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1.
Kosa, Matyas.
Direct and multistep conversion of lignin to biofuels.
Degree: PhD, Chemistry and Biochemistry, 2012, Georgia Tech
URL: http://hdl.handle.net/1853/45836 
► Lignin is the second most abundant biopolymer on Earth, right after cellulose, with a highly complex chemical structure that hinders its possible utilizations. Applications that…
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▼ Lignin is the second most abundant biopolymer on Earth, right after cellulose, with a highly complex chemical structure that hinders its possible utilizations. Applications that utilize lignin in different manners are of great interest, due to its inexpensive nature. Present work is based on the notion of converting lignin into different biofuels that have only a few, however important, advantages over lignin as a direct energy source. The first part of current work (pyrolysis) details the analysis of lignin from a relatively new lignin isolation process called LignoBoost. It is obtained from the pulp and paper industry via CO₂ precipitation of lignin from black liquor (BL). This method is environment friendly, results lignin with minimal oxidation, eliminates the main bottleneck of the Kraft cycle (recovery boiler capacity), and yet leaves enough lignin in the process stream to recover pulping chemicals and generate energy for the pulp mill. Pyrolysis had converted this lignin into bio-oil with high aliphatic content and low oxidation level, all advantageous for application as liquid fuel. The second part of this dissertation proved the theory that lignin degradation and lipid accumulation metabolic pathways can be interconnected. Gram-positive Rhodococcus opacus species, DSM 1069 and PD630 were used to evaluate lignin to lipid bioconversion, starting with ethanol organosolv and Kraft lignin. This conversion is a first step in a multistep process towards biodiesel production, which includes transesterification, after lipids are extracted from the cells. Results clearly indicated that the lignin to lipid bioconversion pathway is viable, by cells gaining up to 4 % of their weight in lipids, while growing solely on lignin as a carbon and energy source.
Advisors/Committee Members: Arthur J. Ragauskas (Committee Chair), Nicholas V. Hud (Committee Member), Preet Singh (Committee Member), Sheldon W. May (Committee Member), Yulin Deng (Committee Member).
Subjects/Keywords: Lignin; Lipid; Oleaginous bateria; Rhodococcus; Beta-ketoadipate; Pyrolysis; Biomass conversion; Biomass energy; Energy crops
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APA (6th Edition):
Kosa, M. (2012). Direct and multistep conversion of lignin to biofuels. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/45836
Chicago Manual of Style (16th Edition):
Kosa, Matyas. “Direct and multistep conversion of lignin to biofuels.” 2012. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/45836.
MLA Handbook (7th Edition):
Kosa, Matyas. “Direct and multistep conversion of lignin to biofuels.” 2012. Web. 23 Jan 2021.
Vancouver:
Kosa M. Direct and multistep conversion of lignin to biofuels. [Internet] [Doctoral dissertation]. Georgia Tech; 2012. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/45836.
Council of Science Editors:
Kosa M. Direct and multistep conversion of lignin to biofuels. [Doctoral Dissertation]. Georgia Tech; 2012. Available from: http://hdl.handle.net/1853/45836
2.
Barks, Hannah Lynn.
Separation and identification of complex mixtures using chromatography mass spectrometry.
Degree: MS, Chemistry and Biochemistry, 2010, Georgia Tech
URL: http://hdl.handle.net/1853/33953
► Here, for the first time, the formation of adenine, hypoxanthine, and guanine from formamide solutions with heating only to 130 degrees C and UV-irradiation in…
(more)
▼ Here, for the first time, the formation of adenine, hypoxanthine, and guanine from formamide solutions with heating only to 130 degrees C and UV-irradiation in the absence of minerals or inorganic salts is shown using LC-MS/MS as the analysis technique. The thesis goes on to demonstrate that the product distributions change drastically when the temperature is increased to 160 degrees C from 130 degrees C, specifically that the amount of hypoxanthine increases with the addition of UV light, and the amount of adenine increases with an increase in temperature. Along with showing the formation of purines in these reactions, the identification of pyrimidines was also achieved by GCxGC-MS. GCxGC-MS was also used to study additional samples, specifically bio-oils, where the type of compounds in the samples were easily identifiable, which allowed for a direct comparison between different types of bio-oils (e.g. Douglas-fir bark, Southern pine bark, and a Southern pine bark-wood mixture).
Advisors/Committee Members: Thomas M. Orlando (Committee Chair), Alfred H. Merrill, Jr. (Committee Member), Facundo M. Fernandez (Committee Member), Jean-Marie D. Dimandja (Committee Member), Nicholas V. Hud (Committee Member).
Subjects/Keywords: Mass spectrometry; Photoexcitation; Purines; Nucleobases; DNA; RNA; Chromatography; Chromatographic analysis; Life Origin
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APA (6th Edition):
Barks, H. L. (2010). Separation and identification of complex mixtures using chromatography mass spectrometry. (Masters Thesis). Georgia Tech. Retrieved from http://hdl.handle.net/1853/33953
Chicago Manual of Style (16th Edition):
Barks, Hannah Lynn. “Separation and identification of complex mixtures using chromatography mass spectrometry.” 2010. Masters Thesis, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/33953.
MLA Handbook (7th Edition):
Barks, Hannah Lynn. “Separation and identification of complex mixtures using chromatography mass spectrometry.” 2010. Web. 23 Jan 2021.
