Use of 2-methylsulfonylethyl as a phosphorus protecting group in oligonucleotide synthesis via a phosphite triester approach

2-Methylsulfonylethoxy dichlorophosphine has been converted into the mono-N-morpholino derivative and applied for the preparation of 5′-O,N-protected d-nucleoside-3$\text{-}\text{?}$phosphoramidites. The latter intermediates could be used in the presence of 1-hydroxybenzotriazole for the formation of 3′-5′-phosphotriester linkages. The MSE protecting group can be removed selectively and fast under mild basic conditions.     

New intermediates for the synthesis of oligonucleotides by the phosphite triester approach

Heterocyclic bases such as triazole and tetrazole have been used to increase selectivity of phosphorylation of nucleosides in oligonucleotide synthesis $\text{via}$ the phosphite triesters.     

亚磷酸三酯法合成葡萄糖磷酸酯

本文叙述了具有一个游离羟基的葡萄糖衍生物与试剂CH3OPCl2反应生成糖的方法, 包括逐步取代试剂上两个氯原子, 将生成的亚磷酸酯氧化成磷酸酯及最后的氨解去甲基反应. 运用这个方法制备了三个单糖磷酸三酯, 四个双糖磷酸三酯及一个双糖磷酸二酯. CH3OPCl2 中第一个氯原子被糖衍生物取代后,第二个氯原子可用被伯醇丶仲醇或另一个糖基取代. 但叔醇在相同条件下不发生取代反应. 两个氯原子被取代后生成的亚磷酸酯是一类不稳定的化合物, 在醇中易被醇解. 应用叔丁胺脱去磷酸甲酯上的甲基生成双糖磷酸二酯是一种较理想的方法. 反应操作简便, 产率高.对二异丙叉葡萄糖磷酸酯衍生物质谱图的主要碎片峰所进行的解析表明, 它们的断裂具有一定的规律, 这个方法可以用鉴定此类化合物的有用手段.     

Synthesis of glucose phosphate derivatives by the phosphite triester method

Synthesis of sugar phosphate derivatives by means of phosphite triester method is described. Seven glucose phosphotriester derivatives have been prepared, i.e. dimethyl, methyl n-propyl, and methyl isopropyl (1, 2:5, 6-di-O-isopropylidene-α-D-glucofuranose-3-) phosphate (5, 7 and 8); methyl bis-(1, 2:5, 6-di-O-isopropylidene-α-D-glucofuranose-3-) phosphate (6); methyl bis-(1, 2, 3, 4-tetra-O-acetyl-β-D-glucopyranose-6-) phosphate (9); methyl bis-(1, 2-O-isopropylidene-3,5-O-benzylidene-α-D-glucofuranose-6-) phosphate (10); and methyl (1, 2, 5, 6-di-O-iso-propylidene-α-D-glucofuranose-3-) (1, 2, 3, 4-tetra-O-acetyl-β-D-glucopyranose-6-) [phosphate (11). The results of the displacement of second chlorine atom of the reagent by different alcohols showed that methanol, n-propanol, isopropanol and as well as the glucose derivatives reacted normally to give the expected phosphite esters which yield the expected phosphate products after oxidation, but not the t-butanol. Removal of methyl group from a phosphotriester linkage can be easily achieved by the action of t-butyl amine and thus, t-butyl ammonium bis-(1, 2:5, 6-di-O-isopropylidene-α-D-glucofuranose-3-) phosphate t-butyl amine salt (12) has been obtained from its parent phosphotriester in nearly quantitative yield. The mass spectra data of di-O-isopropylideneglucose phosphate reveals that the cleavage of these compounds follows a general pattern and can be used for their characterization.     

Large scale synthesis of oligoribonucleotides on PEG by the phosphite triester approach

Large scale synthesis of oligoribonucleotides has been successfully performed on PEG support by the phosphoramidite approach using t-butyldimethylsilyl to protect the 2'-hydroxyl group of ribonucleoside. By means of this procedure, the dodecamer r(AGUGGUCUUUGU) was synthesized in 98.1% average coupling yield, and 55 mg pure product was obtained from one gram of functionalized PEG.     

Solid-phase triester synthesis of modified triuridylates using an effective condensing agent

Triuridylates containing 2-deoxyuridine, 5-bromouridine, and 6-azauridine in various positions of the sequence have been synthesized by the use of an O-nucleophilic nucleotide condensation catalyst — 4-ethoxypyridine N-oxide — under the conditions of the solid-phase triester method.Institute of Molecular Biology and Genetics, Ukrainian SSR Academy of Sciences, Kiev. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 416–421, May–June, 1988.     

