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.

Variation in Miscanthus chemical composition and implications for conversion by pyrolysis and thermo-chemical bio-refining for fuels and chemicals

Different species and genotypes of Miscanthus were analysed to determine the influence of genotypic variation and harvest time on cell wall composition and the products which may be refined via pyrolysis. Wet chemical, thermo-gravimetric (TGA) and pyrolysis-gas chromatography–mass spectrometry (Py-GC–MS) methods were used to identify the main pyrolysis products and determine the extent to which genotypic differences in cell wall composition influence the range and yield of pyrolysis products. Significant genotypic variation in composition was identified between species and genotypes, and a clear relationship was observed between the biomass composition, yields of pyrolysis products, and the composition of the volatile fraction. Results indicated that genotypes other than the commercially cultivated Miscanthus x giganteus may have greater potential for use in bio-refining of fuels and chemicals and several genotypes were identified as excellent candidates for the generation of genetic mapping families and the breeding of new genotypes with improved conversion quality characteristics.

Base modified peptidic nucleic acids: synthesis and crystallographic analysis of intermediates

Peptidic Nucleic Acids (PNAs) are achiral, uncharged nucleic add mimetics, with a novel backbone composed of N-(2-aminoethyl)glycine units attached to the DNA bases through carboxymethylene linkers. With the aim of extending and improving upon the molecular recognition properties of PNAs, the aim of this work was to synthesjse PNA building block intermediates containing a series of substituted purine bases for subsequent use in automated PNA synthesis. Four purine bases: 2,6~diaminopurine (D), isoGuanine (isoG), xanthine (X) and hypoxanthine (H) were identified for incorporation into PNAs targeted to DNA, with the promise of increased hybrid stability over extended pH ranges together with improvements over the use of adenine (A) in duplex formation, and cytosine (C) in triplex formation. A reliable, high-yielding synthesis of the PNA backbone component N -('2- butyloxycarbonyl-aminoethyl)glycinate ethyl ester was establishecl. The precursor N~(2-butyloxycarbonyl)amino acetonitrile was crystallised and analysed by X-ray crystallography for the first time. An excellent refinement (R = 0.0276) was attained for this structure, allowing comparisons with known analogues. Although chemical synthesis of pure, fully-characterised PNA monomers was not achieved, chemical synthesis of PNA building blocks composed of diaminopurine, xanthine and hypoxanthine was completely successful. In parallel, a second objective of this work was to characterise and evaluate novel crystalline intermediates, which formed a new series of substituted purine bases, generated by attaching alkyl substituents at the N9 or N7 sites of purine bases. Crystallographic analysis was undertaken to probe the regiochemistry of isomers, and to reveal interesting structural features of the new series of similarly-substituted purine bases. The attainment of the versatile synthetic intermediate 2,6-dichloro~9- (carboxymethyl)purine ethyl ester, and its homologous regioisomers 6-chloro~9- (carboxymethyl)purine ethyl ester and 6-chloro-7-(carboxymethyl)purine ethyl ester, necessitated the use of X-ray crystallographic analysis for unambiguous structural assignment. Successful refinement of the disordered 2,6-diamino-9-(carboxymethyl) purine ethyl ester allowed comparison with the reported structure of the adenine analogue, ethyl adenin-9-yl acetate. Replacement of the chloro moieties with amino, azido and methoxy groups expanded the internal angles at their point of attachment to the purine ring. Crystallographic analysis played a pivotal role towards confirming the identity of the peralkylated hypoxanthine derivative diethyl 6-oxo-6,7-dihydro-3H-purlne~3,7~djacetate, where two ethyl side chains were found to attach at N3 and N7,

Novel materials for membrane separation processes

The aim of this work was to synthesise a series of hydrophilic derivatives of cis-1,2-dihydroxy-3,5-cyclohexadiene (cis-DHCD) and copolymerise them with 2-hydroxyethyl methacrylate (HEMA), to produce a completely new range of hydrogel materials. It is theorised that hydrogels incorporating such derivatives of cis-DHCD will exhibit good strength and elasticity in addition to good water binding ability. The synthesis of derivatives was attempted by both enzymatic and chemical methods. Enzyme synthesis involved the transesterification of cis-DHCD with a number of trichloro and trifluoroethyl esters using the enzyme lipase porcine pancreas to catalyse the reaction in organic solvent. Cyclohexanol was used in initial studies to assess the viability of enzyme catalysed reactions. Chemical synthesis involved the epoxidation of a number of unsaturated carboxylic acids and the subsequent reaction of these epoxy acids with cis-DHCD in DCC/DMAP catalysed esterifications. The silylation of cis-DHCD using TBDCS and BSA was also studied. The rate of aromatisation of cis-DHCD at room temperature was studied in order to assess its stability and 1H NMR studies were also undertaken to determine the conformations adopted by derivatives of cis-DHCD. The copolymerisation of diepoxybutanoate, diepoxyundecanoate, dibutenoate and silyl protected derivatives of cis-DHCD with HEMA, to produce a new group of hydrogels was investigated. The EWC and mechanical properties of these hydrogels were measured and DSC was used to determine the amount of freezing and non-freezing water in the membranes. The effect on EWC of opening the epoxide rings of the comonomers was also investigated