Vancouver:
Barks HL. Separation and identification of complex mixtures using chromatography mass spectrometry. [Internet] [Masters thesis]. Georgia Tech; 2010. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/33953.
Council of Science Editors:
Barks HL. Separation and identification of complex mixtures using chromatography mass spectrometry. [Masters Thesis]. Georgia Tech; 2010. Available from: http://hdl.handle.net/1853/33953
3.
Ovat, Asli.
Design, synthesis and evaluation of cysteine protease inhibitors.
Degree: PhD, Chemistry and Biochemistry, 2009, Georgia Tech
URL: http://hdl.handle.net/1853/33822
► Cysteine proteases are important drug targets due to their involvement in many biological processes such as protein turnover, digestion, blood coagulation, apoptosis, cell differentiation, cell…
(more)
▼ Cysteine proteases are important drug targets due to their involvement in many biological processes such as protein turnover, digestion, blood coagulation, apoptosis, cell differentiation, cell signaling, and the immune response. In this thesis, we have reported the design, synthesis and evaluation of clan CA and clan CD cysteine protease inhibitors.
Aza-peptidyl Michael acceptor and epoxide inhibitors for asparaginyl endopeptidases (legumains) from the bloodfluke, Schistosoma mansoni (SmAE) and the hard tick, Ixodes ricinus (IrAE) were designed and synthesized. SARs were similar, but with some notable exceptions. Both enzymes prefer disubstituted amides to monosubstituted amides in the P1' position and potency increased as we increased the hydrophobicity of the inhibitor in this position. Extending the inhibitor to P5 resulted in increased inhibitory potency, especially against IrAE, and both enzymes prefer small over large hydrophobic residues in the P2 position. Aza-peptide Michael acceptor inhibitors are more potent than aza-peptide epoxide inhibitors and, for some of these compounds, second order inhibition rate constants are the fastest yet discovered.
We have also synthesized aza-peptidyl Michael acceptor and epoxide inhibitors for the parasitic cysteine proteases; cruzain, rhodesain. We have found that monosubstituted amides were favored over disubstituted amides indicating the involvement of the amide hydrogen in a H-bond network. We have shown that aza-peptide epoxides were as potent as Michael acceptors and we have obtained compounds with IC50 values as low as 20 nM.
We have worked on the synthesis of heterocyclic peptidyl α-ketoamides, peptidyl ketones and aza-peptidyl ketones as calpain inhibitors. We have synthesized peptidyl α-ketoamides with nucleotide bases in the primed region to create compounds that can cross the blood-brain barrier. We have improved the potency by introducing a hydrophobic group on the adenine ring. We have obtained compounds with Ki values in the nanomolar range. We have designed peptidyl aminoketones as a new class of inhibitors for calpain. Peptidyl aminoketones were less potent than peptidyl α-ketoamides but still reasonable inhibitors of calpain that have the potential to cross the BBB.
Advisors/Committee Members: Powers, James C. (Committee Chair), Christoph J. Fahrni (Committee Member), Jonathan D. Glass (Committee Member), Nicholas V. Hud (Committee Member), Sheldon W. May (Committee Member).
Subjects/Keywords: Legumain; Calpain; Protease; Cysteine; Cysteine proteinases; Cysteine proteinases Inhibitors; Protease inhibitors; Biosynthesis; Epoxy compounds
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APA (6th Edition):
Ovat, A. (2009). Design, synthesis and evaluation of cysteine protease inhibitors. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/33822
Chicago Manual of Style (16th Edition):
Ovat, Asli. “Design, synthesis and evaluation of cysteine protease inhibitors.” 2009. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/33822.
MLA Handbook (7th Edition):
Ovat, Asli. “Design, synthesis and evaluation of cysteine protease inhibitors.” 2009. Web. 23 Jan 2021.
Vancouver:
Ovat A. Design, synthesis and evaluation of cysteine protease inhibitors. [Internet] [Doctoral dissertation]. Georgia Tech; 2009. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/33822.
Council of Science Editors:
Ovat A. Design, synthesis and evaluation of cysteine protease inhibitors. [Doctoral Dissertation]. Georgia Tech; 2009. Available from: http://hdl.handle.net/1853/33822
Georgia Tech
4.
Gadsby, Elizabeth Deibler.
Drug/DNA Interactions and Condensation
Investigated with Atomic Force Microscopy.
Degree: PhD, Chemistry and Biochemistry, 2004, Georgia Tech
URL: http://hdl.handle.net/1853/5113
► Atomic force microscopy (AFM) is a particularly useful tool, for obtaining structural information about drug-nucleic acid interactions. The mode of drug binding intercalation versus groove…
(more)
▼ Atomic force microscopy (AFM) is a particularly useful tool, for obtaining structural information about drug-nucleic acid interactions. The mode of drug binding intercalation versus groove binding can be determined from images acquired on individual DNA molecules as the length of a DNA molecule increases in direct proportion to the number of intercalators bound to it.
The efforts of this research were directed toward elucidating the mode of binding of a series of drugs based on polymers of naphthalenetetracarboxyl diimide (NDI) interacting with a linearized DNA plasmid. During the course of the investigation of these drugs, DNA intercalation was confirmed as the mode of binding and the binding affinity estimated. Unexpectedly, concentration-dependent formation of secondary DNA structures including condensates was observed. DNA toroids, spheres, and rods were imaged and measured. Conformations that are believed to be intermediate condensate forms were also identified at lower poly-NDI concentrations. Models for the DNA condensation process have been proposed.
