A Novel Real-time Fluorescence Mutant-allele-specific Amplification Method for Rapid Single Nucleotide Polymorphism Analysis

Current methods for single nucleotide polymorphism (SNP) analysis are time-consuming and complicated. We aimed at development of one-step real-time fluorescence mutant-allele-specific amplification (MASA) method for rapid SNP analysis. The method is a marriage of two technologies: MASA primers for target DNA and a double-stranded DNA-selective fluorescent dye, SYBR Green I. Genotypes are separated according to the different threshold cycles of the wild-type and mutant primers. K-rar oncogene was used as a target to validate the feasibility of the method. The experimental results showed that the different genotypes can be clearly discriminated by the assay. The real-time fluorescence MASA method will have an enormous potential for fast and reliable SNP analysis due to its simplicity and low cost.     

New phosphonic analogs of aspartic and glutamic acid by aminoalkylation of trivalent phosphorus chlorides with ethyl acetyloacetate or ethyl levulinate and benzyl carbamate

Preparation of the phosphonic analogs of -methylaspartic (4 a–d), glutamic (7 a–b) and -methylpyroglutamic (5 a–b) acids by aminoalkylation of trivalent phosphorus chlorides with ethyl esters of oxoalkyloacids and benzyl carbamate is described. The phosphonic analogs of pyroglutamic acid (8 a–b) was obtained by the cyclization of the corresponding esters (9 a–b). The stability of the phosphonic analogs of pyroglutamic acid in acidic and alkaline media was also studied.

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Die Herstellung von neuen Phosphonanalogen der Asparagin- und Glutaminsäure in der Reaktion von trivalenten Phosphorchloriden mit Ethyl-acetyloacetat oder Ethyl-lävulinat bzw. Benzylcarbaminat

Zusammenfassung Es wurde die Darstellung der Phosphonanalogen der -Methylasparaginsäure (4 a–d), Glutamin- (7 a–b) und -Methylpyroglutaminsäure (5 a–b) in der Reaktion der trivalenten Phosphorchloride und der Oxoalkansäureethylester sowie des Benzylcarbaminats beschrieben. In der Ringschlußreaktion der Ester (9 a–b) erhält man Phosphonanaloge der Pyroglutaminsäure. Die Stabilität der Analogen der Pyroglutaminsäure wurde in sauren und alkalischen Medien geprüft.

     

Selective one-pot synthesis of substituted pyrrole-3-phosphonates from α-cyanomethyl-β-ketoesters

A one-step synthesis of 5-alkoxypyrrole-3-phosphonates is presented starting from suitable α-cyanomethyl-β-ketophosphonates. The key step in the synthesis involves a one-pot addition and heteroannulation sequence. The zinc perchlorate-catalyzed addition of alcohols to the nitrile carbon of α-cyanomethyl-β-ketophosphonates followed by annulation furnished 5-alkoxypyrrole-3-phosphonates. The addition-annulation process is carried out in the presence of water and 4,5-dihydro-5-oxo-1H-pyrrole-3-phosphonates (pyrrolinones) are obtained in good yields.     

亚氨基二乙酸—硅胶键合相的合成及其在核苷酸分析中的应用

以大孔微球硅胶（３０ｎｍ，８μｍ）为基体，经γ－氨丙基三乙氧基硅烷活化与间隔臂氯代环氧丙烷反应后，再与螯合剂亚氨基二乙酸键合，后者与铜离子（Ⅱ）螯合后，构成定位金属离子亲和色谱固定相。用磷酸盐缓冲溶液（ｐＨ＝７．０）作流动相，经紫外吸收检测（２６０ｎｍ）对核苷酸混合物进行了高效液相色谱分析，取得较满意的结果。     

Mitsunobu reactions of nucleoside analogs using triisopropyl phosphite-DIAD

Herein, we report the use of triisopropyl phosphite (TIP) as an effective substitute for triphenylphosphine in the Mitsunobu reaction of nucleoside analogs. In addition, the use of triphenyl phosphite as an alternative reagent for the expensive hexamethylphosphorous triamide (HMPT) in the Véliz-Beal bromination protocol is reported.     