Migration of additives from thermoplastic polymers

A homologous series of ultra-violet stabilisers containing 2-hydroxybenzophenone (HBP) moiety as a uv absorbing chromophore with varying alkyl chain lengths and sizes were prepared by known chemical synthesis. The strong absorbance of the HBP chromophore was utilized to evaluate the concentration of these stabilisers in low density polyethylene films and concentration of these stabilisers in low density polyethylene films and in relevant solvents by ultra-violet/visible spectroscopy. Intrinsic diffusion coefficients, equilibrium solubilities, volatilities from LDPE films and volatility of pure stabilisers were studied over a temperature range of 5-100oC. The effects of structure, molecular weight and temperature on the above parameters were investigated and the results were analysed on the basis of theoretical models published in the literature. It has been found that an increase in alkyl chain lengths does not change the diffusion coefficients to a significant level, while attachment of polar or branched alkyl groups change their value considerably. An Arrhenius type of relationship for the temperature dependence of diffusion coefficients seems to be valid only for a narrow temperature range, and therefore extrapolation of data from one temperature to another leads to a considerable error. The evidence showed that increase in additive solubility in the polymer is favoured by lower heat of fusions and melting points of additives. This implies the validity of simple regular solution theory to provide an adequate basis for understanding the solubility of additives in polymers The volubility of stabilisers from low density polyethylene films showed that of an additive from a polymer can be expressed in terms of a first-order kinetic equation. In addition the rate of loss of stabilisers was discussed in relation to its diffusion, solubility and volatility and found that all these factors may contribute to the additive loss, although one may be a rate determining factor. Stabiliser migration from LDPE into various solvents and food simulants was studied at temperatures 5, 23, 40 and 70oC; from the plots of rate of migration versus square root time, characteristic diffusion coefficients were obtained by using the solution of Fick's diffusion equations. It was shown that the rate of migration depends primarily on partition coefficients between solvent and the polymer of the additive and also on the swelling action of the contracting media. Characteristic diffusion coefficients were found to approach to intrinsic values in non swelling solvents, whereas in the case of highly swollen polymer samples, the former may be orders of magnitude greater than the latter.

The characterisation and optimisation of modified herbaceous grasses for identifying pyrolisis-oil quality traits

The primary objective of this work is to relate the biomass fuel quality to fast pyrolysis-oil quality in order to identify key biomass traits which affect pyrolysis-oil stability. During storage the pyrolysis-oil becomes more viscous due to chemical and physical changes, as reactions and volatile losses occur due to aging. The reason for oil instability begins within the pyrolysis reactor during pyrolysis in which the biomass is rapidly heated in the absence of oxygen, producing free radical volatiles which are then quickly condensed to form the oil. The products formed do not reach thermodynamic equilibrium and in tum the products react with each other to try to achieve product stability. The first aim of this research was to develop and validate a rapid screening method for determining biomass lignin content in comparison to traditional, time consuming and hence costly wet chemical methods such as Klason. Lolium and Festuca grasses were selected to validate the screening method, as these grass genotypes exhibit a low range of Klason /Acid Digestible Fibre lignin contents. The screening methodology was based on the relationship between the lignin derived products from pyrolysis and the lignin content as determined by wet chemistry. The second aim of the research was to determine whether metals have an affect on fast pyrolysis products, and if any clear relationships can be deduced to aid research in feedstock selection for fast pyrolysis processing. It was found that alkali metals, particularly Na and K influence the rate and yield of degradation as well the char content. Pre-washing biomass with water can remove 70% of the total metals, and improve the pyrolysis product characteristics by increasing the organic yield, the temperature in which maximum liquid yield occurs and the proportion of higher molecular weight compounds within the pyrolysis-oil. The third aim identified these feedstock traits and relates them to the pyrolysis-oil quality and stability. It was found that the mineral matter was a key determinant on pyrolysis-oil yield compared to the proportion of lignin. However the higher molecular weight compounds present in the pyrolysis-oil are due to the lignin, and can cause instability within the pyrolysis-oil. The final aim was to investigate if energy crops can be enhanced by agronomical practices to produce a biomass quality which is attractive to the biomass conversion community, as well as giving a good yield to the farmers. It was found that the nitrogen/potassium chloride fertiliser treatments enhances Miscanthus qualities, by producing low ash, high volatiles yields with acceptable yields for farmers. The progress of senescence was measured in terms of biomass characteristics and fast pyrolysis product characteristics. The results obtained from this research are in strong agreement with published literature, and provides new information on quality traits for biomass which affects pyrolysis and pyrolysis-oils.

Heterogeneous catalysts for clean technology:spectroscopy, design, and monitoring

Reactive, but not a reactant. Heterogeneous catalysts play an unseen role in many of today's processes and products. With the increasing emphasis on sustainability in both products and processes, this handbook is the first to combine the hot topics of heterogeneous catalysis and clean technology. It focuses on the development of heterogeneous catalysts for use in clean chemical synthesis, dealing with how modern spectroscopic techniques can aid the design of catalysts for use in liquid phase reactions, their application in industrially important chemistries - including selective oxidation, hydrogenation, solid acid- and base-catalyzed processes - as well as the role of process intensification and use of renewable resources in improving the sustainability of chemical processes. With its emphasis on applications, this book is of high interest to those working in the industry.

Degradable poly(ethylene glycol)-based hydrogels:synthesis, physico-chemical properties and in vitro characterization

Designing degradable hydrogels is complicated by the structural and temporal complexities of the gel and evolving tissue. A major challenge is to create scaffolds with sufficient mechanical properties to restore initial function while simultaneously controlling temporal changes in the gel structure to facilitate tissue formation. Poly(ethylene glycol) was used in this work, to form biodegradable poly(ethylene glycol)-based hydrogels with hydrolyzable poly-l-lactide segments in the backbone. Non-degradable poly(ethylene glycol) was also introduced in the formulation to obtain control of the degradation profile that encompasses cell growth and new tissue formation. The dependence on polymer composition was observed by higher degradation profiles and decreased mechanical properties as the content of degradable segments was increased in the formulation. Based on in vitro tests, no toxicity of extracts or biomaterial in direct contact with human adipose tissue stem cells was observed, and the ultraviolet light treatment did not affect the proliferation capacity of the cells.