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You searched for subject:(DNA mimicry). Showing records 1 – 3 of 3 total matches.

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University of Edinburgh

1. Stephanou, Augoustinos S. Biophysical study of the DNA charge mimicry displayed by the T7 Ocr protein.

Degree: PhD, 2010, University of Edinburgh

The homodimeric Ocr protein of bacteriophage T7 is a molecular mimic of a bent double-stranded DNA molecule ~24 bp in length. As such, Ocr is a highly effective competitive inhibitor of the bacterial Type I restriction modification (R/M) system. Thus, Ocr facilitates phage infection of the bacterial cell to proceed unhindered by the action of the R/M defense system. The main aim of this work was to understand the basis of the DNA mimicry displayed by Ocr. The surface of the protein is replete with acidic residues, most or all of which mimic the phosphate backbone of DNA. Aspartate and glutamate residues on the surface of Ocr were either mutated or chemically modified in order to investigate their contribution to the tight binding between Ocr and the EcoKI Type I R/M enzyme. Single or double mutations of Ocr had no discernable effect on binding to EcoKI or its methyltransferase component (M.EcoKI). Chemical modification was then used to specifically modify the carboxyl moieties of Ocr, thereby neutralizing the negative charges on the protein surface. Ocr samples modified to varying degrees were analysed to establish the extent of derivatisation prior to extensive biophysical characterisation to assess the impact of these changes in terms of binding to the EcoKI R/M system. The results of this analysis revealed that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by at least ~800-fold. In addition, based on the known 3-D structure of the protein, a set of multiple mutations were introduced into Ocr aimed at eliminating patches of negative charge from the protein surface. Specifically, between 5 and 17 acidic residues were targeted for mutation (Asp and Glu to Asn and Gln, respectively). Analysis of the in vivo activity of the mutant Ocr along with biophysical characterisation of the purified proteins was then performed. Results from these studies identified regions of the Ocr protein that were critical in forming a tight association with the EcoKI R/M system. Furthermore by comparing the relative contribution of different groups of acidic residues to the free energy of binding, the actual mechanism by which Ocr mimics the charge distribution of DNA has been delineated.

Subjects/Keywords: 571.4; homodimeric Ocr protein; bacteriophage T7; DNA mimicry; Orc

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

APA (6th Edition):

Stephanou, A. S. (2010). Biophysical study of the DNA charge mimicry displayed by the T7 Ocr protein. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/4348

Chicago Manual of Style (16th Edition):

Stephanou, Augoustinos S. “Biophysical study of the DNA charge mimicry displayed by the T7 Ocr protein.” 2010. Doctoral Dissertation, University of Edinburgh. Accessed June 25, 2019. http://hdl.handle.net/1842/4348.

MLA Handbook (7th Edition):

Stephanou, Augoustinos S. “Biophysical study of the DNA charge mimicry displayed by the T7 Ocr protein.” 2010. Web. 25 Jun 2019.

Vancouver:

Stephanou AS. Biophysical study of the DNA charge mimicry displayed by the T7 Ocr protein. [Internet] [Doctoral dissertation]. University of Edinburgh; 2010. [cited 2019 Jun 25]. Available from: http://hdl.handle.net/1842/4348.

Council of Science Editors:

Stephanou AS. Biophysical study of the DNA charge mimicry displayed by the T7 Ocr protein. [Doctoral Dissertation]. University of Edinburgh; 2010. Available from: http://hdl.handle.net/1842/4348