Ultimately, this research furthers the understanding of DNA condensation which can be applied to gene delivery systems and anti-viral agents. It may also help direct the development of better drugs based on the insight of poly-intercalators interactions with DNA.
Advisors/Committee Members: Lawrence A. Bottomley (Committee Chair), L. Andrew Lyon (Committee Member), Loren D. Williams (Committee Member), Nicholas V. Hud (Committee Member), William D. Hunt (Committee Member).
Subjects/Keywords: Atomic force microscopy; DNA; Condensation; Intercalation; Drug interaction
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APA (6th Edition):
Gadsby, E. D. (2004). Drug/DNA Interactions and Condensation
Investigated with Atomic Force Microscopy. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/5113
Chicago Manual of Style (16th Edition):
Gadsby, Elizabeth Deibler. “Drug/DNA Interactions and Condensation
Investigated with Atomic Force Microscopy.” 2004. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/5113.
MLA Handbook (7th Edition):
Gadsby, Elizabeth Deibler. “Drug/DNA Interactions and Condensation
Investigated with Atomic Force Microscopy.” 2004. Web. 23 Jan 2021.
Vancouver:
Gadsby ED. Drug/DNA Interactions and Condensation
Investigated with Atomic Force Microscopy. [Internet] [Doctoral dissertation]. Georgia Tech; 2004. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/5113.
Council of Science Editors:
Gadsby ED. Drug/DNA Interactions and Condensation
Investigated with Atomic Force Microscopy. [Doctoral Dissertation]. Georgia Tech; 2004. Available from: http://hdl.handle.net/1853/5113
Georgia Tech
5.
Conwell, Christine C.
Kinetic and Thermodynamic Factors Govern DNA Condensate Size and Morphology.
Degree: PhD, Chemistry and Biochemistry, 2004, Georgia Tech
URL: http://hdl.handle.net/1853/5213
► It is well known that multivalent cations can cause DNA to condense from solution to form high-density nanometer scale particles. However, several fundamental questions concerning…
(more)
▼ It is well known that multivalent cations can cause DNA to condense from solution to form high-density nanometer scale particles. However, several fundamental questions concerning the phenomenon of DNA condensation remain unanswered. DNA condensation in vitro has been of interest for many years as a model of naturally occurring DNA packaging (e.g. chromatin, sperm head and virus capsid packing). More recently, DNA condensation has been of interest in optimizing artificial gene delivery, where packaging genes to an optimal size is essential to developing efficient uptake and delivery systems. The research presented in this dissertation provides an in depth biophysical study of the factors that control DNA condensate size and morphology. Millimolar changes in the ionic strength of the solution were found to alter the size of toroidal condensates. Variations in the order of addition of the counterions also significantly changed the size and morphology of the condensates. Studies were also performed to investigate the effects of static curvature and increased DNA flexibility on DNA condensation. These include the addition of static bending by sequence directed curvature, dynamic bending through protein-DNA interactions and reducing DNA persistence length by condensing single-stranded DNA. Several new models of DNA condensation are proposed based on the experimental data presented in this thesis.
Advisors/Committee Members: Nicholas V. Hud (Committee Chair), James C. Powers (Committee Member), L. Andrew Lyon (Committee Member), Loren D. Williams (Committee Member), Mark R. Prausnitz (Committee Member).
Subjects/Keywords: Gene delivery; Toroids; Condensation; DNA
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APA (6th Edition):
Conwell, C. C. (2004). Kinetic and Thermodynamic Factors Govern DNA Condensate Size and Morphology. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/5213
Chicago Manual of Style (16th Edition):
Conwell, Christine C. “Kinetic and Thermodynamic Factors Govern DNA Condensate Size and Morphology.” 2004. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/5213.
MLA Handbook (7th Edition):
Conwell, Christine C. “Kinetic and Thermodynamic Factors Govern DNA Condensate Size and Morphology.” 2004. Web. 23 Jan 2021.
Vancouver:
Conwell CC. Kinetic and Thermodynamic Factors Govern DNA Condensate Size and Morphology. [Internet] [Doctoral dissertation]. Georgia Tech; 2004. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/5213.
Council of Science Editors:
Conwell CC. Kinetic and Thermodynamic Factors Govern DNA Condensate Size and Morphology. [Doctoral Dissertation]. Georgia Tech; 2004. Available from: http://hdl.handle.net/1853/5213
Georgia Tech
6.
Rohatgi, Priyanka.
Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules.
