The thesis entitled “New DNA-Targeting Small Molecules as Potential Anticancer Agents and for in vivo Specificity toward Enhanced Silk Production” encompasses design, computational calculations, and syntheses of diverse small molecular scaffolds to explicitly target duplex and higher order DNA morphologies (G-quadruplex DNA). Some of these molecules have a potential as anticancer agents. Besides, an attempt has been made elucidate the importance of novel oligopyrrole carboxamides in the enhancement of silk yield, hence proving to a boon in the field of sericulture. The work has been divided into six chapters. Chapter 1. DNA Binding Small Molecules as Anticancer Agents Figure 1. DNA targeting by small molecules. Cancer has always been a dreadful disease and continues to attract extensive research investigations. Various targets have been identified to restrain cancer. Among these DNA happens to be the most explored one. A wide variety of small molecules, often referred to as “ligands”, has been synthesized to target numerous structural features of DNA (Figure 1). The sole purpose of such molecular design has been to interfere with the transcriptional machinery in order to drive the cancer cell toward apoptosis. The mode of action of the DNA targeting ligands focuses either on the sequence-specificity by groove binding and strand cleavage, or by identifying the morphologically distinct higher order structures like that of the G-quadruplex DNA. Chapter 2. Ligand 5, 10, 15, 20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-type Human G-Quadruplex DNA over its other Polymorphs The binding of ligand 5, 10, 15, 20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA (Figure 2). Figure 2. Ligand TMPyP4 prefers parallel propeller-type G-quadruplex DNA morphology. Chapter 3. A Theoretical Analysis on the Selective Stabilization of Intermolecular G-quadruplex RNA with a bis-Benzimidazole Ligand EtBzEt over TMPyP4 in K+ Environment Ever since the discovery of G-quadruplex RNA, a constant urge exists to target these higher order RNA conformations. These structures play a significant role in the transcriptional and translational mechanism. Herein we have determined the mode and extent of association of certain G-quadruplex DNA binding bisbenzimidazole ligand (EtBzEt) in comparison to a known porphyrin ligand (TMPyP4). We have performed docking studies of the known G-quadruplex DNA binding ligands with the parallel propeller G-quadruplex RNA (PPR) to determine the most potent binding conformation which showed EtBzEt to be a better RNA binder than others. Furthermore, a molecular dynamics (MD) simulation (6 ns) was performed for the most stable docked complex in explicit solvent environment. The role of K+ ions, Hoogsteen hydrogen bond formation and backbone dihedral angle between the tetrads were carefully analyzed during the entire simulation run to determine the stability of each ligand associated PPR complex. All the analyses conclusively showed that while TMPyP4 merely stabilized the PPR, the ligand EtBzEt stabilized PPR very efficiently (Figure 3). Figure 3. Stabilzation and destabilization by EtBzEt and TMPyP4, repectively. Red and green ovals represent EtBzEt and TMPyP4, repectively. Chapter 4A. Design and Synthesis of New DNA Binding Fe(III) and Co(II) Salen Complexes with Pendant Oligopyrrole Carboxamides Extensive research on these oligopyrrole carboxamides has shown their specificity toward AT-rich sequences with high binding affinity. Here we have designed and synthesized Fe (III)-and Co (II)-based salen complexes attached with minor groove targeting oligopyrrole carboxamide side-chains (Figure 4). While the ligands showed excellent activity toward DNA damage, they also exhibited high affinity toward the minor grooves of the ds-DNA. This was also reflected in the high efficiency of the ligands toward cancer cell cytotoxicity. Further studies revealed that the ligands resulted in prominent nuclear condensation and fragmentation thereby driving the cells toward apoptosis. The presence of metal coordinated salen moiety conjugated with positively charged pendants ending with minor groove binding oligopyrrole carboxamides might have resulted in the increased activity of the ligands toward DNA targeting and cancer cell death. Figure 4. Chemical structures of the ligands used in this study. Chapter 4B. Design and synthesis of novel oligopyrrole based salen metal complexes and their efficiency toward stabilization of G-quadruplex