The 7-deazaguanosine nucleosides queuosine (Q) and archaeosine (G⁺) are two of the most structurally complex modified nucleosides found in tRNA. Q is found exclusively in the wobble position of tRNAGUN coding for the amino acids asparagine, aspartate, histidine and tyrosine in eukarya and bacteria, while (G⁺) occurs in nearly all archaeal tRNA at position 15. In archaea preQ₀ is inserted into tRNA by the enzyme tRNA-guanine transglycosylase (TGT), which catalyzes the exchange of guanine with preQ₀ to produce preQ₀-tRNA. The first objective of this study was to identify and characterize the enzyme(s) catalyzing the conversion of preQ₀-tRNA to G+-tRNA. Comparative genomics identified a protein family possibly involved in the final steps of archaeosine biosynthesis, which was annotated as TgtA2. Structure based alignments comparing TGT and TgtA2 revealed that TgtA2 lacked key TGT catalytic residues and contained an additional module. The gene corresponding to "tgtA2" from "Methanocaldococcus jannaschii (mj1022)" was cloned, expressed and the purified recombinant enzyme characterized. Recombinant MjTgtA2 was shown to convert preQ₀-tRNA to G⁺-tRNA using glutamine, asparagine or NH₄⁺ as nitrogen donors in an ATP-independent reaction. This is the only example of the conversion of a nitrile to a formamidine known in biology. QueF catalyzes the reduction of preQ₀ to 7-aminomethyl-7-deazaguanine preQ₀ in the queuosine biosynthetic pathway. The second aim of this study was the transient state kinetic analysis of substrate binding and catalysis by the enzyme QueF, as well as investigation of the effects of ligands on its quaternary structure. Gel filtration and sedimentation equilibrium analyses indicated that QueF exists as a hybrid population in a rapid equilibrium between decamer and pentamer states. Addition of preQ₀ to QueF resulted in shifting the equilibrium towards the decamer state, as did the addition of divalent metals. Potassium chloride at high concentrations was found to disrupt the quaternary structure of QueF. Intrinsic tryptophan and NADPH fluorescence was used to determine the substrate binding to QueF by stopped-flow kinetic studies. Studies on the binding of preQ₀ to QueF in conjuction with binding NADPH to the QueF mutant E78A-thioimide intermediate suggested a two-step mechanism consisting of a fast bimolecular process and a subsequent slower unimolecular process, while the binding of preQ₀ to the C55A mutant was monophasic, consisting of only the fast bimolecular process. Thioimide formation was monitored by UV-Vis; under single turnover conditions the data fit well to single exponential rise. However, at high preQ₀ concentrations two phases could be observed. The reduction of the thioimide was determined under single turnover conditions by both UV-Vis and fluorescence, and comparable rates were obtained from both techniques. These results indicate that the binding of preQ₀ and NADPH to QueF, as well as thioimide formation, are very rapid; and that reduction of the thioimide is most likely the rate limiting step. Analysis of component rates suggests structural changes occur between these steps, further limiting the overall rate.

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Reaction progress kinetic analysis (RPKA) is a powerful tool for determining kinetic parameters of catalytic reactions. Many of the published articles that have used RPKA have employed reaction calorimetry for obtaining sufficient data to be reliable. The use of gas uptake measurements, in place of calorimetry is explored in this Thesis. Chapter 2 details the use of gas uptake measurements in establishing the order with respect to substrate and gas for the rhodium catalysed hydrogenation of 1-octene. Previous studies have used initial rate measurements to establish these orders and the reaction cycle is well known. The use of RPKA allows the same information to be established in two reactions. Chapter 3 focuses on the rhodium catalysed hydroformylation of 1-octene as it involves the reaction of one substrate with two gases. Using RPKA it is possible to determine the order in substrate and the overall order in gas, but it was found difficult to determine the order with respect to the individual gases using RPKA alone. Chapter 4 shows the palladium catalysed methoxycarbonylation of vinyl acetate. The reaction has two substrate concentrations changing simultaneously as well as a gas. This chapter shows that by careful design of experiments the orders with respect to each of these substrates and CO can be determined in minimal numbers of experiments. Chapter 5 focuses on the methoxycarbonylation of alkynes, which uses RPKA in complex multistep reactions, to establish if RPKA can be used to determine the kinetics with respect to the individual reacting components for each step. This study focuses on the methoxycarbonylation of phenylacetylene to produce methyl cinnamate as well as the methoxycarbonylation of both terminal and internal linear alkynes. These linear alkynes carbonylate to produce an α,β-unsaturated ester. The double bond is isomerised from its conjugated position along the chain to the terminal position where it is trapped and carbonylated to produce an α,ω-dieter product.

