Chemical synthesis of oligonucleotides containing (M+4) guanine

HPLC MS/MS has shown great potential in the measurement of DNA oxidative damage. Its accuracy depends on the use of multiply isotopically labelled internal standards. In this report, multiply isotopically labelled (M + 4) guanine internal standards were prepared in the form of base, nucleoside, as well as DNA oligomer. To our knowledge, this is the first chemical synthesis of oligomers containing (M + 4) guanine, and we believe that they can be used to develop a procedure that can make further improvement to the existing analytical procedures. Copyright © Taylor & Francis, Inc.

A combinatorial approach to the chemical synthesis and biological evaluation of 3,4,5-trisubstiituted furan-2(5H)-ones

Many important natural products contain the furan-2(5H)-one structure. The structure of this molecule lends itself to manipulation using combinatorial techniques due to the presence of more than one site for the attachment of different suhstituents. By developing different reaction schemes at the three sites available for attachment on the furan-2(5H)-one scaffold, combinatorial chemistry techniques can be employed to assemble libraries of novel furan 2(5H)-ones. These libraries can then be entered into various biological screening programmes. This approach will enable a vast diversity or compounds to be examined, in the hope or finding new biologically active Iead structures. The work in this thesis has investigated the potential that combinatorial chemistry has in the quest for new biologically active lead structures based on the furan-2(5H)-one structure. Different reactions were investigated with respect to their suitability for inclusion in a library. Once sets of reactions at the various sites had been established, the viability of these reactions in the assembly of combinatorial libraries was investigated. Purification methods were developed, and the purified products entered into suitable biological screening tests. Results from some of these tests were optimised using structure activity relationships, and the resulting products re-screened. The screening tests performed were for anticancer and antimicrobial activity, cholecystokinin (CCK-B) antagonism and anti-inflammatory activity (in the quest for novel cyclo-oxygenase (COX-2) selective non-steroidal anti-inflammatory drugs). It has been shown that many reactions undergone by the furan-2(5H)-one structure are suitable for the assembly of a combinatorial library. Investigation into the assembly of different libraries has been carried out with initial screening results included. From this work, further investigation into combinatorial library assembly and structure activity relationships of screened reaction products can be undertaken.

Chemical synthesis of DNA and RNA containing thio-substituted bases and their post-synthetic modifications

Modified oligonucleotides containing sulphur group have been useful tools for studies of carcinogenesis, protein or nucleic acid structures and functions, protein-nucleic acid interactions, and for antisense modulation of gene expression. One successful example has been the synthesis and study of oligodeoxynucleotides containing 6-thio-2'-deoxyguanine. 6-Thio-2-deoxyguanosine was first discovered as metabolic compound of 6- mercaptopurine (6-MP). Later, it was applied as drug to cure leukaemia. During the research of its toxicity, a method was developed to use the sulphur group as a versatile position for post-synthetic modification. The advantage of application of post-synthetic modification lies in its convenience. Synthesis of oligomers with normal sequences has become routine work in most laboratories. However, design and synthesis of a proper phosphoramidite monomer for a new modified nucleoside are always difficult tasks even for a skilful chemist. Thus an alternative method (post-synthetic method) has been invented to overcome the difficulties. This was achieved by incorporation of versatile nucleotides into oligomers which contain a leaving group, that is sufficiently stable to withstand the conditions of synthesis but can be substituted by nucleophiles after synthesis, to produce, a series of oligomers each containing a different modified base. In the current project, a phosphoramidite monomer with 6-thioguanine has been successfully synthesised and incorporated into RNA. A deprotection procedure, which is specific for RNA was designed for oligomers containing 6-thioguanosine. The results were validated by various methods (UV, HPLC, enzymatic digestion). Pioneer work in utilization of the versatile sulphur group for post-synthetic modification was also tested. Post-synthetic modification was also carried out on DNA with 6- deoxythioguanosine. Electrophilic reagents with various functional groups (alphatic, aromatic, fluorescent) and bi-functional groups have been attached with the oligomers.

Chemical synthesis of isotopically labelled (M+4) purine nucleosides and their incorporation into DNA oligomers