Degree: PhD, Chemistry and Biochemistry, 2006, Georgia Tech
URL: http://hdl.handle.net/1853/19852
► Small molecule dependent molecular switches that control gene expression are important tool in understanding biological cellular processes and for regulating gene therapy. Nuclear receptors are…
(more)
▼ Small molecule dependent molecular switches that control gene expression are important tool in understanding biological cellular processes and for regulating gene therapy. Nuclear receptors are ligand activated transcription factors that have been engineered to selectively respond to synthetic ligands and used as regulators of gene expression. In this work the retinoid X receptor (RXR), has been used to develop an inducible molecular switch with a near drug like compound LG335. Three RXR variants (Q275C; I310M; F313I), (I268A; I310A; F313A; L436F), (I268V; A272V; I310M; F313S; L436M) were created via site-directed mutagenesis and a structure based approach, such that they preferentially bind to the synthetic ligand LG335 and not its natural ligand, 9-cis retinoic acid. These variants show reverse ligand specificity as designed and have an EC50 for LG335 of 80 nM, 30 nM, 180 nM, respectively. The ligand binding domains of the RXR variants were fused to a yeast transcription factor Gal4 DNA binding domain. This modified chimeric fusion protein showed reverse response element specificity as designed and recognized the Gal4 response element instead of the RXR response element. The modified RXR protein did not heterodimerize with wild type RXR or with other nuclear receptor such as retinoic acid receptor. These RXR-based molecular switches were tested in retroviral vectors using firefly luciferase and green fluorescence protein and they maintain their inducible behavior with LG335. These experiments demonstrate the orthogonality of RXR variants and their possible use in regulating gene therapy.
Advisors/Committee Members: Donald F. Doyle (Committee Chair), C. David Sherrill (Committee Member), H.Trent Spencer (Committee Member), Joseph M. LeDoux (Committee Member), Nicholas V. Hud (Committee Member).
Subjects/Keywords: Protein engineering; Nuclear receptor; Gene therapy; Inducible system; Molecular switches; Gene therapy; Ligands (Biochemistry); Protein engineering
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APA (6th Edition):
Rohatgi, P. (2006). Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/19852
Chicago Manual of Style (16th Edition):
Rohatgi, Priyanka. “Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules.” 2006. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/19852.
MLA Handbook (7th Edition):
Rohatgi, Priyanka. “Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules.” 2006. Web. 23 Jan 2021.
Vancouver:
Rohatgi P. Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules. [Internet] [Doctoral dissertation]. Georgia Tech; 2006. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/19852.
Council of Science Editors:
Rohatgi P. Engineering Protein Molecular Switches To Regulate Gene Expression with Small Molecules. [Doctoral Dissertation]. Georgia Tech; 2006. Available from: http://hdl.handle.net/1853/19852
Georgia Tech
7.
Nayak, Satish Prakash.
Design, Synthesis and Characterization of Multiresponsive Microgels.
Degree: PhD, Chemistry and Biochemistry, 2005, Georgia Tech
URL: http://hdl.handle.net/1853/6845
► This thesis is geared towards using hydrogel nanoparticles in various biotechnological applications. The polymer that was used in making these nanoparticles was poly(N-isopropylacrylamide), which is…
(more)
▼ This thesis is geared towards using hydrogel nanoparticles in various biotechnological applications. The polymer that was used in making these nanoparticles was poly(N-isopropylacrylamide), which is a thermoresponsive polymer. These particles were used in making fast responsive polymer films, which can be used in optics. It was observed that the rate of deswelling increased as the concentration of the nanoparticles in the film was increased. These particles were also used in making photoresponsive materials. In this case a photoresponsive dye (malachite green) was conjugated to these nanoparticles and in presence of light of appropriate wavelength the particles undergo a phase transition. A core/shell construct was synthesized where the core was composed of degradable cross-links and the shell of composed of non-degradable cross-links. The degradable cross-linker had vicinal diols, which can be cleaved by sodium periodate. Hence after degrading the core, hollow particles were obtained. Zwitterionic particles were made by incorporating a cationic and anionic comonomer. These microgels go from a positively charged state to zwitterionic to negatively charged state on increasing the pH. One of the important potential applications for these microgels is drug delivery. Microgels were used for targeting cancer cells. Folic acid was used as the targeting ligand. The microgels were conjugated with folic acid and were able to target cells that overexpress folate receptors. In one other application core/shell microgels were made which exhibit pore-size dependent permeation of proteins.
Advisors/Committee Members: Dr. L. Andrew Lyon (Committee Chair), Dr. Christopher W. Jones (Committee Member), Dr. Jiri Janata (Committee Member), Dr. Marcus Weck (Committee Member), Dr. Nicholas V. Hud (Committee Member).
Subjects/Keywords: pNIPAm; Core/Shell; Nanoparticles; Hydrogels; Polymers; Thin films; Polymers Thermal properties; Polymers Optical properties; Nanoparticles Synthesis; Colloids
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APA (6th Edition):
Nayak, S. P. (2005). Design, Synthesis and Characterization of Multiresponsive Microgels. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/6845
Chicago Manual of Style (16th Edition):
Nayak, Satish Prakash. “Design, Synthesis and Characterization of Multiresponsive Microgels.” 2005. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/6845.
MLA Handbook (7th Edition):
Nayak, Satish Prakash. “Design, Synthesis and Characterization of Multiresponsive Microgels.” 2005. Web. 23 Jan 2021.
Vancouver:
Nayak SP. Design, Synthesis and Characterization of Multiresponsive Microgels. [Internet] [Doctoral dissertation]. Georgia Tech; 2005. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/6845.
Council of Science Editors:
Nayak SP. Design, Synthesis and Characterization of Multiresponsive Microgels. [Doctoral Dissertation]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/6845
Georgia Tech
8.
Ndlebe, Thabisile S.
Oxidative Damage in DNA: an Exploration of Various DNA Structures.