DNA DNA targeting has been the key strategy toward the restriction of cancer cell proliferation. In a similar effort, we have designed and synthesized novel salen based Ni(II) and Pd(II) metal complexes with positively charged flanking side-chains comprising attached N-methylpyrrole carboxamides of varying lengths (Figure 5). The ligands showed efficient stabilization of the G-quadruplex DNA morphologies, with specificity over the duplex DNA. Sufficient inhibition of the telomerase activity was observed by the TRAP-LIG assay which was ascertained by the prominent restriction of cancer cell proliferation in the long-term cell viability assay. The ligands exhibited condensation and fragmentation of the nucleus when observed under confocal microscopy which is indicative of the cells undergoing apoptosis. Further annexin V-FITC and PI dual staining showed apoptosis to be the mechanistic pathway underlying the cancer cell cytotoxicity by the ligands. Modeling studies clearly showed the stacking of the salen moiety over the G-tetrads with the association of the pendant oligopyrrole carboxamide units to the grooves. Figure 5. Chemical structures of the ligands used in this study. Chapter 5A. Role of Metal Ions in Novel Fluorescein based Salen and Salphen Complexes toward Efficient DNA Damage and their Effect on Cancer Cells Metal ions play an important role toward DNA damage and numerous ligands have been synthesized for their use in anticancer therapy. Herein, we have designed and synthesized Fe(III) and Co(II) based salen/salphens by bridging two fluorescein moieties with varying spacers (Figure 6). Although the ligands exhibit dual binding mode, the more flexible salen ligands prefer to associate to the minor groove of the DNA while the relatively rigid salphen ligands show greater intercalation. The biophysical experiments reveal better binding affinity of the salphens toward duplex DNA as compared to the salen ligands. The metal coordination resulted in efficient DNA cleavage of plasmid at low ligand concentrations. The ligands also showed cancer cell cytotoxicity, cellular internalization with apoptosis as the proposed mechanism for cell death. Figure 6. Chemical structures of the salen and salphen ligands used in this study. Chapter 5B. Fluorescein based Salen and salphen Complexes as stabilizers of the Human G-quadruplex DNA and Promising Telomerase Inhibitors Metal based salen complexes have been considered as an important scaffold toward targeting of DNA structures. In the present work we have designed and synthesized nickel(II)-and palladium(II)-salen and salphen ligands by using fluorescein as the backbone to provide an extended aromatic surface (Figure 7). The ligands exhibit sufficient affinity toward the human telomeric G-quadruplex (G4) DNA in preference to the duplex DNA and also exhibit promising inhibition of telomerase activity. This is ascertained by their potency in the long-term cell viability assay which shows significant cancer cell cytotoxicity in presence of the ligands. Confocal microscopy showed cellular internalization followed by nuclear localization. Considerable population at the sub-G1 phase of the cell cycle showed cell death via apoptotic pathway. Figure 7. Chemical structures of the ligands used in this study. Chapter 6. Knockdown of Broad-Complex Gene Expression of Bombyx mori by Oligopyrrole carboxamides Enhances Silk Production Bombyx mori (B. mori) is important due to its major role in the silk production. Though DNA binding ligands often influence gene expression, no attempt has been made to exploit their use in sericulture. The telomeric heterochromatin of B. mori is enriched with 5′-TTAGG-3′ sequences. These sequences were also found to be present in several genes in the euchromatic regions. We examined three synthetic oligopyrrole carboxamides that target 5′-TTAGG-3′ sequences in controlling the gene expression in B. mori (Figure 8). The ligands did not show any defect or feeding difference in the larval stage, crucial for silk production. The compounds caused silencing of various isoforms of the broad-complex transcription factor and cuticle proteins which resulted in late pupal developmental defects. This study shows for the first time use of oligopyrrole carboxamide drugs in controlling gene expression in B. mori and their long term use in enhancing silk production. Figure 8. Chemical structures of the ligands used in this study (top) and increased cocoon size on ligand treatment.

