Open Access Theses and Dissertations

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You searched for subject:(Deoxyribonucleotides Synthesis). Showing records 1 – 2 of 2 total matches.

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Oregon State University

1. McGaughey, Kathleen M. The effects of protein associations on pyrimidine deoxyribonucleotide biosynthesis.

Degree: PhD, Biochemistry, 2001, Oregon State University

URL: http://hdl.handle.net/1957/29400 

The faithful replication of DNA depends on the appropriate balance of DNA precursors. From studies conducted in bacteriophage T4, models for deoxyribonucleotide biosynthesis producing pools appropriate for DNA replication have made it possible to understand more complex systems. A portion of that body of evidence supports the concept that deoxyribonucleotide biosynthesis for bacteriophage T4 is carried out by an association of enzymes and other cellular components in a complex called the dNTP synthetase complex. This dissertation explores potential direct protein-protein interactions within this complex for the preparation of pyrimidine deoxyribonucleotides. Direct associations for enzymes involved in pyrimidine deoxyribonucleotide biosynthesis were examined by affinity chromatography. It was determined that there was a significant direct relationship between T4 thymidylate synthase and T4 dCMP deaminase, between T4 dCTPase/dUTPase and T4 dCMP deaminase as well. The interaction between thymidylate synthase and dCMP deaminase was significantly influenced by the presence of dCTP, a positive effector of dCMP deaminase. Furthermore, protein associations changed the kinetic character of pyrimidine deoxyribonucleotide production. T4 dCTPase/dUTPase, a member of the dNTP synthetase complex, significantly alters the kinetic nature of thymidylate synthase by working with thymidylate synthase in a reciprocal relationship. T4 single-stranded DNA binding protein, a member of the replication complex, alters the activity of thymidylate synthase as well. Attempts to isolate a kinetically coupled complex from two or more constituent proteins of the dNTP synthetase complex were frustrated by protein degradation to fragments under 10 kDa in size. Pyrimidine deoxyribonucleotide synthesis is located between the significant energy investment of ribonucleotide reductase and phosphate attachments by kinases to prepare the deoxyribonucleotide molecules for DNA replication. In bacteriophage T4, intermediate reactions are driven by mass action but are modulated by subtleties including direct protein associations and the presence of small molecules that influence enzyme function. Through these and potentially similar controls, pools of deoxyribonucleotides are prepared and delivered in a timely, balanced manner to the DNA replication apparatus. Advisors/Committee Members: Mathews, Christopher K. (advisor).

Subjects/Keywords: Deoxyribonucleotides  – Synthesis

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

APA (6th Edition):

McGaughey, K. M. (2001). The effects of protein associations on pyrimidine deoxyribonucleotide biosynthesis. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/29400

Chicago Manual of Style (16th Edition):

McGaughey, Kathleen M. “The effects of protein associations on pyrimidine deoxyribonucleotide biosynthesis.” 2001. Doctoral Dissertation, Oregon State University. Accessed December 15, 2019. http://hdl.handle.net/1957/29400.

MLA Handbook (7th Edition):

McGaughey, Kathleen M. “The effects of protein associations on pyrimidine deoxyribonucleotide biosynthesis.” 2001. Web. 15 Dec 2019.

Vancouver:

McGaughey KM. The effects of protein associations on pyrimidine deoxyribonucleotide biosynthesis. [Internet] [Doctoral dissertation]. Oregon State University; 2001. [cited 2019 Dec 15]. Available from: http://hdl.handle.net/1957/29400.

Council of Science Editors:

McGaughey KM. The effects of protein associations on pyrimidine deoxyribonucleotide biosynthesis. [Doctoral Dissertation]. Oregon State University; 2001. Available from: http://hdl.handle.net/1957/29400


University of Lethbridge

2. University of Lethbridge. Faculty of Arts and Science. Computational modeling of the hydrolysis of 2'-deoxyribonucleic acids .

Degree: 2009, University of Lethbridge

URL: http://hdl.handle.net/10133/1292 

The mechanism for the hydrolysis of 2′-deoxyribonucleosides is examined using computational chemistry techniques. Initially, a model capable of accurately predicting the mechanism and activation barrier for the uncatalyzed hydrolysis of 2′-deoxyuridine is designed. It is found that the smallest model includes both explicit and implicit solvation during the optimization step. Next, this hybrid solvation model is applied to four natural nucleosides, namely 2′-deoxyadenosine, 2′-deoxycytidine, 2′-deoxyguanosine and thymidine. The hybrid model correctly predicts the trend in activation Gibbs energies for the pyrimidines and purines, separately. Finally, the concepts developed during the generation of the uncatalyzed hydrolysis model are applied to the mechanism of action of a glycosylase enzyme, namely human uracil DNA glycosylase. A hybrid ONIOM approach is utilized to study the experimentally proposed two-step mechanism. Results regarding the protonation state of His148 are inconclusive, and future directions are proposed.

Subjects/Keywords: Deoxyribonucleotides  – Synthesis; Hydrolysis; Chemical engineering; DNA; Dissertations, Academic

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

APA (6th Edition):

Science, U. o. L. F. o. A. a. (2009). Computational modeling of the hydrolysis of 2'-deoxyribonucleic acids . (Thesis). University of Lethbridge. Retrieved from http://hdl.handle.net/10133/1292

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):

Science, University of Lethbridge. Faculty of Arts and. “Computational modeling of the hydrolysis of 2'-deoxyribonucleic acids .” 2009. Thesis, University of Lethbridge. Accessed December 15, 2019. http://hdl.handle.net/10133/1292.

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

MLA Handbook (7th Edition):

Science, University of Lethbridge. Faculty of Arts and. “Computational modeling of the hydrolysis of 2'-deoxyribonucleic acids .” 2009. Web. 15 Dec 2019.

Vancouver:

Science UoLFoAa. Computational modeling of the hydrolysis of 2'-deoxyribonucleic acids . [Internet] [Thesis]. University of Lethbridge; 2009. [cited 2019 Dec 15]. Available from: http://hdl.handle.net/10133/1292.

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

Council of Science Editors:

Science UoLFoAa. Computational modeling of the hydrolysis of 2'-deoxyribonucleic acids . [Thesis]. University of Lethbridge; 2009. Available from: http://hdl.handle.net/10133/1292

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

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