SOLID-PHASE SYNTHESIS OF OLIGODEOXYNUCLEOTIDES CONTAINING 3′-S-PHOSPHOROTHIOLATE LINKAGES

For the first time a fully automated procedure has been developed for the incorporation of a 3′-S-phosphorothiolate linkage into DNA, using phosphorothioamidite monomers. Coupling yields with either of the activators 5-ethylthiotetrazole or 4,5-dicyanoimidazole were in the range of 80–90%. Coupling yields were equally good when performed on either a 0.2 or 1 μmole reaction column, thus facilitating large scale synthesis.     

Synthesis of phosphorothioamidites derived from 3'-thio-3'-deoxythymidine and 3'-thio-2',3'-dideoxycytidine and the automated synthesis of oligodeoxynucleotides containing a 3'-S-phosphorothiolate linkage

The synthesis of N4-benzoyl-5′-O-dimethoxytrityl-2′,3′-dideoxy-3′-thiocytidine and its phosphorothioamidite is described for the first time, together with a shortened procedure for the preparation of 5′-O-dimethoxytrityl-3′-deoxy-3′-thiothymidine and its corresponding phosphorothioamidite. The first fully automated coupling procedure for the incorporation of a phosphorothioamidite into a synthetic oligodeoxynucleotide has been developed, which conveniently uses routine activators and reagents. Coupling yields using this protocol were in the range of 85–90% and good yields of singularly modified oligonucleotides were obtained. Coupling yields were also equally good when performed on either a 0.2 or 1 µmol reaction column, thus facilitating large scale syntheses required for mechanistic studies.     

Synthesis of Modified Nucleosides. Palladium-Catalysed Couplings of Organostannanes or Organoboranes with Pyrimidine Nucleosides

Abstract

Coupling of suitably protected 5-iodouridine or 5-iodo-2′-deoxyuridine with either arylboronic acids or aryltrimethylstannanes in the presence of a palladium catalyst gave moderate yields of the corresponding 5-aryluridines and 5-aryC2′-deoxyuridines. 5-Hydroxyuridine was converted into 5-(trifluoromethanesulphonyl)uridine in good yield and the triacetate of this modified nucleoside also underwent palladium-catalysed couplings with a variety of organostannanes to produce the 5-substituted uridine in excellent yield.     

Highly efficient chemical synthesis of 2''-O-methyloligoribonucleotides and tetrabiotinylated derivatives; novel probes that are resistant to degradation by RNA or DNA specific nucleases.

2'-O-Methyloligoribonucleotides have been synthesised on solid phase from base protected 5'-O-dimethoxytrityl-2'-O-methylribonucleoside-3'-O-(2-cyanoethyl N,N-diisopropylphosphoramidites) using 5-(4-nitrophenyl)-1H-tetrazole as activator. Coupling yields greater than 99% were achieved, as judged by trityl cation release. The preparation of a modified 2'-deoxycytidine building block bearing an N4-(5-trifluoroacetylaminopentyl) spacer is also described. The latter compound enabled the chemical synthesis of 2'-O-methyloligoribonucleotide probes carrying several 5'- terminal biotinylation sites (in general four modified residues were used), which can be conveniently 32P end-labelled enzymatically using polynucleotide kinase. Used in conjunction with streptavidin-containing derivatives, such biotinylated probes have important applications in biochemical purification and electron microscopy of RNA-protein complexes. The 2'-O-methyloligoribonucleotides are completely resistant to degradation by either RNA or DNA specific nucleases. In contrast, nucleases with dual RNA/DNA specificity show a complete spectrum of cleavage rates.     

Application of high-performance liquid chromatographic peptide purification to protein microsequencing by solid-phase Edman degradation

Peptide purification via high-performance liquid chromatography (HPLC) and solid-phase sequencing were integrated to form a system allowing the determination of complete sequence information on a microscale without the use of radiolabels or modified phenylisothiocyanate. Mixtures of peptides (500 pmol to 10 nmol) resulting from proteolytic digestion or chemical cleavage were applied directly to reverse-phase columns. The columns, equilibrated in either 10 mm KP_i or 0.05% trifluoroacetic acid, were then developed using acetonitrile gradients. Eluates were monitored nondestructively by direct ultraviolet detection at both 214 and 254 nm. Each peak was collected as a discrete fraction, and purity was assessed by amino acid analysis prior to covalent attachment to a solid support for sequence analysis. Activation of the peptide carboxyl terminus via a water soluble carbonyldiimide was the solid-phase coupling method used 90% of the time. Coupling yields averaged 52% of starting material. Sequence analysis was performed in the range 100 pmol to 4 nmol of coupled peptide. Phenylthiohydantoin-amino acids were identified by reverse-phase HPLC using ultraviolet detection.     