Rapid preparation of hexanucleotide triester blocks fior use in polydeoxyribonucleotide synthesis

Hexanucleotide phosphotriester blocks suitable for use in the construction of polydeoxyribonucleotides can be synthesized in high yield by a rapid procedure involving simple extractive purification of intermediates.     

Linkers for oligonucleotide microarray synthesis

A number of linkers for microchip-based (microarray) synthesis of oligonucleotides were synthesized here using photolabile intermediates. The resulting linkers are designed for covalent immobilization on slides containing both hydroxyl and amino groups.The first series of linkers was intended for the synthesis of oligonucleotide arrays for hybridization analysis. These linkers provide a strong covalent bond with the slide surface when amino groups in oligonucleotide heterocyclic bases are deprotected.The second series of linkers allows to cleave the synthesized oligonucleotides from the support on which they were synthesized. Furthermore, the use of such linkers yields oligonucleotides devoid of the phosphate group at their 3′ end.The obtained linkers were successfully tested in the synthesis of oligonucleotides on a microchip for subsequent hybridization analysis and assembly of a DNA fragment.     

Facile synthesis of oligonucleotide phosphoroselenoates

Se-(2-cyanoethyl)phthalimide was synthesized from di-(2-cyanoethyl) diselenide. This reagent was found to be an efficient selenium transfer reagent in the synthesis of selenophosphates. Thus, nucleotide H-phosphonate diesters that are formed in situ through the H-phosphonate chemistry undergo quantitative reaction with Se-(2-cyanoethyl)phthalamide. The resulting Se-(2-cyanoethyl) oligonucleotide phosphoroselenoate triesters are subsequently deprotected to give oligonucleotide phosphoroselenoate diesters in excellent yields.     

A method for solid-phase synthesis of oligonucleotide 5'-peptide-conjugates using acid-labile alpha-amino protections

We describe the development of a solid-phase technique for the synthesis of 5'-peptide-oligonucleotide conjugates (POCs) with a uniform protection strategy for the nucleic acid and the peptide fragments. On the alpha-amino function, the amino acid building blocks were protected with the 2-(biphenyl-4-yl)propan-2-yloxycarbonyl (Bpoc) group. This protection is removed during the stepwise peptide elongation by the same acidic conditions used for removal of the dimethoxytrityl (DMT) group used in the oligonucleotide assembly (3% trichloroacetic acid, 2 min). The 2-(3,5-dimethoxyphenyl)propan-2-yloxycarbonyl (Ddz) group was also tested. With this somewhat more stable group, a prolonged contact with the acid (at least 16 min) was required for accomplishing complete alpha-amino deprotection, which resulted in some degree of depurination of the acid-sensitive DNA chain. Base-labile acyl protections were adopted for the side-chains of histidine, lysine, and the nucleobase amino functions. These were all removed in the final deblocking step by ammonolysis. This uniform protection scheme for the peptide and the oligonucleotide enabled the total stepwise synthesis of model conjugates in the 3' --> N direction with high efficiency and purity.     

Active monomeric nucleotide intermediate in the oligonucleotide synthesis

The interaction of 3′ - O - acetylthymidine - 5′ - phosphate (pT-Ac) and p - nitrophenylphosphate (pPhNO₂) with triisopropylbenzenesulphonyl chloride (TPS) in pyridine was studied by the pulsed NMR spectroscopy on ³¹P nuclei. The esters investigated were shown to convert to the corresponding disubstituted pyrophosphates, trisubstituted tripolyphosphates and compounds showing a singlet displaced 5–8 ppm from the original ester. The latter are the main final products of the interaction of nucleotide and pPhNO₂ with TPS. The investigation of the chemical conversion of a pT-Ac derivative with a 5·1 ppm shift showed that this product is a powerful phosphorylating reagent. It was shown that this active derivative contains one P atom in accordance with the structure of monomeric metaphosphoric acid ester proposed by Todd for these compounds. The reaction of monomeric metaphosphate with 5′-O-tritylthymidine results information of a compound, containing stoichiometric amounts of pT-Ac and 5′ - O - tritylthymidilyl - (3′ → 5′) - 3′ - O - acetylthymidine residues. This compound was identified as a trisubstituted P¹ - 5′ - O - trityl - P¹ - P² -bis -(3′ - O - acetylthymidine) - pyrophosph     