Detection of single nucleotide polymorphisms using electrospray ionization mass spectrometry: validation of a one-well assay and quantitative pooling studies

Single nucleotide polymorphisms (SNPs) are currently being mapped and databased at a remarkable pace, providing a viable means for understanding disease susceptibility, differential drug response and human evolution. Consequently, there is an increasing demand for SNP genotyping technologies that are simple, rapid, cost effective and readily amenable to automation for high-throughput analyses. In this study, we improved the Survivor Assay, a SNP detection method based on electrospray ionization mass spectrometry (ESI-MS), with several developments. One improvement is the development of a one-well assay, requiring no off-line purification of the polymerase chain reaction product, achieved by simple addition of reagent solution into a single well. Another is the on-line separation of magnesium and dideoxynucleotides using an in-house made monolithic metal chelating column, eliminating any off-line sample preparation prior to mass spectrometric analysis. Here the Survivor Assay is extended from a proof-of-principle concept to a validated method by genotyping six SNPs from five different regions of human genomic DNA in 55 individual samples with 100% accuracy. This improved Survivor Assay eliminates the tedious and time-consuming steps of sample preparation, minimizes sample handing and offers a high-throughput analysis of SNPs by ESI-MS. The current combined preparation and analysis time is 2 min per sample. The simplicity of this method has potential for full automation and parallel chromatography and, thus, reduced analysis time. In addition, we have adapted the Survivor Assay for quantitative SNP analysis in pooled DNA samples. The capabilities and sensitivity of this approach were evaluated. We demonstrate that an allele occurring at a frequency of 2% can consistently be quantitated.     

Applications of homemade kit in mutation detection of genes

With the accomplishment of Human Genome Project (HGP), single nucleotide polymorphism (SNP) and mutation detection in human genome are becom-ing a new researching focus. These researches can help us to understand the phenotype diversity of indi-vidual, disease susceptibility and drug resistance of different colonies. Traditional method used for muta-tion detection is slab gel electrophoresis, which re-mains labor-intensive and time-consuming because of the requirement of radioactivity or te…     

Synthesis of (α-substituted α-aminophosphinic and α-aminophosphonic acids

The reaction of ketoximes with hypophosphorous acid resulted in previously unknown -substituted--aminophosphinic acids, which were oxidized into the corresponding -substituted--aminophosphonic acids.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2729–2732, November, 1996.     

A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

Summary The effect of the substitution in position 1 on the low-energy conformations of the oxytocin/vasopressin 20-membered ring was investigated by means of molecular mechanics. Three representative substitutions were considered: -mercapto-,-dimethyl)propionic acid (Dmp), (-mercapto-,-cyclopentamethylene)propionic acid (Cpp), both forming strong antagonists, and (,-dimethyl--mercapto)propionic acid (-Dmp), forming analogs of strongly reduced biological activity, with the -mercaptopropionic (Mpa) residue taken as reference. Both ECEPP/2 (rigid valence geometry) and AMBER (flexible valence geometry) force fields were employed in the calculations. Three basic types of backbone conformations were taken into account which are distinguished by the type of -turn at residues 3 and 4: 1/III, II, and I/III, all types containing one or two intra-annular hydrogen bonds. The allowed (ring-closed) disulfide-bridge conformations were searched by an algorithm formulated in terms of scanning the disulfide-bridge torsional angle C-S-S-C. The ECEPP/2 and AMBER energies of the obtained conformations were found to be in reasonable agreement. Two of the low-energy conformers of the [Mpa¹]-compound agreed very well with the cyclic part of the two conformers found in the crystal structure of [Mpa¹]-oxytocin. An analysis of the effect of -substitution on relative energies showed that the conformations with the N-C-CH₂-CH₂ (₁) and C-CH₂-CH₂-S (₁) angles of the first residue around (–100°, 60°) and (100°, –60°) are not affected; this in most cases implies a left-handed disulfide bridge. In the case of -substitution the allowed values of ₁ are close to ± 60°. This requirement, being in contradiction to the one concerning -substitution, could explain the very low biological activity of the -substituted analogs. The conformational preferences of substituted compounds can largely be explained by the analysis of local interactions within the first residue. Based on the selection of the conformations which are low in energy for both the reference and -substituted compounds, two distinct types of possible binding conformations were proposed, the first one being similar to the crystal conformer with a left-handed disulfide bridge, the second one having a right-handed bridge, but a geometry different from that of the crystal conformer with the right-handed bridge. The first type of disulfide-bridge arrangement is equally favorable for both I/III and II types of backbone structure, while the second one is allowed only for the II type of backbone. No conformation of the I/III type has a low enough energy to be considered as a possible binding conformation for all of the active compounds studied in this work.     

Superbeads: immobilization in "sweet" chemistry

Enzymatic oligosaccharide synthesis using recombinant glycosyltransferases is able to overcome the difficulties associated with chemical methods. Nonetheless, sugar nucleotide regeneration cycles are necessary for the glycosylation. The multistep enzyme reaction can be efficiently carried out on superbeads that are prepared by immobilizing multienzyme mixtures on bead support through fused binding domains.