Predictable and Reproducible Yields in the Anchoring of Dmt-nucleoside-succinates to Highly Loaded Aminoalkyl-Polystyrene Resins

Abstract

Coupling of DMT-nucleoside-succinates¹ onto aminomethyl-polystyrene has been fine tuned in order to allow the preparation of DMT-nucleoside-resins with the desired substitution degree in reproducible yields.     

Immobilization of glycoenzymes through carbohydrate side chains.

Glucoamylase, peroxidase, glucose oxidase, and carboxypeptidase Y were covalently bound to water-insoluble supports through their carbohydrate side chains. Two approaches were used. First, the carbohydrate portions of the enzymes were oxidized with periodate to generate aldehyde groups. Treatment with amines (ethylenediamine or glycyltyrosine) and borohydride provided groups through which the protein could be immobilized. Ethylenediamine was attached to glucoamylase, peroxidase, glucose oxidase, and carboxypeptidase Y to the extent of 24, 20, 30, and 15 mol/mol of enzyme, respectively. These derivatives were coupled to an aminocaproate adduct of CL-Sepharose via an N-hydroxysuccinimide ester or to CNBr-activated Sepharose. Coupling yields were in the range of 37–50%. Retained activities of the bound aminoalkyl-enzymes were 41% (glucoamylase), 79% (peroxidase), 71% (glucose oxidase), 83% (carboxypeptidase Y). A glycyltyrosine derivative of carboxypeptidase Y was bound to diazotized arylamine-glass. Coupling yield was 42% and retained esterase activity was 84%. In the second approach, the enzyme was adsorbed to immobilized concanavalin A and the complex was crosslinked. Adsorption of carboxypeptidase Y on immobilized concanavalin A followed by crosslinking with glutaraldehyde was also effective. The bound enzyme retained 96% of the native esterase activity and showed very good operational stability.     

Efficient synthesis of DNA dumbbells using template-induced chemical ligation in double-stranded polynucleotides closed by minihairpin fragments

The chemical ligation of 17 50-54-membered nicked DNA dumbbells with different closing fragments, nick positions, and nucleotides facing the nick were investigated. T4, T5, GTA4C, GCGA2GC, and GCGA3GC sequences were chosen as the closing fragments. The nicks were placed in the center of the duplex stem or were adjacent to the closing fragments. N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide and cyanogen bromide were used as the condensing agents. We showed that the ligation efficiency is 10%-90% depending on the sequence of the closing fragments, nick position, and nucleotides facing the nick. Coupling yields of 80%-90% were observed when the nick was situated in the middle of the molecule between two T residues or was adjacent to GCGA2GC or GCGA3GC minihairpins. In the last case, the reacting 3'-phosphate and 5'-hydroxy groups were brought close together by only two base pair minihairpins. The coupling yields did not depend on the nature of the condensing agent. On the basis of the results obtained, we believe a rational design of nicked DNA dumbbells has been developed for efficient chemical synthesis of closed dumbbells.     

Ready to use p-Benzoquinone activated supports for biochemical coupling,with special applications for laccase immobilization

Summary A new type of p-Benzoquinone activated support (agarose, polyvinyl alcohol, chitosan) which can be stored for more than one year, is described. Coupling yields of 10–95% were obtained for various compounds (propylamine, serum albumin, alpha-amylase). A retained activity of 150% for the immobilized laccase, was obtained. This peculiar result is probably due to the presence of hydroquinone groups on the support, which, as a substrate of laccase, can generate a simultancous affinity retention of the enzyme.     

Synthesis and biological activity of some unsaturated 6-azauracil acyclonucleosides

A useful route is described for obtaining Z and E unsaturated alkylating agents 3 and 4. Coupling 6-azauracils 5 and 6 with unsaturated alkylating agent followed by the deprotection with H+ resin gave acyclonucleosides 11-14 in good overall yields. Unsaturated acyclonucleosides phosphonates 19 and 20 were prepared using potassium carbonate as base and 4-bromobut-2-enyl diethyl phosphonate 16 as the alkylating agent. The introduction of a propargyl group at the N-3 position of acyclonucleosides 7, 8 17, 18, 19, and 20 was achieved using potassium carbonate in DMF.     

