Gene Expression Levels from Next Generation Sequencing Data
… tags using a tagging restriction enzyme whose recognition site is ligated upstream of the recognition site of the anchoring enzyme.</p> <p>In this thesis we present two novel expectation-maximization algorithms for inference of isoform- and/or gene-specific expression levels from RNA-Seq and …
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Protein mis-folding and human disease
… that bind at the amyloid recognition site of SAP, and the X-ray<br/>crystal structures were determined at atomic resolution.<br/><br/>A secondary aim of this work was to understand the enhanced amyloidogenic<br/>potential of L55P and V30M transthyretin (TTR) protein. TTR …
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Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods
… interactions at JNK's D-recruitment site, making them a good candidate for specific non-ATP competitive inhibitors. However, (-)-zuonin A inhibits 80% of JNK catalyzed reactions at saturating levels, while (+)-zuonin A only inhibits 15%. Molecular docking and molecular dynamics …
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Patterns in the sequence context of protein disulfide bonds
… searched for conserved patterns that may reflect recognition sites by the disulfide bond forming enzyme protein disulfide isomerase (PDI). Several methods of classifying disulfide bonds were explored, and each class was analyzed for conserved sequence patterns. To maximize the chances of finding a …
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DNA Binding Protein’s Structure, Mechanism, and Functional Relevance; From Filament Formation of SgrAI to Helicase Activity of B19V-NS1
… sequences, known as primary and secondary sites. Depending on the type of recognition site SgrAI is bound to, SgrAI has a dimeric form or a filamentous form. The dimeric form of SgrAI is an inactive structure which can cleave only primary site sequences slowly. On the other hand, when it is …
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Protein purification and cDNA cloning of suGF1 : a sea urchin nuclear DNA-binding factor
… of the early histone gene battery, and the recognition site contains 11 contiguous Gs which are incorporated into a positioned nucleosome core in vitro. suGFI may be a member of a family of Gstring factors which could be involved in the developmental regulation of unrelated genes in various …
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Exogenously-introduced Homing Endonucleases Catalyze Double-stranded DNA Breaks in Aedes aegypti
… to test rHEs in Ae. aegypti were successful. Recognition sequences for various rHEs were introduced into Ae. aegypti through germline transformation, and imperfect repair at each of these exogenous sites was evaluated. In mosquitoes containing a single exogenous HE site, imperfect gap repair …
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Identification and Biochemical Characterization of Ghrelin O-Acyltransferase (GOAT)
… reaction strictly depends on the GOAT recognition site comprising three of the four N-terminal amino acids of proghrelin: Gly-1, Ser-3, and Phe-4. A pentapeptide containing only the N-terminal five amino acids of ghrelin is octanoylated by the enzyme. Moreover, I have demonstrated that …
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Bacterial expression of radio-labeled recombinant proteins for studying AHR signalling
… removal from the fusion partner via a thrombin recognition site as well as the incorporation of an in vitro phosphorylation site. The proteins were then expressed and column purified from E. coli. Once the proteins were expressed and purified they were cleaved from the thioredoxin fusion partner …
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Understanding Membrane Curvature Sensing
… and sensing of membrane curvature combined with recognition of specific cargo. Endophilin consists of a curvature-sensitive BAR domain followed by an SH3 (Src-homology 3) domain and has recently been identified in a clathrin-independent endocytosis pathway, FEME (fast endophilin-mediated …
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Binding mechanism of K88ab pili produced by enterotoxigenic Escherichia coli
… present on the protein moiety are a part of the recognition site for K88ab pili of receptor polypeptides in brush border membrane. Differences were obtained in the binding patterns of K88ab pili when brush border membranes were prepared from small intestines obtained from 2-, 21-, and 42-day-old …
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Genetic and Biochemical Characterization of the Mechanisms Concerning the TraR/AAI/TraM Mediated Quorum Sensing That Regulates Ti Plasmid Conjugation
… lactone, the cis-acting recognition site tra box located in the promoter region of the target gene and the antiactivator TraM that negatively modulates TraR activity. Using a combination of genetic and biochemical approaches, I have analyzed how these four elements …
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The Importance of RNA Sequence and Structure in the Assembly and Function of Signal Recognition Particle
Signal recognition particle (SRP), the ribonucleoprotein responsible for the recognition and targeting of nascent secretory proteins to the endoplasmic reticulum, is composed of 7SL RNA, along with six polypeptides. Earlier work in our lab identified a homolog of 7SL RNA in S. pombe, showed by gene …
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Mechanisms of Cytokine-Induced IGF -I Insensitivity in Cancer Cells
… a cyclin A promoter reporter. Deletion of an E2F recognition site from this reporter eliminates the regulatory effects of both IGF-I and TNFalpha/IL-1beta on cyclin A transcription, indicating an essential role for E2F-1 in mediating this cross talk. Moreover, knockdown experiments using E2F-1 …
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