Tübingen, Univ., Diss., 2008.

Univ., Diss.--Göttingen, 1992.

Maintenance of the levels of nucleoside triphosphates (NTPs) as well as their corresponding deoxy derivatives (dNTPs) is crucial to all growth and developmental processes. The enzyme nucleoside diphosphate kinase (NDK) utilises an autophosporylated enzyme intermediate to catalyse the transfer of 5’ terminal phosphate from NTPs (mostly ATP) to nucleoside diphosphates (NDPs) via a reversible mechanism as given below. N1TP + NDK ↔N1DP+ −NDK-His* (1) N2DP + NDK-His* P ↔N2TP + NDK−His. (2) In the γ-phosphoryl group transfer, the highly conserved His 117 active site residue becomes autocatalytically phosphorylated, in the enzyme intermediate (NDK-H*). This phosphoryl group is transferred to ribo-or deoxyribonucleotides (N2DP) in a substrate non-specific manner. In addition to its fundamental role in nucleotide metabolism, NDP kinase is also involved in a number of cellular regulatory functions such as growth and developmental control, tumor metastasis suppression, signal transduction and so on. From mycobacterial genera, NDK of Mycobacterium tuberculosis (MtNDK) has been crystallised, structure was solved and biochemical functions were elucidated. However, there has not been any such study on the NDK of Mycobacterium smegmatis, except on the possible interaction with other proteins which modulates the NTP synthesising activity of MsNDK, towards specific NTPs. M. smegmatis, being a saprophytic, fast growing and non-pathogenic mycobacterium that is widely used as an experimental model mycobacterial system to study various biological processes in mycobacteria, it was thought appropriate to study NDK from this organism. The outcome of current study is presented in five chapters. The First Chapter gives a detailed introduction on the structural and functional aspects of NDK from diverse organisms, from bacteria to humans. Chapter 2. Molecular Cloning, Expression and Characterisation of Biochemical Activities of Nucleoside Diphosphate Kinase from Mycobacterium smegmatis mc 155 The research work starts with the molecular cloning, overexpression, purification, and characterisation of biochemical activities of recombinant MsNDK protein. In brief, ndk gene from M. smegmatis (Msndk) has been cloned, efficiently overexpressed as a soluble 6xHis-tagged recombinant protein, purified through affinity chromatography, and its biochemical characterisation for ATPase, GTPase and NTP synthesising activities have been demonstrated. Catalytic mutant of MsNDK, MsNDK-H117Q, was generated using site-directed mutagenesis approach and H117 was shown to be essential for the catalytic activity. Further experiments revealed that it is the same H117 that is required for mediating autophosphorylation as well, which is an intermediate in the transphosphorylation reaction of NDK. Chapter 3. Characterisation of Oligomerisation Property of M. smegmatis Nucleoside Diphosphate Kinase: the Possible Role of Hydrogen Bond and Hydrophobic Interactions The present study revealed that presence of homodimer of MsNDK could be observed in the presence of heat and SDS. Chemical cross-linking experiments revealed that MsNDK forms dimer, tetramer and hexamer. Homology modeling of MsNDK on the MtNDK crystal structure supported the existence of hexamer as three homodimers. Gln 17, Ser 24 and Glu 27 were found to be positioned at the dimer interface. Mutations on these residues did not abolish the stability of the respective mutant dimers in the presence of SDS and heat. Modeled structure of MsNDK revealed the existence of hydrophobic interactions at the dimer interface. In silico approach helped in mapping the existence of hydrophobic interactions at the dimer interface as two consecutive β-strands. Exposure of hydrophobic residues, using organic solvent methanol, abolished the dimer completely, indicating the vital role of hydrophobic interactions in the dimer stability. In solution, the native MsNDK was found to be a hexamer. Chapter 4. Mycobacterial Nucleoside Diphosphate Kinase Functions as GTPase Activating Protein for Mycobacterial Cytokinetic Protein FtsZ In Vitro Mammalian, plant, and bacterial NDKs can function as GTPase activating protein (GAP) for small G proteins namely, p21 Ras, Rad, and Rho-GTPases in animals and Pra1, Pra2, and GPA1 in Arabidopsis thaliana in vitro. We examined whether NDK of M. tuberculosis (MtNDK) can function as GAP in vitro for the cytokinetic protein FtsZ of Mycobacterium tuberculosis (MtFtsZ), which is a protein with a classical G-protein fold, possessing GTP-binding and GTPase activities (like G proteins). Both MtNDK and MsNDK could function as GAP for MtFtsZ and FtsZ of M. smegmatis (MsFtsZ) respectively in vitro. Similarly, MtNDK could function as GAP for MsFtsZ and reciprocally MsNDK could function as GAP from MtFtsZ. Interaction of NDK with respective FtsZ could be observed. Physiological implications of GAP activity of NDK on FtsZ are discussed. Chapter 5. Transcriptional Analyses of Nucleoside Diphosphate Kinase Gene of Mycobacterium smegmatis mc 155 Although there are studies on the structural and functional aspects of NDK, there are not many studies available on the transcriptional analysis of nucleoside diphosphate kinase (NDK) gene expression in general and nothing in particular in mycobacterial systems. Therefore we studied the transcriptional analysis of expression of Msndk gene, in order to map the Transcriptional Start Site (TSS), identification of promoter elements, and elucidated of transcriptional activity of the promoters. Expression of Msndk gene was analysed in exponential growth phase and under two different stress conditions wherein DNA replication gets arrested. Hydroxy Urea (HU), which reduce dNTP pools by inhibiting ribonucleotide reductase and Phenethyl Alcohol (PEA), which affects membrane structure resulting in DNA replication arrest, were used. Two transcripts and their promoter elements were mapped and their promoter activities were demonstrated. The profile of transcripts was found to be identical under the three different conditions examined.