Development of accurate and sensitive analytical methods to measure the level of biomarkers, such as 8-oxo-guanine or its corresponding nucleoside, 8-oxo-2’-deoxyguanosine, has become imperative in the study of DNA oxidative damage in vivo. Of the most promising techniques, HPLC-MS/MS, has many attractive advantages. Like any method that employs the MS technique, its accuracy depends on the use of multiply, isotopically-labelled internal standards. This project is aimed at making available such internal standards. The first task was to synthesise the multiply, isotopically-labelled bases (M+4) guanine and (M+4) 8-oxo-guanine. Synthetic routes for both (M+4) guanine and (M+4) 8-oxo-guanine were designed and validated using the unlabelled compounds. The reaction conditions were also optimized during the “dry runs”. The amination of the 4-hydroxy-2,6-dichloropyrimidine, appeared to be very sensitive to the purity of the commercial [15]N benzylamine reagent. Having failed, after several attempts, to obtain the pure reagent from commercial suppliers, [15]N benzylamine was successfully synthesised in our laboratory and used in the first synthesis of (M+4) guanine. Although (M+4) bases can be, and indeed have been used as internal standards in the quantitative analysis of oxidative damage, they can not account for the errors that may occur during the early sample preparation stages. Therefore, internal standards in the form of nucleosides and DNA oligomers are more desirable. After evaluating a number of methods, an enzymatic transglycolization technique was adopted for the transfer of the labelled bases to give their corresponding nucleosides. Both (M+4) 2-deoxyguanosine and (M+4) 8-oxo-2’-deoxyguanosine can be purified on micro scale by HPLC. The challenge came from the purification of larger scale (>50 mg) synthesis of nucleosides. A gel filtration method was successfully developed, which resulted in excellent separation of (M+4) 2’-deoxyguanosine from the incubation mixture. The (M+4) 2’-deoxyguanosine was then fully protected in three steps and successfully incorporated, by solid supported synthesis, into a DNA oligomer containing 18 residues. Thus, synthesis of 8-oxo-deoxyguanosine on a bigger scale for its future incorporation into DNA oligomers is now a possibility resulting from this thesis work. We believe that these internal standards can be used to develop procedures that can make the measurement of oxidative DNA damage more accurate and sensitive.

On the active site in H3PW12O40/SiO2 catalysts for fine chemical synthesis

The surface environment and structural evolution of silica supported phosphotungstic acid (H3PW12O40) catalysts have been investigated as a function of acid loading. H3PW12O40 clusters are deposited intact upon the silica surface, adopting a Stranksi-Krastanov growth mode forming a two-dimensional adlayer which saturates at 45wt% acid. Intimate contact with the silica support perturbs the local chemical environment of three tungstate centres, which become inequivalent with those in the remaining cluster, suggesting an adsorption mode involving three terminal W==O groups. Above the monolayer, H3PW12O40 clusters form three-dimensional crystallites with physico-chemical properties indistinguishable from those in the bulk heteropoly acid. These H3PW12O40/SiO2 materials are efficient for the solventless isomerisation of α-pinene under mild reaction conditions. Activity scales directly with the number of accessible perturbed tungstate sites at the silica interface; these are the active species.

Catalysing sustainable fuel and chemical synthesis

Concerns over the economics of proven fossil fuel reserves, in concert with government and public acceptance of the anthropogenic origin of rising CO2 emissions and associated climate change from such combustible carbon, are driving academic and commercial research into new sustainable routes to fuel and chemicals. The quest for such sustainable resources to meet the demands of a rapidly rising global population represents one of this century’s grand challenges. Here, we discuss catalytic solutions to the clean synthesis of biodiesel, the most readily implemented and low cost, alternative source of transportation fuels, and oxygenated organic molecules for the manufacture of fine and speciality chemicals to meet future societal demands.

Characterization of silver nanoparticles prepared by wet chemical method and their antibacterial and cytotoxicity activities

Purpose: To investigate the efficiency of silver nanoparticles synthesized by wet chemical method, and evaluate their antibacterial and anti-cancer activities. Methods: Wet chemical method was used to synthesize silver nanoparticles (AgNPs) from silver nitrate, trisodium citrate dehydrate (C6H5O7Na3.2H2O) and sodium borohydride (NaBH4) as reducing agent. The AgNPs and the reaction process were characterized by UV–visible spectrometry, zetasizer, transmission electron microscopy (TEM) and scanning electron microscopy (SEM) equipped with energy dispersive spectroscopy (EDS). The antibacterial and cytotoxic effects of the synthesized nanoparticles were investigated by agar diffusion method and MTT assay respectively. Results: The silver nanoparticles formed were spherical in shape with mean size of 10.3 nm. The results showed good antibacterial properties, killing both Gram-positive and Gram-negative bacteria, and its aqueous suspension displayed cytotoxic activity against colon adenocarcinoma (HCT-116) cell line. Conclusion: The findings indicate that silver nanoparticles synthesized by wet chemical method demonstrate good cytotoxic activity in colon adenocarcinoma (HCT-116) cell lines and strong antibacterial activity against various strains of bacteria.

Symmetry and shape issues in nanostructure growth

Symmetry plays a key role in dictating the equilibrium morphology of crystals. However, several growth morphologies that deviate from the point group symmetry are routinely observed under several different growth conditions. In this article, we present a summary of symmetry-breaking mechanisms that are operative for crystals grown from the vapour phase as well as those formed as a result of wet chemical synthesis. This understanding is crucial for rationalizing the variety of morphologies observed during nanocrystal synthesis and also providesa rational framework for the synthesis of anisotropic nanostructures.

