Synthesis of a Gene Coding for Vasoactive intestinal Peptide (VIP)

Abstract

A solid phase phosphoramidite triester coupling approach was used for the synthesis of the 16 fragments of a gene coding for human/porcine VIP. The design, synthesis, purification, subcloning and sequencing of the gene will be described.     

Convenient synthesis of a propargylated cyclic (3'-5') diguanylic acid and its "click" conjugation to a biotinylated azide

The ribonucleoside building block, N2-isobutyryl-2'-O-propargyl-3'-O-levulinyl guanosine, was prepared from commercial N2-isobutyryl-5'-O-(4,4'-dimethoxytrityl)-2'-O-propargyl guanosine in a yield of 91%. The propargylated guanylyl(3'-5')guanosine phosphotriester was synthesized from the reaction of N2-isobutyryl-2'-O-propargyl-3'-O-levulinyl guanosine with N2-isobutyryl-5'-O-(4,4'-dimethoxytrityl)-2'-O-tert-butyldimethylsilyl-3'-O-[(2-cyanoethyl)-N,N-diisopropylaminophosphinyl] guanosine and isolated in a yield of 88% after P(III) oxidation, 3'-/5'-deprotection, and purification. The propargylated guanylyl(3'-5')guanosine phosphotriester was phosphitylated using 2-cyanoethyl tetraisopropylphosphordiamidite and 1H-tetrazole and was followed by an in situ intramolecular cyclization to give a propargylated c-di-GMP triester, which was isolated in a yield of 40% after P(III) oxidation and purification. Complete N-deacylation of the guanine bases and removal of the 2-cyanoethyl phosphate protecting groups from the propargylated c-di-GMP triester were performed by treatment with aqueous ammonia at ambient temperature. The final 2'-desilylation reaction was effected by exposure to triethylammonium trihydrofluoride affording the desired propargylated c-di-GMP diester, the purity of which exceeded 95%. Biotinylation of the propargylated c-di-GMP diester was easily accomplished through its cycloaddition reaction with a biotinylated azide derivative under click conditions to produce the biotinylated c-di-GMP conjugate of interest in an isolated yield of 62%.     

Purification and characterization of a phosphoric triester hydrolase from the tufted apple bud moth, Platynota idaeusalis (Walker)

Whole body homogenates from azinphosmethyl-resistant fifth instars of the tufted apple bud moth demonstrated 11.8-fold elevated phosphoric triester hydrolase (methyl paraoxonase) activity as compared to susceptible insects of the same species. Elevated phosphoric triester hydrolase (PTEH) activity associated with resistance was also found in the Colorado potato beetle but not in the German cockroach or tobacco budworm. Phosphoric triester hydrolase activity in the tufted apple bud moth was minimal in resistant and susceptible third instars and in adult males and females and was highest in whole body homogenates and in the alimentary canal of resistant fifth instars. A microtiterplate assay was developed, which successfully diagnosed resistance in individual fifth instars based on increased phosphoric triester hydrolase (methyl paraoxonase) activity. Phosphoric triester hydrolase was purified 289-fold from fifth instars of resistant bud moths, but any additional resolution resulted in the loss of enzyme activity. Phosphoric triester hydrolase demonstrated an apparent molecular weight of 41,000 with an isoelectric point of 5.28. Methyl paraoxonase activity was increased by calcium, cobalt, manganese, and octylthio-1,1,1-trifluoro-2-propanone and decreased by mercury, phosphate ions, tin, and ethylenediaminetetraacetic acid. Iron, potassium chloride, lithium, magnesium, sodium chloride, and lead had no effect.     

Conjugated Antisense Oligonucleotides for Inhibition of Human Cytomegalovirus In Vitro

Abstract

Several thiono triester containing oligonucleotide phosphorothioates linked with a lipophilic group have been synthesized. Some of these modified antisense oligonucleotides show potent anti-HCMV activity as well as improved cellular association and nuclease resistance.     

NBS-DMSO as a nonaqueous nonbasic oxidation reagent for the synthesis of oligonucleotides

A new method for the oxidation of nucleoside phosphite triester into phosphate triester under nonbasic and nonaqueous conditions using NBS-DMSO in CH(3)CN has been developed. The utility of this method for solution- and solid-phase synthesis of oligonucleotide is demonstrated.     