<p> N-[(9-β-D-ribofuranosyl-9H-purin-6-yl)carbamoyl]- threonine, a hypermodified nucleoside found in transfer RNA represents the archetype structure of a group of synthetic ureidopurines which promote cell division in plants. L-threonine was shown to be incorporated into this nucleoside in Tobacco tissue and Rhizopogon roseolus transfer RNA. Also, this nucleoside was isolated as a free molecule in Rhizopogon roseolus growth medium.</p> <p> Chromatographic analysis of an enzymic hydrolysate of 3 g of yeast transfer RNA failed to indicate the presence of a lipophilic derivative of PCT riboside. It is concluded that PCT riboside occurs in transfer RNA with a free carboxyl group.</p> / Thesis / Master of Science (MSc)

<p> Attempts to prepare silicone oligonucleotide copolymers are complicated by the large difference in hydrophobicity in the two materials. Two approaches were followed to overcome this challenge. Initially, highly sterically hindered tetraisopropyldisiloxanes were used to bind 5'-0-(4,4'-dimethoxytrityl)-thyrnidine at the 5'-0H. These compounds proved to be hydrolytically more stable than the analogous dimethylsiloxane compounds, which were also prepared. Alternatively, Si-C bonds, which are hydrolytically stable, can be used to bind the two species together. Introduction of allyl ether by traditional Williamson conditions was followed by hydrosilylation with hydride terminated (Si-H) silicone, catalyzed by using platinum complexes, to give the nucleoside-functionalized silicone. We also introduced an epoxy group to one end of a silicone chain and found it to be stable to hydrolysis. Once the epoxy group binds nucleoside-functionalized silicone to solid phase, it is expected that the nucleoside-functionalized silicone via a trimethylene spacer linkage might be a starter for preparation of oligonucleotide-functionalized silicones in future work. </p> / Thesis / Master of Science (MSc)

The immune-reactive sperm are kept separate from the body by epithelial barriers such as the blood-testis barrier (BTB). While these barriers are beneficial for the protection of sperm from toxicants, they can make treating these areas difficult due to preventing the entry of pharmacological agents. This is especially an issue in the treatment of HIV and Ebola infection based on the ample evidence that these viruses are able to survive and spread from within the male genital tract (MGT), but only a few antiviral drugs are known to access the MGT. Transporters that line the epithelial barriers of the MGT, especially the BTB, are important for determining whether or not a drug is able to penetrate into the MGT through transepithelial transport. Several nucleoside analogs (NSA), which are used to treat HIV infection and leukemias, are known to be able to accumulate in seminal plasma, which makes them a useful tool for understanding transepithelial transport for the BTB. The purpose of these studies is to characterize the transport profile for the MGT, in particular the BTB, to gain a better understanding of how xenobiotics, especially ones based on nucleosides, can access the MGT. The chief finding of this work is the discovery of a transepithelial transport pathway expressed by Sertoli cells that allows for the entry of nucleosides (necessary for germ cell development) and NSA into the MGT. This pathway depends on equilibrative nucleoside transporter (ENT) 1 uptake and ENT2 efflux and occurs in both rats and humans. These studies provide the foundation for being able to predict the penetration of novel drugs into the MGT.