Kinetics and thermodynamics of synthesis of palm oil-based trimethylolpropane triester using microwave irradiation

Enhancement of reaction performance utilizing microwave irradiation has drawn so much interest due to its shorter reaction time and low catalyst loading. These advantages are particularly significant from kinetics and thermodynamics perspectives. This study aimed to investigate the kinetics and thermodynamics of microwave-assisted transesterification of palm oil-based methyl ester into biolubricant. The transesterification reaction of palm oil methyl ester (PME) and trimethylolpropane (TMP) was conducted at 110–130 °C for 90 min under vacuum condition. Sodium methoxide was employed as the catalyst at 0.6 wt% of reactants fixed at molar ratio of 4:1 (PME: TMP). The experimental data were fitted with the second-order reversible reaction kinetics mechanisms. The data were solved via Runge-Kutta 4,5 order using MATLAB software. Analysis on the data revealed that the reaction rate constants at temperatures of 110–140 ℃ were in the range of 0.01–0.63 [(w/w)(min)]⁻¹, with standard errors of 0.0026–0.0228 within 99.99% prediction interval. Microwave-assisted reaction obtained 17.0 kcal/mol of activation energy. This method reduced activation energy by 49% as compared to the conventional heating. Activation energy and time-periodic energy assessment showed that the reaction was endothermic. The reaction at 130 °C is the easiest to activate. The positive Gibbs free energy (ΔG > 0) found using Eyring-Polanyi equation indicated that the transesterification was non-spontaneous and endergonic.     

O-selectivity and utility of phosphorylation mediated by phosphite triester intermediates in the N-unprotected phosphoramidite method

Previously, O-selective phosphorylation on polymer supports in the N-unprotected phosphoramidite method could not be carried out because the amino groups of dA and dC have high reactivity toward tervalent phosphorus(III)-type phosphitylating reagents. In this paper, we developed a new coupling strategy named the "activated phosphite method" in which the phosphitylation is mediated by phosphite triester intermediates 1. Application of 1-hydroxybenzotriazole as the promoter to the solid-phase synthesis resulted in excellent O-selectivity of more than 99.7%. This O-selectivity was explained by the frontier molecular orbital interactions between the reactive intermediates and the nucleophiles such as the amino or hydroxyl groups of nucleosides. Furthermore, longer oligonucleotides were synthesized not only by a manual operation but also by a DNA synthesizer. The utility of our new method was demonstrated by the successful synthesis of a base-labile modified oligodeoxyribonucleotide having 4-N-acetyldeoxycytidine residues. Finally, DNA 20-mers containing dA or dC could be synthesized in good yields by use of a combined reagent of 6-trifluoromethyl-1-hydroxybenzotriazole and benzimidazolium triflate.     

In-situ synthesis of PHEMA magnetic nanogels via photochemical method

One-pot synthesis of magnetic nanogels via photochemical method is reported in this paper. Poly(2-hydroxyethyl methacrylate)(PHEMA) magnetic nanogels are synthesized by in-situ polymeriza-tion of 2-hydroxyethyl methacrylate(HEMA) and N,N'-methylene-bis-(acrylamide)(MBA) in Fe3O4 aqueous suspension under UV irradiation. The structure and compositions of magnetic nanogels are characterized by FTIR,TGA,SEM,TEM and PCS. TGA measurement indicates that magnetic nanogels contain 90% magnetite. Both naked Fe3O4 and magnetic nanogels are superparamagnatic at room temperature according to magnetization curves. The swollen capability of the hydrogel shell is proved by contrasting the particles sizes obtained by SEM,TEM and PCS. Particle diameters can be manipu-lated by changing monomer concentration and irradiation time. A mechanism of the coating process is proposed.     

Nucleosides and nucleotides. 3. Polycondensation of thymidine-3'-phosphate by the triester method

Condensation of a mixture of 25 mole per cent of 5′-O-p-methoxy-trityl-thymidine3′-[(β-cyanoethyl)phosphate] and 75 mole per cent of thymidine 3′-[(β-cyanoethyl)phosphate] in pyridine yielded a mixture of oligonucleotides, the largest being the pentanucleotide. It was demonstrated that longer chains are not obtained due to the formation of a C-pyridinium-thymidine nucleotide. For avoiding this undesired side reaction, the condensation was carried out using sym.-collidine as solvent. The analogous side reaction was not observed, longer chains of oligonucleotide were not obtained, however.