University of Texas Southwestern Medical Center

2. Nulf, Christopher J. Peptide Nucleic Acid (PNA) Hybridization to Nucleic Acid Targets.

Degree: 2004, University of Texas Southwestern Medical Center

Peptide nucleic acid (PNA) is a DNA/RNA mimic that offers many advantages for hybridization to nucleic acid targets. The simple premise of Watson-Crick base-pairing presents PNAs with a number of diverse applications ranging fromnanotechnology to antisense therapeutics. I studied the synthesis and characterization of novel tethered PNA molecules (bisPNAs) designed to assemble two individual DNA molecules through Watson-Crick base pairing. The spacer regions linking the PNAs were varied in length and contained amino acids with different electrostatic properties. I observed that bisPNAs effectively assembled oligonucleotides that were either the exact length of the PNA or that contained overhanging regions that projected outwards. In contrast, DNA assembly was much less efficient if the oligonucleotides contained overhanging regions that projected inwards. Surprisingly, the length of the spacer region between the PNA sequences did not greatly affect the efficiency of DNA assembly. Reasons for inefficient assembly of inward projecting DNA oligonucleotides include non-sequence-specific intramolecular interactions between the overhanging region of the bisPNA and steric conflicts that complicate binding of two inward projecting strands. These results suggested that bisPNA molecules can be used for self-assembling DNA nanostructures. The Hepatitis C Virus (HCV) RNA genome contains a conserved tertiary structure known as the internal ribosomal entry site (IRES) necessary for cap-independent translation. I tested the hypothesis that antisense peptide nucleic acid (PNA) and locked nucleic acid (LNA) oligomers can bind IRES sequences and block translation. Using a lipid-mediated approach to introduce antisense PNAs and LNAs into cells, my data suggested that PNAs and LNAs could inhibit HCV IRES-dependent translation. PNA or LNA oligomers targeting different regions of the HCV IRES demonstrated a sequencespecific dose-response inhibition of translation with EC50 values of 50-150 nM. IRESdirected inhibition of gene expression widens the range of mechanisms for antisense inhibition by PNAs and LNAs and may provide further therapeutic lead compounds for the treatment of HCV. It is important to compare and contrast the biological activities of PNAs against other nucleotide analogs. Presented herein are collaborations involving comparisons of my PNAs against siRNA, 2'-O-methoxyethyl RNA, and morpholinos. Antisense PNAs were demonstrated to cause isoform-specific inhibition of protein expression of Caveolin. imilarly, PNAs demonstrated the ability to re-direct splicing activity of Insulin Receptor a-Subunit pre-mRNA. Also, antisense PNAs targeting the Chordino gene demonstrated "knock-down" morphologies similar to "knock-out" mutants in developing Zebrafish embryos. Collectively, these results suggest that PNAs are comparable in function to other oligonucleotide analogs and across many experimental platforms. Advisors/Committee Members: Corey, David R..

Subjects/Keywords: Mimicry, DNA; Oligonucleotides; Peptide Nucleic Acids

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

APA (6th Edition):

Nulf, C. J. (2004). Peptide Nucleic Acid (PNA) Hybridization to Nucleic Acid Targets. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/348

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

Chicago Manual of Style (16th Edition):

Nulf, Christopher J. “Peptide Nucleic Acid (PNA) Hybridization to Nucleic Acid Targets.” 2004. Thesis, University of Texas Southwestern Medical Center. Accessed June 25, 2019. http://hdl.handle.net/2152.5/348.

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

MLA Handbook (7th Edition):

Nulf, Christopher J. “Peptide Nucleic Acid (PNA) Hybridization to Nucleic Acid Targets.” 2004. Web. 25 Jun 2019.

Vancouver:

Nulf CJ. Peptide Nucleic Acid (PNA) Hybridization to Nucleic Acid Targets. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2004. [cited 2019 Jun 25]. Available from: http://hdl.handle.net/2152.5/348.

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

Council of Science Editors:

Nulf CJ. Peptide Nucleic Acid (PNA) Hybridization to Nucleic Acid Targets. [Thesis]. University of Texas Southwestern Medical Center; 2004. Available from: http://hdl.handle.net/2152.5/348

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


University of Toledo Health Science Campus

3. Prinz, Deborah Marie. Development and Characterization of the Immune Response Induced by Peptides and DNA Constructs that Mimic the Capsular Polysaccharide of Neisseria Meningitidis Serogroup C.