Synthesis of Racemic 5-Substituted 1-(2,3-Dihydroxypropyl)-6-azauracils and Their Isosteric Isomers

Abstract

Acyclic nucleoside analogues of antiviral DHPA and HPMPA have been prepared. Coupling of silylated 6-azauracils with benzyl glycidyl ether and stannic chloride followed by the deprotection with boron trichloride gave 1-(2,3-dihydroxypropyl)-6-azauracils (3) in good overall yields. Reaction of silylated 6-azauracil and epichlorohydrin with or without catalytic stannic chloride afforded 1-(2-chloro-3-hydroxypropyl)-6-azauracil (4a) and 1-(3-chloro-2-hydroxypropyl)-6-azauracil (6a) respectively. Coupling of silylated 6-azaisocytosine under the same reaction conditions provided 1-(2,3-dihydroxypropyl)-6-azaisocytosine (9) and 1-(2-chloro-3-hydroxypropyl)-6-azaisocytosine (10) respectively. None of the compounds exhibited significant antiviral activity against herpes simplex viruses.     

Ferrocene-avidin conjugates for bioelectrochemical applications.

Coupling of ferrocene moieties to avidin via a flexible spacer molecule yields a conjugate which combines the unique biotin-binding properties of avidin with the reversible redox characteristics of ferrocenes. Synthesis of the conjugate has been optimised and the conjugates were characterised bio- and electrochemically. Covalent immobilisation of the conjugate on gold electrodes in a dense monolayer results in electrodes with a high binding capacity for biotinylated molecules as well as good electron transfer properties. The application potential of such electrodes for bioelectrochemical systems is demonstrated by electrochemical reduction of hydrogen peroxide under mild conditions catalysed by a bound biotin-microperoxidase MP11 conjugate.     

Microbial energetics and stoichiometry for biodegradation of aromatic compounds involving oxygenation reactions

Oxygenation reactions significantly alter the energy and electron flows and, consequently, the overall stoichiometry for the microbial utilization of aromatic compounds. Oxygenation reactions do not yield a net release of electrons, but require an input of electrons to reduce oxygen molecules. The biodegradation pathway of phenanthrene as a model compound was analyzed to determine the impact of oxygenation reactions on overall stoichiometry using the half-reaction method. For individual oxygenation reactions, the half-reaction method for analyzing the electron and energy flows must be modified, because the reactions do not release electrons for synthesis or energy generation. Coupling the oxygenation reaction to subsequent reaction steps provides a net electron release for the coupled reactions. Modeling results indicate that oxygenation reactions increase the oxygen requirement and reduce the cell yield, compared to the conventional mineralization represented by hydroxylation reactions in place of oxygenations. The computed yields considering oxygenation reactions conform better to empirical yields reported in the literature than do yields computed by the hydroxylation single-step methods. The coupled-reaction model also is consistent with information about the ways in which micro-organisms that degrade aromatics accumulate intermediates, regulate degradation genes, and organize enzyme clusters.     

Folic acid conjugates with photosensitizers for cancer targeting in photodynamic therapy: Synthesis and photophysical properties

Recent researches in photodynamic therapy have focused on novel techniques to enhance tumour targeting of anticancer drugs and photosensitizers. Coupling a photosensitizer with folic acid could allow more effective targeting of folate receptors which are over-expressed on the surface of many tumour cells. In this study, different folic acid–OEG-conjugated photosensitizers were synthesized, characterized and their photophysical properties were evaluated. The introduction of an OEG does not significantly improve the hydrophilicity of the FA–porphyrin. All the FA-targeted photosensitizers present good to very good photophysical properties. The best one appears to be Ce6. Molar extinction coefficient, fluorescence and singlet oxygen quantum yields were determined and were compared to the corresponding photosensitizer alone.     