Preparation and Characterization of MWCNT/ZnO nanoparticles Hybrid

ZnO nanoparticles (ZnO NPs) were grown on the surface of multiwall carbon nanotubes (MWCNTs) by a wet chemical synthesis route. The anchoring of ZnO NPs on acid-treated MWCNTs was achieved under remarkably mild reaction conditions (low temperature, atmospheric pressure, without any capping agents and no need for subsequent thermal annealing). MWCNT/ZnO NPs hybrid samples with varying loading of ZnO NPs are prepared. A very high degree of dispersion of ZnO NPs over the surface of MWCNT was achieved by suitably controlling the ratio of ZnO NPs and MWCNTs in the solution. The hybrid sample was characterized by electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy (XPS). Transmission electron microscope images of the as-prepared MWCNT/ZnO NPs hybrid reveal that mono-dispersed ZnO NPs are anchored stably on functionalized MWCNTs. The interaction of ZnO NPs with MWCNT surface was interpreted through XPS analysis.

Phase formation and stability of alloy phases in free nanoparticles: some insights

This paper explores phase formation and phase stability in free nanoparticles of binary alloys. A procedure for estimating the size and composition dependent free energies incorporating the contributions from the interfaces has been presented. Both single phase solid solution and two phase morphology containing interphase interfaces have been considered. A free energy scenario has been evaluated for two binary alloy systems Ag-Ni and Ag-Cu to predict the microstructure of the alloy nanoparticles at different size ranges as a function of composition. Both Ag-Cu and Ag-Ni systems exhibit wide bulk immiscibility. Ag-Ni nanoparticles were synthesized using the wet chemical synthesis technique whereas Ag-Cu nanoparticles were synthesized using laser ablation of a Ag-Cu target immersed in distilled water. Microstructural and compositional characterization of Ag-Ni and Ag-Cu nanoparticles on a single nanoparticle level was conducted using transmission electron microscopy. Nanoparticle microstructures observed from the microscopic investigation have been correlated with thermodynamic calculation results. It is shown that the observed two phase microstructure consisting of Ag-Ni solid solution in partial decomposed state coexisting with pure Ag phases in the case of Ag-Ni nanoparticles can be only be rationalized by invoking the tendency for phase separation of an initial solid solution with increase in nanoparticle size. Smaller sized Ag-Ni nanoparticles prefer a single phase solid solution microstructure. Due to an increase in particle size during the synthesis process the initial solid solution decomposes into an ultrafine scale phase separated microstructure. We have shown that it is necessary to invoke critical point phenomenon and wetting transition in systems showing a critical point that leads to phase separated Ag-Ni nanoparticles providing a catalytic substrate for the nucleation of equilibrium Ag over it. In the case of the Ag-Cu system, we report the experimental observation of a core shell structure at small sizes. This can be rationalized in terms of a metastable solid solution. It is argued that the nucleation barrier can prevent the formation of biphasic morphology with an internal interface. In such a situation, demixing of the solid solution can bring the system to a lower energy configuration. This has lead to the observed core-shell morphology in the Ag-Cu system during room temperature synthesis.

Effect of the nature of a transition metal dopant in BaTiO3 perovskite on the catalytic reduction of nitrobenzene

In the present study, we have synthesized Fe, Co and Ni doped BaTiO3 catalyst by a wet chemical synthesis method using oxalic acid as a chelating agent. The concentration of the metal dopant varies from 0 to 5 mol% in the catalysts. The physical and chemical properties of doped BaTiO3 catalysts were studied using various analytical methods such as X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), BET surface area and Transmission electron microscopy (TEM). The acidic strength of the catalysts was measured using a n-butylamine potentiometric titration method. The bulk BaTiO3 catalyst exhibits a tetragonal phase with the P4mm space group. A structural transition from tetrahedral to cubic phase was observed for Fe, Co and Ni doped BaTiO3 catalysts with an increase in doped metal concentration from 1 to 5 mol%. The particle sizes of the catalysts were calculated from TEM images and are in the range of 30-80 nm. All the catalysts were tested for the catalytic reduction of nitrobenzene to azoxybenzene. The BaTiO3 catalyst was found to be highly active and less selective compared to the doped catalysts which are active and highly selective towards azoxybenzene. The increase in selectivity towards azoxybenzene is due to an increase in acidic strength and reduction ability of the doped metal. It was also observed that the nature of the metal dopant and their content at the B-site has an impact on the catalytic reduction of nitrobenzene. The Co doped BaTiO3 catalyst showed better activity with only 0.5 mol% doping than Fe and Ni doped BaTiO3 catalysts with maximum nitrobenzene conversion of 91% with 78% selectivity to azoxybenzene. An optimum Fe loading of 2.5 mol% in BaTiO3 is required to achieve 100% conversion with 93% selectivity whereas Ni with 5 mol% showed a conversion of 93% and a azoxybenzene selectivity of 84%.