Degree: PhD, College of Graduate Studies, 2005, University of Toledo Health Science Campus

Carbohydrate antigens, such as the capsular polysaccharide of Neisseria meningitidis, are considered T-independent in nature. T-independent antigens do not require T cell help to elicit an immune response and do not generate immunologic memory formation. Carbohydrate antigens have limited responses as immunogens and fail to elicit protective levels of antibodies in children less than 2 yr of age. In order to increase the immunogenicity of a capsular polysaccharide, it must be converted into a T-dependent antigen. T-dependent antigens have the ability to associate with major histocompatibility complex (MHC) molecules and be presented to T cells. This generates a memory response and overcomes the immune tolerance associated with carbohydrate antigens in the young. One method of converting a carbohydrate into a T-dependent antigen is though the use of molecular mimicry. Molecular mimicry is defined as the ability of structurally unrelated molecules to exert the same biological effect. The concept of mimicry is based on the idiotypic network that suggests mimicry is the function of reproducing the binding interaction between an antibody and antigen. Recent studies have extended this concept by demonstrating the potential of phage display libraries in selecting peptides capable of mimicking the capsular polysaccharide, and thus eliciting anti-polysaccharide antibodies when used an immunogens. A natural extension of the observation that peptides can mimic polysaccharides is the development of DNA constructs that encode peptide mimics of capsular polysaccharides. DNA constructs have been shown to induce long lasting humoral and cellular responses, and can easily be altered to manipulate the magnitude and orientation of the desired immune response. Therefore, multiple DNA encoded epitope sequences representing specific carbohydrate and protein epitopes can be included in the construct design. Therefore, DNA immunization may be useful against encapsulated organisms by directing the response to specific polysaccharide as well as protein epitopes. The following studies will describe the selection and evaluation of an immunogenic peptide mimic of N. meningitidis serogroup C capsular polysaccharide (MCPS). The studies will further describe the design of a multi-epitope DNA construct encoding a peptide mimic of MCPS, and will evaluate and characterize the anti-MCPS immune response in a murine model. Advisors/Committee Members: Westerink, M.D., M.A. Julie (Advisor).

Subjects/Keywords: Health Sciences, Immunology; DNA Vaccines; Capsular Polysaccharide; Neisseria Meningitidis; Peptide Mimicry; Multi-epitope DNA Constructs

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

APA (6th Edition):

Prinz, D. M. (2005). Development and Characterization of the Immune Response Induced by Peptides and DNA Constructs that Mimic the Capsular Polysaccharide of Neisseria Meningitidis Serogroup C. (Doctoral Dissertation). University of Toledo Health Science Campus. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=mco1121695211

Chicago Manual of Style (16th Edition):

Prinz, Deborah Marie. “Development and Characterization of the Immune Response Induced by Peptides and DNA Constructs that Mimic the Capsular Polysaccharide of Neisseria Meningitidis Serogroup C.” 2005. Doctoral Dissertation, University of Toledo Health Science Campus. Accessed June 25, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=mco1121695211.

MLA Handbook (7th Edition):

Prinz, Deborah Marie. “Development and Characterization of the Immune Response Induced by Peptides and DNA Constructs that Mimic the Capsular Polysaccharide of Neisseria Meningitidis Serogroup C.” 2005. Web. 25 Jun 2019.

Vancouver:

Prinz DM. Development and Characterization of the Immune Response Induced by Peptides and DNA Constructs that Mimic the Capsular Polysaccharide of Neisseria Meningitidis Serogroup C. [Internet] [Doctoral dissertation]. University of Toledo Health Science Campus; 2005. [cited 2019 Jun 25]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=mco1121695211.

Council of Science Editors:

Prinz DM. Development and Characterization of the Immune Response Induced by Peptides and DNA Constructs that Mimic the Capsular Polysaccharide of Neisseria Meningitidis Serogroup C. [Doctoral Dissertation]. University of Toledo Health Science Campus; 2005. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=mco1121695211

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