Synthesis of human insulin gene. Part I. Development of reversed-phase chromatography in the modified triester method. Its application in the rapid and efficient synthesis of eight deoxyribooligonucleotides fragments constituting human insulin A DNA.

Preparative reversed-phase thin layer chromatography on silanized silica-gel (RP-2 and RP-18) has been developed to purify triester deoxyribooligonucleotides prepared by the modified triester method. The effectiveness of this technique has been demonstrated in the rapid synthesis of eight pure deoxyribooligonucleotides constituting the sequence of human insulin A DNA. The sequence of each of the deoxyribooligonucleotides was confirmed by the two-dimensional mobility-shift method of finger-printing.     

Synthesis of phosphate-branched oligonucleotides

A solid-phase synthesis for phosphate-branched oligonucleotides is described. The method is based on coupling of a single nucleoside phosphorodiamidite to terminal hydroxyl functions of two solid-supported oligonucleotides. After oxidation of the phosphite triester obtained to a phosphate triester, the third branch is assembled by conventional phosphoramidite chemistry.     

Enzymatic and Hybridization Properties of Oligonucleotide Analogues Containing Novel Phosphotriester Internucleotide Linkage

Abstract

Enhanced cellular uptake, stable and discriminating hybridization and increased stability in biological media are of particular interest for oligonucleotides of potential therapeutic application. Additionally, toxicity or immunogenicity of the oligonucleotide analogues and their biodegradation products should be minimized by minimal alteration of the biological structure and effort and cost of bulk production should be as low as possible by using a standard automated synthesis protocol. Oligonucleotide phosphotriesters with oligoethyleneglycol substituents show promise to ideally combine all these advantages. Here we describe the hybridization properties and the stability of modified oligonucleotides containing triester internucleotide linkages substituted with α,ω-dihydroxy-(3,6-dioxa)-octan-1-yl group (“triethyleneglycol triester linkages”) towards enzymatic degradation. The triester linkages are stable towards exo- and endonucleases. Regardless of number and position of triester linkages, the modified oligonucleotides showed practically no decrease of T_m in hybridization studies with complementary biological oligonucleotides. In further enzymatic studies the modified oligonucleotides were highly stable towards nucleases in human blood serum.     

Efficient synthesis of the cholinephosphate phospholipid headgroup

In search of an efficient method to prepare cholinephosphate headgroups in phospholipids under mild conditions (where the diacylglycerol moiety is not subject to oxidation), a method was developed for phosphorylation using a trialkyl phosphite and I2. The active intermediate is a phosphoryl iodide formed by oxidation of the phosphite with I2. 2-Bromoethanol, dimethyl chlorophosphite, and an alcohol (diglyceride) are converted to a phosphate triester in a one-pot reaction with high yield. In the second reaction, the phosphate triester is demethylated, and the ethyl bromide group is converted to choline by treatment with aqueous trimethylamine. This procedure is applied to the synthesis of hexadecylphosphocholine, and 1,2-didecanoyl-1-deoxy-1-thio-sn-glyceryo-3-phosphocholine.     

Further improvements on the phosphotriester synthesis of deoxyribooligonucleotides and the oligonucleotide directed site-specific mutagenesis of E. coli lipoprotein gene.

Two improvements that greatly enhance the rate of phosphotriester oligonucleotide synthesis are described: 1) use of hindered primary amines, e.g. t-butyl amine for decyanoethylation of oligonucleotide triester intermediates, and 2) a simplified isolation procedure that eliminates the tedious bicarbonate extraction after each condensing reaction. Using the improved procedures, oligonucleotide fragments can be synthesized as rapidly as using solid phase chemistry. The final products are purer than those obtained by solid phase chemistry since each intermediate block is purified by chromatography. The technique has been used to synthesize five oligonucleotide fragments (size 15 to 20) for the purpose of performing guided site-specific mutagenesis on a cloned E. coli lipoprotein gene.     

The chemical composition of uropygial gland secretions from ralliformes

The uropygial gland wax from rails contains ester waxes, triester waxes and triglycerides. The ester waxes are composed of mainly methyl-substituted fatty acids with predominantly n-alkanols. Methyl-branched alcohols are only found in minor amounts. The occurrence of 2,6,10- and 4,8,12-trimethyl-substituted acids can be used as chemotaxonomie markers. The triester waxes contain n-fatty acids, n-alkanols and alkyl-hydroxymalonic acids.     