Degree: PhD, Chemistry and Biochemistry, 2006, Georgia Tech
URL: http://hdl.handle.net/1853/11467
► Research efforts to determine the causes, effects and locations of mutations within the human genome have been widely pursued due to their role in the…
(more)
▼ Research efforts to determine the causes, effects and locations of mutations within the human genome have been widely pursued due to their role in the development of various diseases. The main cause of mutations in vivo is oxidative damage to DNA via oxidants and free radical species. Numerous studies have been performed in vitro to determine how oxidative damage is induced in DNA. Most of these in vitro studies require photosensitizers to initiate the oxidative damage through various mechanisms. For the purposes of this research, all the photosensitizers that were used initiated oxidative damage in DNA through the electron transfer mechanism. In the charge transport studies, an anthraquinone photosensitizer was covalently linked to the 5 end of DNA by a short carbon tether in order to determine the pattern of damage induced along the length of the DNA. Anthraquinone preferentially damages guanine bases. Our first work sought to determine the effects of charge transport through guanine rich quadruplex DNA dimers. The dimers were formed by the combination of two hairpins with duplex overhangs extending beyond the quadruplex region. This enabled the optimal comparison of the effects of charge transport between duplex and quadruplex DNA structures. Another area of research we pursued in this area was to determine the effects of charge transport in M-DNA (a novel DNA conformation that was reported to form in the presence of zinc ions at a pH above 8). Earlier work on M-DNA suggested that it behaved like a molecular wire. Our research attempted to determine the effects of charge transport on this structure in order to show the behavior of a DNA molecular wire as compared to the standard studies performed in this area on normal B-DNA structures. Lastly, in collaboration with Dr. Ramaiah and colleagues we designed some viologen linked acridine photosensitizers which were tested for any ability to cleave GGG bulges. In preliminary studies, these viologen linked acridine derivatives showed preferential cleavage for guanine bases. They were not covalently bound to DNA, although they could potentially form non covalent interactions with DNA such as intercalation and/or groove binding. Our overall research goal was to determine the extent and overall effect of oxidative damage (using different photosensitizers) on the various DNA structures mentioned above.
Advisors/Committee Members: Dr. Gary B. Schuster (Committee Chair), Bridgette Anne Barry (Committee Member), Donald F. Doyle (Committee Member), Nicholas V. Hud (Committee Member), Roger M. Wartell (Committee Member).
Subjects/Keywords: DNA structures; Oxidative damage; Charge transport in DNA; M-DNA; FRET; Quadruplex DNA; DNA photocleavage; Viologen linked acridine derivatives; DNA Structure; DNA Analysis
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APA (6th Edition):
Ndlebe, T. S. (2006). Oxidative Damage in DNA: an Exploration of Various DNA Structures. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/11467
Chicago Manual of Style (16th Edition):
Ndlebe, Thabisile S. “Oxidative Damage in DNA: an Exploration of Various DNA Structures.” 2006. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/11467.
MLA Handbook (7th Edition):
Ndlebe, Thabisile S. “Oxidative Damage in DNA: an Exploration of Various DNA Structures.” 2006. Web. 23 Jan 2021.
Vancouver:
Ndlebe TS. Oxidative Damage in DNA: an Exploration of Various DNA Structures. [Internet] [Doctoral dissertation]. Georgia Tech; 2006. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/11467.
Council of Science Editors:
Ndlebe TS. Oxidative Damage in DNA: an Exploration of Various DNA Structures. [Doctoral Dissertation]. Georgia Tech; 2006. Available from: http://hdl.handle.net/1853/11467
Georgia Tech
9.
Schlientz, Nathan William.
Charge Migration through Duplex DNA: A Study of the Mechanism for Charge Migration and Oxidative Damage.
Degree: PhD, Chemistry and Biochemistry, 2006, Georgia Tech
URL: http://hdl.handle.net/1853/11484
► DNA sequences containing contiguous AA or TT mismatches, as well as sequences containing a 3-deazacytidine analogue were synthesized. Irradiation of anthraquinone abstracts an electron from…
(more)
▼ DNA sequences containing contiguous AA or TT mismatches, as well as sequences containing a 3-deazacytidine analogue were synthesized. Irradiation of anthraquinone abstracts an electron from the DNA. The loss of an electron from double-stranded DNA results in the formation of a radical cation that migrates through the DNA where it reacts irreversibly with H2O or O2 at GG steps. Subsequent treatment with piperidine or Fpg enzyme cleaves the backbone of the DNA at the site of reaction. DNA oligomers were designed to contain contiguous AA, TT, or G3-deazacytidine mismatches. It was revealed that the mismatches destabilize the duplex DNA; however, there is no measurable effect on the overall secondary structure of the DNA. The contiguous (AA)n mismatch, where n lt 7, was shown to have no effect on charge migration efficiency. In contrast, the contiguous (TT)n mismatch, where n gt 2, was shown to have near complete inhibition of charge migration through the mismatch region. Charge migration through the G3-deazacytidine mismatch was shown to have no effect on charge migration efficiency as well. Interestingly, reaction at the (G3-deazacytidine)2 base pairs revealed a change in the ratio of oxidative damage at the Gs. In (GC)2 base pairs, the ratio of damage at the two Gs is 10:1 with the majority of damage occurring at the 5-G. However, the (G3-deazacytidine)2 base pairs had an equal distribution of damage at the 5 and 3-Gs, with the amount of total reactivity equaling the (GC)2 base pairs. These findings indicate that the base composition in mismatched DNA determines the effect on charge migration efficiency and trapping reactivity.