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

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The gas phase reactions of atomic chlorine with hydrogen sulfide, ammonia, benzene, and ethylene are investigated using the laser flash photolysis / resonance fluorescence experimental technique. In addition, the kinetics of the reverse processes for the latter two elementary reactions are also studied experimentally. The absolute rate constants for these processes are measured over a wide range of conditions, and the results offer new accurate information about the reactivity and thermochemistry of these systems. The temperature dependences of these reactions are interpreted via the Arrhenius equation, which yields significantly negative activation energies for the reaction of the chlorine atom and hydrogen sulfide as well as for that between the phenyl radical and hydrogen chloride. Positive activation energies which are smaller than the overall endothermicity are measured for the reactions between atomic chlorine with ammonia and ethylene, which suggests that the reverse processes for these reactions also possess negative activation energies. The enthalpies of formation of the phenyl and β-chlorovinyl are assessed via the third-law method. The stability and reactivity of each reaction system is further rationalized based on potential energy surfaces, computed with high-level ab initio quantum mechanical methods and refined through the inclusion of effects which arise from the special theory of relativity. Large amounts of spin-contamination are found to result in inaccurate computed thermochemistry for the phenyl and ethyl radicals. A reformulation of the computational approach to incorporate spin-restricted reference wavefunctions yields computed thermochemistry in good accord with experiment. The computed potential energy surfaces rationalize the observed negative temperature dependences in terms of a chemical activation mechanism, and the possibility that an energized adduct may contribute to product formation is investigated via RRKM theory.

Aptamers are synthetic nucleic acid molecules designed to bind with high specificity and affinity to a selected target. The aptamer selection method, called the systematic evolution of ligands by exponential enrichment (SELEX), was first described in 1990 and has been adapted for the selection of aptamers for a number of applications. One such application is the selective targeting of cells for therapeutic delivery. This thesis explores this application with the selection and characterisation of internalising aptamers specific to the T lymphocyte specific receptor, CD7. The CD7 receptor is expressed on thymus derived progenitor lymphocytes and remains after T cell activation and expression of the CD4 receptor. As such, the CD7 receptor is a noteworthy target for lymphocyte cancers, HIV-1 and other T lymphocyte tropic viruses. A heterogeneous pool of internalising CD7-aptamers was enriched through six rounds of positive selection in a stably transduced CD7-HeLa cell line. Aptamers were selected using a modified whole cell SELEX method that selected specifically for internalising aptamers. Aptamer specificity for CD7-HeLa cells over HeLa cells was screened by flow cytometry. CD7 specific aptamers were screened for binding after blocking CD7-HeLa cells with an anti-CD7 antibody. Eight CD7 specific aptamer clones were selected from CD7-HeLa screening for evaluation in Jurkat cells (T lymphocyte cell line endogenously expressing the CD7 receptor). Three aptamer clones showed high level binding to Jurkat cells by flow cytometry (CSIR 3.14, CSIR 3.37 and CSIR 3.42). Kinetic analysis of aptamer internalisation was analysed using flow cytometry and determined to be within the femtomolar range. Aptamer CSIR 3.14 had a dissociation constant of 2.1 fM and an association rate of 4.7 ± 2.4 × 105 Molar-1minute-1, aptamer CSIR 3.37 had a dissociation constant of 0.23 fM and an association rate of 4.3 ± 3.3 × 106 Molar-1minute-1 and aptamer CSIR 3.42 had a dissociation constant of 1.1 fM with an association rate of 7.9 ± 5.1 × 105 Molar-1minute-1. Aptamer CSIR 3.14 internalisation was tracked by confocal microscopy and the kinetics calculated with an association rate of 6.3 × 104 Molar-1minute-1 and Kd of 13 fM. Deletions within the CSIR 3.14 sequence that altered the predicted structures significantly reduced the aptamer binding. Combined, the data presented in this thesis identifies aptamer CSIR 3.14 as a lymphocyte specific internalising aptamer with potential for therapeutic delivery.

Hon Wan Chee Nicole Wendy. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 85-87). / Abstracts in English and Chinese. / THESIS COMMITTEE --- p.ii / ABSTRACT (English version) --- p.iii / ABSTRACT (Chinese version) --- p.v / ACKNOWLEDGEMENTS --- p.vii / TABLE OF CONTENTS --- p.viii / LIST OF FIGURES --- p.x / LIST OF TABLES --- p.xiii / Chapter CHAPTER 1. --- General Introduction / Chapter Section 1.1 --- Introduction --- p.1 / Chapter Section 1.2 --- Electronic Structure Calculation --- p.2 / Chapter Section 1.3 --- Molecular Dynamics --- p.10 / Chapter CHAPTER 2. --- Ab Initio Molecular Dynamics Study on Thermal Dissociation of Azomethane / Chapter Section 2.1 --- Introduction / Chapter Section 2.2 --- Computational Method --- p.17 / Chapter Section 2.3 --- Results and Discussion --- p.21 / Chapter Section 2.4 --- Conclusion --- p.47 / Chapter CHAPTER 3. --- "Ab Initio Molecular Dynamics Study on Fluxionality of IF7, TeF7- and iof6-" / Chapter Section 3.1 --- Introduction --- p.49 / Chapter Section 3.2 --- Computational Method --- p.52 / Chapter Section 3.3 --- Analysis --- p.55 / Chapter Section 3.4 --- Results and Discussion --- p.56 / Chapter Section 3.5 --- Conclusion --- p.83 / REFERENCES --- p.85