This thesis considers atom`s attributes, which affects shape of molecules. It describes rules that are basic for molecule creation. This text features basic attributes and rules, which affects the final shape of molecule. Next part of this text explains several ways to display molecule. Following parts of this thesis describes several ways how to store and represent atom and molecules in computer technology along with solution of these problems that are used for this thesis.

No description available.

Thesis (MSc)--Stellenbosch University, 2012. / Please refer to full text for abstract.

Homocysteine (Hcy) has been identified as a primary risk factor for atherosclerosis as it induces endothelial cell (EC) activation/dysfunction and thus potentially initiating atherosclerotic plaque formation. There is accumulating evidence indicating a key role for oxidative stress in mediating Hcy atherogenic effects. The aim of this study was to evaluate the effects of chronic treatment with Hcy on EC activation and to explore the role of oxidative stress in these effects. Human umbilical vein endothelial cells (HUVEC) were cultured and treated chronically with DL-Hcy for 5-9 days. An in vitro flow system was also used to characterize the different types of interactions between DL-Hcy-treated HUVEC and neutrophils under physiological flow conditions. EC activation was studied by characterizing the activation of the JNK pathway and the up-regulation of different cell adhesion molecules (CAM) and cytokines, using different techniques including western blot, immunohistochemical staining, enzyme-linked immunosorbent assay and polymerase chain reaction. The role of oxidative stress was investigated by measuring the production of ROS and evaluating the efficiency of antioxidants. Furthermore, the role of nitric oxide and nitric oxide synthase in modulating Hcy effects was investigated. Chronic treatment with DL-Hcy did not kill the EC however, it inhibited cell proliferation. Furthermore, this treatment induced EC activation/dysfunction which was characterized by sustained activation of the JNK pathway, which in turn mediated up-regulation of E-selectin, ICAM-1 and to lesser extent P-selectin. Furthermore, DL-Hcy induced production of IL-8 protein. These CAM and chemokines collectively mediated different interactions between DL-Hcy-treated HUVEC and neutrophils under flow conditions including tethering, rolling, adherence and transmigration. DL-Hcy was also shown to induce significant ROS generation which mediated activation of the JNK pathway. Antioxidants restored DL-Hcy-induced interactions under flow to the basal level. DL-Hcy was shown to induce eNOS uncoupling which mediated, at least in part, the DL-Hcy-induced ROS production. Furthermore, short term treatment with NO inhibited DL-Hcy-induced HUVEC:neutrophil interactions in a cGMP-independent manner. In summary, this research showed that DL-Hcy has several proatherogenic effects, mediated at least in part by the JNK pathway, and induces EC activation/dysfunction priming for atherosclerosis initiation. The data supports that oxidative stress mediates the majority of Hcy atherosclerotic effects. Antioxidants tested, JNK inhibitors and NO showed promising results in reversing all DL-Hcy effects and restoring EC normal status.

No description available.