Advisors/Committee Members: Gary B. Schuster (Committee Chair), David M. Collard (Committee Member), Laren M. Tolbert (Committee Member), Nicholas V. Hud (Committee Member), Uzi Landman (Committee Member).
Subjects/Keywords: Radical cation; Charge transfer; Deazacytidine; DNA; Oxidative damage; Charge migration; DNA; Charge transfer; Cations
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APA (6th Edition):
Schlientz, N. W. (2006). Charge Migration through Duplex DNA: A Study of the Mechanism for Charge Migration and Oxidative Damage. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/11484
Chicago Manual of Style (16th Edition):
Schlientz, Nathan William. “Charge Migration through Duplex DNA: A Study of the Mechanism for Charge Migration and Oxidative Damage.” 2006. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/11484.
MLA Handbook (7th Edition):
Schlientz, Nathan William. “Charge Migration through Duplex DNA: A Study of the Mechanism for Charge Migration and Oxidative Damage.” 2006. Web. 23 Jan 2021.
Vancouver:
Schlientz NW. Charge Migration through Duplex DNA: A Study of the Mechanism for Charge Migration and Oxidative Damage. [Internet] [Doctoral dissertation]. Georgia Tech; 2006. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/11484.
Council of Science Editors:
Schlientz NW. Charge Migration through Duplex DNA: A Study of the Mechanism for Charge Migration and Oxidative Damage. [Doctoral Dissertation]. Georgia Tech; 2006. Available from: http://hdl.handle.net/1853/11484
Georgia Tech
10.
Vilfan, Igor D.
DNA Condensate Morphology - Examples from the Test Tube and Nature.
Degree: PhD, Chemistry and Biochemistry, 2005, Georgia Tech
URL: http://hdl.handle.net/1853/7172
► DNA condensates have attracted the attention of biophysicists, biochemists and polymer physicists for more than thirty years. In the biological community, the quest to understand…
(more)
▼ DNA condensates have attracted the attention of biophysicists, biochemists and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g. gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. The thesis includes an analysis of the kinetic and thermodynamic factors governing DNA condensate morphology in solution, and discusses implications for future applications of DNA condensation in vitro as a model system for testing theories of polyelectrolyte collapse. In addition, DNA condensation by folded bovine protamine, a naturally occurring multivalent oligopeptide responsible for packing genomic DNA in bovine sperm cells, has been studied as well. The analysis of morphology, size, DNA strand packing density, and the stability of structural integrity of DNA condensates obtained with folded bovine protamines suggests that we have reconstituted native sperm cell chromatin. The results of this study were used to model the local structure of bovine sperm cell chromatin.
Advisors/Committee Members: Nicholas V. Hud (Committee Chair), Donald F. Doyle (Committee Member), Loren D. Willliams (Committee Member), Rigoberto Hernandez (Committee Member), Roger M. Wartell (Committee Member).
Subjects/Keywords: Polyelectrolytes; Nucleation; Growth; Toroid; Chromatin
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APA (6th Edition):
Vilfan, I. D. (2005). DNA Condensate Morphology - Examples from the Test Tube and Nature. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/7172
Chicago Manual of Style (16th Edition):
Vilfan, Igor D. “DNA Condensate Morphology - Examples from the Test Tube and Nature.” 2005. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/7172.
MLA Handbook (7th Edition):
Vilfan, Igor D. “DNA Condensate Morphology - Examples from the Test Tube and Nature.” 2005. Web. 23 Jan 2021.
Vancouver:
Vilfan ID. DNA Condensate Morphology - Examples from the Test Tube and Nature. [Internet] [Doctoral dissertation]. Georgia Tech; 2005. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/7172.
Council of Science Editors:
Vilfan ID. DNA Condensate Morphology - Examples from the Test Tube and Nature. [Doctoral Dissertation]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/7172
Georgia Tech
11.
Roberts, Lezah Wilette.
Effect of Netropsin on One-electron Oxidation of DNA.
Degree: PhD, Chemistry and Biochemistry, 2005, Georgia Tech
URL: http://hdl.handle.net/1853/7228
► One electron oxidation of DNA has been studied extensively over the years. When a charge is injected into a DNA duplex, it migrates through the…
(more)
▼ One electron oxidation of DNA has been studied extensively over the years. When a charge is injected into a DNA duplex, it migrates through the DNA until it reaches a trap. Upon further reactions, damage occurs in this area and strand cleavage can occur. Many works have been performed to see what can affect this damage to DNA. Netropsin is a minor groove binder that can bind to tracts of four to five A:T base pairs. It has been used in the studies within to determine if it can protect DNA against oxidative damage, caused by one-electron oxidation, when it is bound within the minor groove of the DNA. By using a naphthacenedione derivative as a photosensitizer, several DNA duplexes containing netropsin binding sites as well as those without binding sites, were irradiated at 420 nm, analyzed, and visualized to determine its effect on oxidative damage. It has been determined netropsin creates a quenching sphere of an average of 5.8 * 108 Šwhether bound to the DNA or not. Herein we will show netropsin protects DNA against oxidative damage whether it is free in solutions or bound within the minor groove of a DNA duplex.