Nucleic acids are important bio-macromolecules in living systems. They are involved in important functions like gene expression and regulation. Nucleoside triphosphates serve as precursors for biochemical synthesis of modified nucleic acids and nucleotide coenzymes. The modification of nucleic acids, particularly at nucleobases, can expand the function and chemical properties of nucleic acid. Herein, we report the chemical synthesis of a novel thiol-modified nucleoside S-(3-(acetylthio)propyl)-5-(mercaptomethyl)-uridine and the corresponding nucleotide via a “new synthetic methodology” developed in our laboratory. The synthesized triphosphate was used for RNA transcription. The activity and nuclease resistance of the transcribed RNA is studied. The results showed that the properties of the nucleotide with thiol functionality are as good as the native. The modified RNA can be used for RNA/protein complex structure studies and gold nanoparticles stabilizer. They can also serve as a probe in DNA/RNA microchip surface functionalization for detection of various diseases and pathogens.

Thesis (Ph. D.)--University of Virginia, 2008. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.

A significant focus of toxicological research is the identification of electrophiles that covalently modify DNA to form addition products (adducts). These products can be generated when aryl radical species react at the C8-site of 2'-deoxyguanosine (dG) to form C8-aryl-dG adducts, which are mutagenic lesions. While this form of DNA modification is detrimental, C8-aryl-dG adducts also possess intriguing properties that can be exploited for beneficial purposes. This thesis is an investigation of one mechanism believed to contribute to the mutagenicity of C8-aryl-dG adducts, as well as a study of the photophysical properties of adducts that allow for their application as fluorescent probes. A common property of C8-aryl-dG adduction is accompaniment of abasic site formation. To determine how the C8-aryl moiety contributes to sugar loss, UV-Vis spectroscopy has been employed to determine hydrolysis kinetics, with C8-aryl-dG adducts found to be more prone than dG to acid-catalyzed hydrolysis. Despite adduct reactivity in acidic media, all adducts are relatively stable at pH 7, suggesting they are unlikely intermediates of abasic site formation at physiological pH. These results have allowed for development of a new rationale for depurination observed upon C8-aryl-dG adduction within duplex DNA. The determination of photophysical parameters of C8-heteroaryl-dG adducts reveals that these nucleosides behave as fluorophores with high fluorescence quantum yields (φfl). These adducts also exhibit emission sensitivity to their solvent environment and H-bonding interactions. C8-Heteroaryl-dG adducts were incorporated in the oligonucleotide 5'-CTCG1G2CG3CCATC, at the G1 and G3 sites, that contains the recognition sequence of the NarI Type II restriction enzyme. Hybridization of the modified NarI oligonucleotides to the complementary strand containing either the C or G nucleobase opposite the adduct allowed for characterization of duplex structures by circular dichroism (CD), UV melting temperature analysis and fluorescence spectroscopy. Results suggest that the C8-heteroaryl-dG adduct favours an anti conformation with base-paired with C, while a syn conformation is favoured when base-paired to G. Adduct conformation of bulky C8-dG adducts is believed to be correlated with their known mutagenic activity. C8-Heteroaryl-dG modified nucleosides could therefore be used as fluorescent models of these adducts to aid in elucidation of adduct-induced mutagenesis in biological systems. / NSERC

<p>Nucleoside transport into the cell plays a key role in providing building blocks for DNA and RNA synthesis, terminating adenosine signaling, and delivering nucleoside-analog drugs to their targets. Concentrative nucleoside transporters (CNTs) constitute one of the classes of membrane transporters responsible for the cellular uptake of nucleosides and nucleoside-derived drugs. We solved the first structure of a member of the CNT family, vcCNT, by X-ray crystallography, revealing the overall architecture of the transporter, delineating the locations of the nucleoside- and sodium-binding sites, and providing insight into the mechanism of transport. Next we examined the molecular origins of nucleoside and nucleoside-drug selectivity by solving structures of the transporter bound to different nucleosides and drugs and measuring their binding affinities for vcCNT to determine energetically important interactions. We then used this information to design a compound that is better transported by and subtype-selective for human CNTs. Finally, we probed the role of sodium in the ion-coupled transport of nucleosides using binding and transport studies and developed a hypothesis for the structural basis of sodium coupling. Taken together, these studies helped to elucidate the molecular mechanism by which CNTs selectively recognize nucleosides and pump them into the cell and provided insight into drug uptake by these transporters, laying a framework for the improvement of targeted nucleoside-drug delivery by CNTs.</p> / Dissertation