Solvent free vapor phase photografting of maleic anhydride onto poly(ethylene terephthalate) and surface coupling of fluorinated probes, PEG, and an RGD-peptide

Poly(ethylene terephthalate) (PET) was photografted in a solvent free vapor of maleic anhydride and benzophenone. After hydrolysis of the initially grafted succinic anhydride groups, the carboxylic PET surfaces were modified by coupling reactions in organic and aqueous solutions. 2,2,2-Trifluoroethylamine and diamino PEGs of molecular weight 3400 and 2000 were reacted with acid chloride groups obtained by treating the PET-COOH surface with PCl(5). Furthermore, fluoro substituted thiols and a cystein terminated RGD containing peptide were bound to PET-COOH surfaces via a disulfide link by a three step coupling sequence. Coupling yields and surface concentrations of the fluoro substituted ligands were calculated from ESCA data. The RGD-peptide surfaces were evaluated by cultivation with rat smooth muscle cells.     

Effects of some oxidising agents,especially ammonium peroxysulfate,on sugar-beet pectins

Sugar-beet pectins contain feruloyl groups linked to the side chains of the rhamnogalacturonan backbone. Coupling reactions may cross-link these macro-molecules. Of several oxidising agents, only hydrogen peroxide-peroxidase and ammonium peroxysulfate were effective, indicating the involvement of free radicals. The effects of peroxysulfate and pectin concentrations, temperature, and the presence of some additives have been investigated mainly by viscometry and chromatography on Sepharose CL-2B. Depending on the concentration of the pectin, the reaction may be used to obtain either water-soluble products of increased molecular weight or gels.     

Palladium-Catalyzed Animation of 6-Chloropurine. Synthesis of N6-Substituted Adenosine Analogues

Abstract

Room-temperature treatment of persilylated 6-chloro-9-β-D-ribofuranosyl-purine with a variety of aliphatic and aromatic amines, in the presence of Pd₂(dba)₃, BINAP and base, leads to N⁶-substituted adenosine analogues in fair to good yields. Coupling of chloropurine with a chiral aziridinyl diester is applied in the synthesis of a potential adenylosuccinate lyase inhibitor.     

Immobilized Human Plasmins: Preparation and Enzymatic Properties

Plasminogen was immobilized on agarose using either a commercially available substituted gel, or the cyanogen bromide (CNBr) activation procedure as a means of coupling the protein to agarose. Coupling the zymogen to the gel followed by its activation with urokinase yielded an immobilized plasmin. The immobilized enzymes have esterase, amidase and protease activity towards lysine and arginine esters, lysine anilide and casein, respectively. They activate plasminogen by a linear non-autocatalytic process. Both enzyme preparations are stable for extended periods of time in the absence of any stabilizing agents, and are not denatured by high salt concentrations or detergents.     

The function of free carboxyl groups in the action of peroxidase and indole-3-acetic acid oxidase

The extracellular peroxidase from cultures of Inonotus radiatus and of peanut (Arachis hypogeaL.) cells as well as the mycelial peroxidase from Trametes versicolor were used for studies of immobilizing this protein either by its free amino or its carboxyl groups. The immobilization process was carried out either on keratin proteins derived from feathers or on polyamide coated over silica gel. Coupling was established either through the free amino or carboxyl groups. In general the indolyl-3-acetic acid oxidase activity of fungal peroxidases exceeds that of peanut peroxidase. When the peroxidase of the three sources was immobilized on the matrices by the free amino groups, little if any effect on the IAA oxidase activity could be measured. However, immobilization through the carboxyl groups resulted in a drastic reduction of indole-3-acetic acid oxidase activity. Since identical amounts of peroxidase were linked in all cases, the loss of indolyl-3-acetic acid oxidase activity implies that the carboxyl group is essential for the active site.     

Ethanol recovery from corn fiber hydrolysate fermentations by pervaporation

Corn fiber, a byproduct of corn wet milling, is an attractive feedstock for biomass ethanol production. Corn fiber was hydrolyzed by dilute sulfuric acid and neutralized by one of two methods: conventional lime treatment or neutralization by strongly basic anion exchange. The anion exchange neutralized (AEN) hydrolysate contained substantially lower levels of the inhibiting compounds furfural, 5-hydroxymethylfurfural, and acetic acid compared to the lime neutralized hydrolysate. In batch fermentations the ethanol yields and final ethanol concentration of the two hydrolysates were similar at 0.32-0.43 g/g and 29-44 g/l, respectively. Sugar consumption in the AEN fermentations was superior. Coupling of a membrane pervaporation unit to a fed-batch fermentation of AEN hydrolysate maintained the ethanol concentration below 25 g/l with complete sugar utilization for approximately 5 days. A concentrated ethanol stream of 17 wt.% ethanol was produced by the pervaporation unit.