Advisors/Committee Members: Gary B. Schuster (Committee Chair), Donald Doyle (Committee Member), Laren Tolbert (Committee Member), Nicholas V. Hud (Committee Member), Roger Wartell (Committee Member).
Subjects/Keywords: Photosensitizer; Charge transfer; Netropsin; TQ; DNA; Electron transfer; One-electron oxidation; Photosensitization, Biological; Charge transfer in biology; DNA Analysis; Oxidation, Physiological
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APA ·
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APA (6th Edition):
Roberts, L. W. (2005). Effect of Netropsin on One-electron Oxidation of DNA. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/7228
Chicago Manual of Style (16th Edition):
Roberts, Lezah Wilette. “Effect of Netropsin on One-electron Oxidation of DNA.” 2005. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/7228.
MLA Handbook (7th Edition):
Roberts, Lezah Wilette. “Effect of Netropsin on One-electron Oxidation of DNA.” 2005. Web. 23 Jan 2021.
Vancouver:
Roberts LW. Effect of Netropsin on One-electron Oxidation of DNA. [Internet] [Doctoral dissertation]. Georgia Tech; 2005. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/7228.
Council of Science Editors:
Roberts LW. Effect of Netropsin on One-electron Oxidation of DNA. [Doctoral Dissertation]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/7228
Georgia Tech
12.
Horowitz, Eric D.
Intercalator-mediated assembly of nucleic acids.
Degree: PhD, Chemistry and Biochemistry, 2009, Georgia Tech
URL: http://hdl.handle.net/1853/33937
► The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to…
(more)
▼ The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to synthesize protein enzymes. This hypothesis, by some interpretations, implies that nucleic acid polymers were the first polymers of life, and must have therefore spontaneously formed from simple molecular building blocks in the "prebiotic soup." Although prebiotic chemists have searched for decades for a process by which RNA can be made from plausible prebiotic reactions, numerous problems persist that stand in the way of a chemically-sound model for the spontaneous generation of an RNA World (e.g., strand-cyclization, heterogeneous backbones, non-selective ligation of activated nucleotides). The Molecular Midwife hypothesis, proposed by
Hud and Anet in 2000, provides a possible solution to several problems associated with the assembly of the first nucleic acids. In this hypothesis, nucleic acid base pairs are assembled by small, planar molecules that resemble molecules which are known today to intercalate the base pairs of nucleic acid duplexes. Thus, the validity and merits of the Molecular Midwife hypothesis can be, to some extent, explored by studying the effects of intercalation on the non-covalent assembly of nucleic acids.
In this thesis, I explore the role of the sugar-phosphate backbone in dictating the structure and thermodynamics of nucleic acid intercalation by using 2′,5′-linked RNA intercalation as a model system of non-natural nucleic acid intercalation. The solution structure of an intercalator-bound 2′,5′ RNA duplex reveals structural and thermodynamic aspects of intercalation that provide insight into the origin of the nearest-neighbor exclusion principle, a principle that is uniformly obeyed upon the intercalation of natural (i.e. 3′,5′-linked) RNA and DNA. I also demonstrate the ability of intercalator-mediated assembly to circumvent the strand-cyclization problem, a problem that otherwise greatly limits the polymerization of short oligonucleotides into long polymers. Together, the data presented in this thesis illustrate the important role that the nucleic acid backbone plays in governing the thermodynamics of intercalation, and provide support for the proposed role of intercalator-mediated assembly in the prebiotic formation of nucleic acids.
Advisors/Committee Members: Nicholas V. Hud (Committee Chair), David Sherrill (Committee Member), Loren Williams (Committee Member), Roger Wartell (Committee Member), Steve Harvey (Committee Member).
Subjects/Keywords: RNA; Intercalation; DNA; Nucleic acids; Origin of life; Template-directed synthesis; Life Origin; Oligonucleotides; Proteins Synthesis; Proteins
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APA ·
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MLA ·
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APA (6th Edition):
Horowitz, E. D. (2009). Intercalator-mediated assembly of nucleic acids. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/33937
Chicago Manual of Style (16th Edition):
Horowitz, Eric D. “Intercalator-mediated assembly of nucleic acids.” 2009. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/33937.
MLA Handbook (7th Edition):
Horowitz, Eric D. “Intercalator-mediated assembly of nucleic acids.” 2009. Web. 23 Jan 2021.
Vancouver:
Horowitz ED. Intercalator-mediated assembly of nucleic acids. [Internet] [Doctoral dissertation]. Georgia Tech; 2009. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/33937.
Council of Science Editors:
Horowitz ED. Intercalator-mediated assembly of nucleic acids. [Doctoral Dissertation]. Georgia Tech; 2009. Available from: http://hdl.handle.net/1853/33937
Georgia Tech
13.
Watkins, Jason Derrick.
X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.
Degree: PhD, Chemistry and Biochemistry, 2008, Georgia Tech
URL: http://hdl.handle.net/1853/26709
► The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. To gain…
(more)
▼ The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. To gain insight into its DNA binding mechanism, we solved the 1.6 Å x-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2 This operator has an A-T at position 9L and T-A at position 9R and is termed DNA9T.