In recent years there has been much progress in the field of cold and ultracold molecular physics and a variety of experimental techniques for producing cold matter now exist. In particular, the generation of trapped molecular ions at mK temperatures has been achieved by sympathetic-cooling with laser-cooled atomic ions. By implementing schemes to selectively prepare and control the internal quantum state of molecular ions, and developing detection techniques, it will be increasingly possible to study cold state-selected chemical collisions in an ion-trap. Most molecular species produced in a selected rovibrational state have a lifetime of a few seconds, before the population is redistributed across numerous rovibrational states by interaction with the ambient blackbody radiation (BBR). Consequently, the investigation of state-selected reaction dynamics at low temperatures in experiments where long time scales (minutes to hours) are required, is hindered. This thesis looks into developing strategies that maintain state selection in molecular ions, allowing one to observe state-selected reactions in cold environments, in particular the state-selected reaction between C₂H⁺₂ and ND₃. Examining reactive ion molecule collisions under cold conditions provides insight into fundamental reaction dynamics, which are thermally averaged out at higher temperatures. A theoretical model is used to investigate laser-driven, blackbody-mediated, rotational cooling schemes for several ¹Σ and ²Π diatomic species. The rotational cooling is particularly effective for DCl⁺ and HCl⁺, for which 92% and >99% (respectively) of the population can be driven into the rovibrational ground state. For the other systems a broadband optical pumping source is found to enhance the population that can be accumulated in the rovibrational ground state by up to 29% more than that achieved when exciting a single transition. The influence of the rotational constant, dipole moments and electronic state of the diatomics on the achievable rotational cooling is also studied. This approach is extended to consider the BBR interaction and rotational cooling of a linear polyatomic ion, C₂H⁺₂, which has a ²Π electronic ground state. The (1-0) band of the ν₅ cis-bending mode is infrared active and strongly overlaps the 300 K blackbody spectrum. Hence the lifetimes of state-selected rotational levels are found to be short compared to the typical timescale of ion trapping experiments. Laser cooling schemes are proposed that could be experimentally viable, which involves simultaneous pumping of a set of closely spaced Q-branch transitions on the ²Δ_5/2-²Π_3/2 band together with two ²Σ⁺– ²Π_1/2 lines. It is shown that this should lead to >70% of total population in the lowest rotational level at 300 K and over 99% at 77 K. In order to identify states of the acetylene ion that could be trapped sufficiently long enough for state-selected reactions in the ion trap with decelerated ND3, the theoretical work has been complemented by experimental investigations into the production of C₂H⁺₂ in selected states, and ion trapping of the same using sinusoidal and digital trapping voltages. Appropriate (2+1) REMPI (Resonance Enhanced Multiphoton Ionization) schemes are used to produce C₂H⁺₂ in different quantum states, with (1+1) Resonance Enhanced Multiphoton Dissociation (REMPD) employed to detect the ion thus produced. The concept of digital ion trapping for ejection onto MCPs is introduced. A comprehensive comparison between sinusoidal and digital trapping fields has been performed with respect to trap depth and stability regions. Programs have been developed to calculate the stability regions for different ions under varying experimental conditions. The trap depth has been derived for both digital and sinusoidal trapping fields. It is observed that as τ increases, the trap depth of a digital trap increases. For τ = 0.293, the trap depth and stability diagram for both sinusoidal and digital trapping fields would be equivalent. The trap depth at which the sinusoidal trap operates experimentally in our research group is ~1.36 eV. In contrast, the experimental parameters at which the digital trap operates generates a trap depth of 1.21 eV. Ca⁺ Coulomb crystals have been formed, stably trapped and stored for extended periods of time in both sinusoidally and digitally time-varying trapping fields. The sympathetic cooling of a diverse range of ions into Ca⁺ Coulomb crystals is demonstrated, again using both sinusoidal and digital trapping fields. Mass spectrometric detection of ionic reaction products using a novel ejection scheme has been developed, where ejection is achieved by switching off the trapping voltage and converting the quadrupole trap into an extractor-repeller pair by providing the ion trap electrodes with appropriate ejection pulses. This technique is developed using a digital trapping voltage rather than the sinusoidal trapping voltage, as ejection with sinusoidal trapping voltages is not clean (resonance circuitry used in the electronics induces ringing after switching off the trapping voltage). Coulomb crystals, both pure Ca⁺ and multi-component crystals, are ejected from the ion trap and the TOF trace obtained is recorded on an oscilloscope. When the integrated, base-line subtracted TOF peak is plotted against the number of ions in a Ca+ crystal and sympathetically-cooled Ca⁺ – CaF⁺ crystal, a linear relationship is obtained. This technique is found to be well mass-resolved, with the signal arising from CaOH⁺ (57 amu) and CaOD⁺ (58 amu) resolvable on the TOF trace. This technique would enable one to monitor a reaction in a Coulomb crystal where the reactant and product species are both either lighter or heavier than calcium, such as the reaction between C₂H⁺₂ and ND₃, something which has not been previously possible. It is, also, potentially a very important technique for reactions with many product channels.