MnFe2O4-Fe3O4 core-shell nanoparticles as a potential contrast agent for magnetic resonance imaging

In recent years, magnetic core-shell nanoparticles have received widespread attention due to their unique properties that can be used for various applications. We introduce here a magnetic core-shell nanoparticle system for potential application as a contrast agent in magnetic resonance imaging (MRI). MnFe2O4-Fe3O4 core-shell nanoparticles were synthesized by the wet-chemical synthesis method. Detailed structural and compositional charaterization confirmed the formation of a core-shell microstructure for the nanoparticles. Magnetic charaterization revealed the superparamagnetic nature of the as-synthesized core-shell nanoparticles. Average size and saturation magnetization values obtained for the as-synthesized core-shell nanoparticle were 12.5 nm and 69.34 emu g(-1) respectively. The transverse relaxivity value of the water protons obtained in the presence of the core-shell nanoparticles was 184.1 mM(-1) s(-1). To investigate the effect of the core-shell geometry towards enhancing the relaxivity value, transverse relaxivity values were also obtained in the presence of separately synthesized single phase Fe3O4 and MnFe2O4 nanoparticles. Average size and saturation magnetization values for the as-synthesized Fe3O4 nanoparticles were 12 nm and 65.8 emu g(-1) respectively. Average size and saturation magnetization values for the MnFe2O4 nanoparticles were 9 nm and 61.5 emu g(-1) respectively. The transverse relaxivity value obtained in the presence of single phase Fe3O4 and MnFe2O4 nanoparticles was 96.6 and 83.2 mM(-1) s(-1) respectively. All the nanoparticles (core-shell and single phase) were coated with chitosan by a surfactant exchange reaction before determining the relaxivity values. For similar nanoparticle sizes and saturation magnetization values, the highest value of the transverse relaxivity in the case of core-shell nanoparticles clearly illustrated that the difference in the magnetic nature of the core and shell phases in the core-shell nanoparticles creates greater magnetic inhomogeneity in the surrounding medium yielding a high value for proton relaxivity. The MnFe2O4-Fe3O4 core-shell nanoparticles exhibited extremely low toxicity towards the MCF-7 cell line. Taken together, this opens up new avenues for the use of core-shell nanoparticles in MRI.

Surface-enhanced Raman scattering from surfactant-free 3D gold nanowire networks substrates

A useful method for the fabrication of three-dimensional gold nanowire networks based on the chemical reduction of HAuCl4 with trisodium citrate was presented. The coverage of the 3D gold nanowire networks was tunable by altering precursor concentration. The as-prepared 3D gold nanowire networks could be used as surface-enhanced Raman scattering (SERS) substrates and examined by 4-aminothiophenol (4-ATP) as a probe molecules.

Rectangular Silver Nanorods: Controlled Preparation, Liquid-Liquid Interface Assembly, and Application in Surface-Enhanced Raman Scattering

In this paper, we for the first time report a polyol method for large-scale synthesis of rectangular silver nanorods in the presence of directing agent and seeds. This method has some clear advantages including simplicity, high quality, and ease of scaleup. Silver nanowires or silver nanorods with a submicrometer diameter could also be facilely prepared when the reaction parameters are slightly changed. Furthermore, a liquid-liquid assembly strategy has been employed to construct uniform rectangular silver nanorod arrays on a solid substrate which could be used as surface-enhanced Raman scattering (SERS) substrates with high SERS activity, stability, and reproducibility. It is found that the SERS spectra obtained from the probe molecules with the different concentrations show different SERS intensifies. As the concentration of 4-aminothiophenol (4-ATP) or rhodamine 6G (R6G) increases, the SERS intensities progressively increase. The enhancement factor for 4-ATP and R6G should be as large as 5.06 x 10(4) or much larger than the value of 5.06 x 10(8), respectively.

Preparation of novel silver-gold bimetallic nanostructures by seeding with silver nanoplates and application in surface-enhanced Raman scattering

Novel silver-gold bimetallic nanostructures were prepared by seeding with silver nanoplates in the absence of any surfactants. During the synthesis process, it was found that the frameworks of silver nanoplates were normally kept though the basal plane of silver nanoplates became rugged. The real morphology of these nanostructures depended on the molar ratio of gold ions to the seed particles. When the molar ratio of gold ions to silver atoms increased from 0.5 to 4, porous or branched silver-gold bimetallic nanostructures could be made. The growth mechanism was qualitatively discussed based on template-engaged replacement reactions and seed-mediated deposition reactions. Due to the unusual structures, they exhibited interesting optical properties. Moreover, they were shown to be an active substrate for surface-enhanced Raman scattering measurements.