Synthesis of oligonucleotides with sequences identical with or analogous to the 3''-end of 16S ribosomal RNA of Escherichia coli: preparation of A-C-C-U-C-C via the modified phosphotriester method.

A combination of two different methods for the synthesis of oligoribonucleotides, i.e. the two-step phosphotriester method with 2-chlorophenyl phosphate as bifunctional phosphate source and the modified triester method with 2,2,2-trichloroethyl 2-chlorophenyl phosphorochloridate as monofunctional phosphate source, is applied for the synthesis of the fully-protected hexaribonucleotide A-C-C-U-C-C. The two-step method is used for the synthesis of the required dinucleotide monophosphates 9, 10 and 11. Application of the modified triester method for the coupling of the oligonucleotide blocks results in the formation of the fully-protected hexamer 15. Furthermore, attention is paid to 2,4,6-triisopropylbenzenesulphonyl 4-nitroimidazolide as a new condensing agent for the coupling of larger oligonucleotide blocks.     

l-Methyl-Z-(2′-Hydroxyphenyl)Imidazole–A Catalytic Phosphate protecting group in deoxyoligonucleotide synthesis

Abstract

The rate of condensation using the phosphate triester method of deoxyoligonucleotide synthesis is dramatically increased by the introduction of a phosphate protecting group bearing a nuclcophilic catalyst in the proper position. Following condensation (resulting in the formation of a phosphate triester) the catalytic protecting group can be removed leaving a dinucleotide, or the condensation reaction can be repeated to synthesize an oligonucleotide. This development is a significant advance in the chemical synthesis of deoxyoligonucleotides.     

Solid-phase synthesis of the nucleopeptide fragment H-Asp-Ser[pAAAGTAAGCC]-Glu-OH from the nucleoprotein of Bacillus subtilis phage phi 29.

The naturally occurring DNA-nucleopeptide H-Asp-Ser[5'-pAAAGTAAGCC-3']-Glu-OH was prepared via a solid-phase phosphite triester approach using N-2-(tert-butyldiphenylsilyloxymethyl)benzoyl protected nucleosides. The oligonucleotide was linked via the extremely base-labile oxalyl ester anchor to the solid support.     

Formation of 4,4'-dimethoxytrityl-C-phosphonate oligonucleotides

Incomplete sulfurization during solid-phase synthesis of phosphorothioate oligonucleotides using phosphoramidite chemistry was identified as the cause of formation of two new classes of process-related oligonucleotide impurities containing a DMTr-C-phosphonate (DMTr=4,4'-dimethoxytrityl) moiety. Phosphite triester intermediates that failed to oxidize (sulfurize) to the corresponding phosphorothioate triester react during the subsequent acid-induced (dichloroacetic acid) detritylation with the DMTr cation or its equivalent in an Arbuzov-type reaction. This leads to formation of DMTr-C-phosphonate mono- and diesters resulting in oligonucleotides modified with a DMTr-C-phosphonate moiety located internally or at the 5'terminal hydroxy group. DMTr-C-phosphonate derivatives are not detected when optimized sulfurization conditions are employed.     

Digestion in vitro of erythritol esters by rat pancreatic juice enzymes

The mechanism of the digestion of erythritol esters was determined using rat pancreatic juice and purified pancreatic lipase (EC 3.1.1.3). Conditions of hydrolysis were used that would selectively activate or inactivate nonspecific lipase or lipase. It was shown that erythritol tetraoleate was hydrolyzed by nonspecific lipase but not by lipase. The initial digestion product was a triester, predominantly erythritol-1,2,3-trioleate. Thus, nonspecific lipase preferentially hydrolyzed the ester of a primary alcohol. In contrast to the results obtained with the tetraester, lipase could remove a fatty acid from the triester but the resulting erythritol-2,3-dioleate was not hydrolyzed by lipase. The selectivity of this hydrolysis and the inability to hydrolyze the diester are attributed to the known specificity of this enzyme to act only on esters of primary alcohols. Nonspecific lipase completely hydrolyzed erythritol tetraoleate to free erythritol in a stepwise manner. The relative rates of these reactions were tetraester --> triester --> diester --> monoester --> erythritol Because of the specificity of pancreatic lipase and the lack of specificity of nonspecific lipase it is likely that this latter enzyme is the primary agent for the hydrolysis of erythritol esters in the intact animal.     