Un échange vigoureux au travers des frontières de la biologie et de la physique se développe autour de nouvelles méthodes et outils, et autour de nouveaux phénomènes. Les objets d’étude au cœur de ce recouvrement multidisciplinaire sont très divers. De manière non exhaustive, il s’agit de nanoparticules, de cellules ou encore d’objets encore plus petits et élémentaires tels que les molécules. Aussi bien pour des applications dans le domaine de la microélectronique que pour l’étude de mécanismes biologiques fondamentaux, l’intégration des objets d’intérêt à l’échelle de l’objet unique est essentielle. Dans le cadre de cette thèse, l’objectif que nous nous sommes fixés est de développer un volet technologique qui permette l’assemblage d’objets micro- ou nanométriques uniques à des endroits bien définis d’une surface solide de façon simple, fiable, bas-coût et parallèle. Pour ce développement, nous nous sommes intéressés tout particulièrement aux nanoparticules d’Au de 100 nm de diamètre, aux bactéries, puis aux molécules d’ADN. Nous décrirons les stratégies développées reposant sur la lithographie douce puis leurs potentialités pour différentes applications dans les domaines de l’analyse médicale et de la détection. / A vigorous trade across the borders of biological and physical sciences is developing around new methods and tools, and around new phenomena. The objects at the heart of this multidisciplinary overlapping are numerous. In a non exhaustive manner, the objects of study can be nanoparticles, cells, or even smaller and more elementary objects such as molecules. For applications in the field of microelectronics as for studies of fundamental biological mechanisms, the integration of these objects of interest at the single object scale is essential. In the frame of this Ph.D. thesis, the objective we pursued is the development of a technological tool-box allowing the assembly of micro- and nano-objects at pre-determined locations of a solid surface, in a simple, reliable, low-cost and parallel manner. For this development, we focused on gold nanoparticles 100 nm in diameter, bacterial cells and DNA molecules in particular. We will describe the strategies developed relying on soft-lithography and their potentialities for different applications in the fields of medical analysis and sensing.

Background: Unfavorable outcomes following periodontal surgeries can be attributed to impaired resolution mechanisms likely due to decreased levels of specialized pro-resolution molecules (SPM). The current study investigates if SPM substrate pools in platelet-rich plasma preparations (PRP) can be increased by essential fatty acid (EFA) and / or aspirin supplementation. Methods: Nineteen healthy volunteers were randomly assigned to take i) aspirin; ii) EFA; iii) aspirin and EFA. Four hours after intake, the lipid precursor pools in PRP were quantified using combined Liquid Chromatography tandem mass spectrometry (LC-MS/MS) and the data statistically analyzed using ANCOVA. Results: Of the 77 metabolites screened, only FFA (18:3) showed a significant interaction effect (p=0.019). By itself, neither EFA (p>0.9) nor aspirin (p>0.4) showed any difference (P>0.4). Multiple comparisons could not identify the differences between groups. Conclusions: There is inadequate data to support oral supplementation of EFA and /or aspirin to increase SPM levels in PRP.

In this work, a new condensed matter approach to the study of excitons based on crystalline thin films of the organic molecule phthalocyanine is introduced. The premise is inspired by a wealth of studies in inorganic semiconductor ternary alloys (such as AlGaN, InGaN, SiGe) where tuning compositional disorder can result in exciton localization by alloy potential fluctuations. Comprehensive absorption, luminescence, linear dichroism and electron radiative lifetime studies were performed on both pure and alloy samples of metal-free octabutoxy-phthalocyanine and transition metal octabutoxy-phthalocyanines, where the metal is Mn, Co, Ni, and Cu. Varying the ratios of the metal to metal-free phthalocyanines in all of these studies, as well as looking across a temperature range from 4 Kelvin up to room temperature is essential for quantifying the exciton wavefunction delocalization in crystalline thin films. A comparative study is performed across organic aromatic ringed molecules of different sizes in the same family: phthalocyanine, naphthalocyanine and tetra-phenyl porphyrin. In an analogy to nanocrystals and their size effects, variations in pi-conjugated ring sizes imply an altering in the number of delocalized electrons, impacting the wavefunction overlap between pi-pi orbitals along the perpendicular axis of neighboring molecules. Finally, complementary measurements that assess crystallinity of the in-house deposited thin films, including individual grain absorption, small angle x-ray scattering images, polarized microscope images and a new unique linear dichroism microscopy dual imaging/luminescence technique are also discussed.