Van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD – NA9T complex suggests that sequence-specificity arises substantially from interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5' TTAA 3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational change. Protein-DNA hydrogen bonding plays a secondary role in specificity.
Advisors/Committee Members: Loren D. Williams (Committee Chair), Donald Doyle (Committee Member), Nicholas V. Hud (Committee Member), Roger Wartell (Committee Member), Stephen Harvey (Committee Member).
Subjects/Keywords: P22 repressor; Direct readout; Indirect readout; Protein binding; DNA-protein interactions; Van der Waals forces
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APA ·
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APA (6th Edition):
Watkins, J. D. (2008). X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/26709
Chicago Manual of Style (16th Edition):
Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/26709.
MLA Handbook (7th Edition):
Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Web. 23 Jan 2021.
Vancouver:
Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Internet] [Doctoral dissertation]. Georgia Tech; 2008. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/26709.
Council of Science Editors:
Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Doctoral Dissertation]. Georgia Tech; 2008. Available from: http://hdl.handle.net/1853/26709
Georgia Tech
14.
Manning, Linda.
The crystal structures of xenobiotic reductase A and B from pseudomonas putida II-B and pseudomonas fluorescens I-C: structural insight into regiospecific reactions with nitrocompounds.
Degree: PhD, Chemistry and Biochemistry, 2005, Georgia Tech
URL: http://hdl.handle.net/1853/36528
► Nitrochemicals are currently widely used as solvents, drugs, biocides, fuels and explosives and are consequently widely distributed in the environment. The reductive nitrite elimination from…
(more)
▼ Nitrochemicals are currently widely used as solvents, drugs, biocides, fuels and explosives and are consequently widely distributed in the environment. The reductive nitrite elimination from explosive compounds is catalyzed by two FMN-dependent, xenobiotic reductases (XenA or XenB). These genes for these regiospecific enzymes were cloned from Pseudomonas putida and P. fluorescens I-C respectively and isolated from the soil of a contaminated World War II munitions manufacturing plant. These enzymes enable the microbes to fulfill their nitrogen requirements from nitroglycerin by catalyzing the regiospecific, NADPH dependent, reductive denitration of nitroglycerin with differing selectivities. The two enzymes also transform a number of additional nitrocompounds in vitro, e.g. TNT and metronidazole, a leading drug in the treatment of Helicobacter pylori, a causative agent of human ulcers. Single crystals were obtained for XenA and XenB and complete X-ray diffraction datasets have been collected and analyzed to better understand these characteristics. The 1.6 Å resolution structure of XenA reveals a dimer of β/α)₈-TIM barrels, but the 2.3 Å resolution structure for XenB is a monomer. The (β/α)₈-TIM barrel protein fold is the most common fold in the PDB. However, the XenA structure exhibits a unique, C-terminal domain-swapped topology. Thus a portion of each active site is comprised of residues from the neighboring monomer. To probe the reaction cycle, crystal structures of ligand complexes and the reduced enzyme have been refined. For example, our structure of the XenA-metronidazole complex shows that ligands bind parallel to the FMN si-face. Our 1.5 Å resolution structure for reduced XenA reveals an FMN isoalloxazine ring with an angle of ~165° along the N5-N10 axis. We have also generated models of the reduced enzyme-nitroglycerin complexes by molecular dynamics. The results with both XenA and XenB reveal differences in enzyme-ligand hydrogen bonding. These differences correlate remarkably well with the regiospecific differences observed for nitrite elimination from nitroglycerin and reduction of TNT by the two enzymes.
Advisors/Committee Members: Allen M. Orville (Committee Chair), Dr. Dale E. Edmondson (Committee Member), Dr. Frank E. Löffler (Committee Member), Dr. Loren D. Williams (Committee Member), Dr. Nicholas V. Hud (Committee Member).
Subjects/Keywords: Nitrocompounds; Flavoprotein; X-ray Crystallography; Xenobiotics; Reductones; Flavoproteins; X-ray crystallography; Nitrogen compounds; Crystals Structure
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APA ·
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MLA ·
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CSE |
Export
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APA (6th Edition):
Manning, L. (2005). The crystal structures of xenobiotic reductase A and B from pseudomonas putida II-B and pseudomonas fluorescens I-C: structural insight into regiospecific reactions with nitrocompounds. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/36528
Chicago Manual of Style (16th Edition):
Manning, Linda. “The crystal structures of xenobiotic reductase A and B from pseudomonas putida II-B and pseudomonas fluorescens I-C: structural insight into regiospecific reactions with nitrocompounds.” 2005. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/36528.
MLA Handbook (7th Edition):
Manning, Linda. “The crystal structures of xenobiotic reductase A and B from pseudomonas putida II-B and pseudomonas fluorescens I-C: structural insight into regiospecific reactions with nitrocompounds.” 2005. Web. 23 Jan 2021.
Vancouver:
Manning L. The crystal structures of xenobiotic reductase A and B from pseudomonas putida II-B and pseudomonas fluorescens I-C: structural insight into regiospecific reactions with nitrocompounds. [Internet] [Doctoral dissertation]. Georgia Tech; 2005. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/36528.
Council of Science Editors:
Manning L. The crystal structures of xenobiotic reductase A and B from pseudomonas putida II-B and pseudomonas fluorescens I-C: structural insight into regiospecific reactions with nitrocompounds. [Doctoral Dissertation]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/36528
. 
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