Polyesters Based on Linoleic Acid for Biolubricant Basestocks: Low-Temperature,Tribological and Rheological Properties

Presently, plant oils which contain high percentage of linoleic acid 1 are perceived to be a viable alternative to mineral oil for biolubricant applications due to their biodegradability and technical properties. In order to get biodegradable lubricant, triester derivatives compounds (1–5) were synthesized and characterized. The processes involved were monoepoxidation of linoleic acid 2, oxirane ring opening 3, esterification 4 and acylation 5. The structures of the products were confirmed by FTIR, ¹H and ¹³C-NMR and LC-MS. The results that showed lowest temperature properties were obtained for triester 5, with a pour point value (PP) of -73°C, highest onset temperature (260°C) and lowest volatility at 0.30%. Viscosity index (VI) increased for the ester’s synthetic compounds (2, 3, 4, 5), while the PP decreased. This behavior is the result of the increase of the chain length of the branching agents. Triester based linoleic acid has improved properties such as low-temperature and tribological properties. These results will make it feasible for plant oil to be used for biolubricants, fuels in chain saws, transmission oil and brake fluid.     

Effects of a trinucleotide ethyl phosphotriester, Gmp(Et)Gmp(Et)U, on mammalian cells in culture

The nonionic 2'-O-methyribooligonucleotide ethyl phosphotriester, Gmp(Et)Gmp(Et)U, is complementary to the...ApCpC...sequence found in the amino acid accepting stem of most tRNAs and the anticodon region of tRNAgly and to the threonine codon of mRNA. Gmp(Et)Gmp(EtU forms hydrogen-bonded complexes with the amino acid accepting stem of tRNApheyeast and unfractionated tRNA Escherichia coli under physiological salt conditions at 37 degrees C as determined by equilibrium dialysis. The extent of phenylalanine aminoacylation of tRNApheE.coli is inhibited 39% by Gmp(Et)Gmp(Et)U at 37 degrees C in solution. The triester is resistant to hydrolysis by serum nucleases and cell lysates. The triester is readily taken up by transformed Syrian hamster fibroblasts growing in monolayer. Within the cell, the triester is deethylated to give the trinucleotide species Gmp(Et)GmpU, GmpGmp(Et)U, and GmpGmpU and is also hydrolyzed to dimeric and monomeric units. Treatment of transformed fibroblasts in monolayer with 25 micronM Gmp(Et)Gmp(Et)U results in a 40% inhibition of cellular protein synthesis with a concurrent slight increase in cellular RNA synthesis during the first 4 h. After 4 h, the rate of cellular protein synthesis begins to recover while RNA synthesis returns to that of the control. Our biochemical studies suggest that inhibition of cellular protein synthesis might be expected if Gmp(Et)Gmp(Et)UGmp(Et)GmpU, GmpGmp(Et)U, and GmpGmpU, which have been taken up by or formed within the cell, physically bind to tRNA and mRNA and inhibit the function of these nucleic acids. The reversible inhibition of protein synthesis may be a consequence of further degradation of the trinucleotide species within the cell as well as to an increase in supply of RNA molecules involved in protein synthesis. The growth of the transformed fibroblasts is inhibited during the first 24 h of incubation with 25 micronM Gmp(Et)Gmp(Et)U after which growth proceeds at a normal rate. In cloning experiments, the number and size of colonies formed by the transformed fibroblasts after 5 days exposure to 25 micronM triester is decreased by 50% relative to untreated controls. The temporary inhibition of cell growth may reflect the transitory inhibition of cellular protein synthesis caused by the triester.     

Sulfurization Efficiency in the Solution Phase Synthesis of Deoxyribonucleoside Phosphorothioates - Comparison of Sulfur Triethylamine with Various Sulfurizing Agents 1

Abstract

Efficient solution-phase synthesis of nucleoside phosphorothioates utilizing phosphoramidite approach is described. Elemental sulfur in combination with triethylamine is the prefered choice for sulfurization of phosphite triester to phosphorothioates.

     

Trichloro-tert.-butyl-cyclic-enediol-phosphate (TCB-CEP), Proposed Reagent for the Syntheses of Oligonucleotides Using the Triester Approach

Abstract

Protected nucleosides, phosphorylated using 4, 5-dimethyl-2-oxo-2-trichloro-tert.-butyl-l, 3, ^λ5-dioxaphos-pholene, can be cleaved to yield either 5′- or 3′-building blocks for triester syntheses.