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.     

Reactions of 3,5-di(tert-butyl)-1,2-benzoquinone with terminal acetylenes in the presence of phosphorus trichloride. ipso-Substitution of the tert-butyl group

The reactions of 3,5-di(tert-butyl)-1,2-benzoquinone with aryl-and alkylacetylenes in the presence of phosphorus trichloride afford 4-aryl(alkyl)-8-tert-butyl-2,6-dichloro-2-oxo-2H-benzo[e][1,2]oxaphosphinines as the major ipso-substitution products of the tert-butyl group by the chlorine atom. 4-Aryl(alkyl)-6,8-di(tert-butyl)-2,5-dichloro-2-oxo-and 4-aryl(alkyl)-6-tert-butyl-2,8-dichloro-2-oxo-2H-benzo[e][1,2]oxaphosphinines were obtained as the minor products. The structures of the stable representatives of this series were confirmed by X-ray diffraction. Dedicated to Academician G. A. Abakumov on the occasion of his 70th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1836–1845, September, 2007.     

Crystal structure and spectroscopic study of di-μ(1,1)-azido-di-μ(0,0-nitrato)tetrakis(3,5-lutidine)dicopper(II), [Cu(N3) (NO3) (3,5-lutidine)2]2

A mixed ligand 12 complex of copper(II) azide with 3,5-lutidine, namely di-(1,1)-azido-di(0,0)-nitrato)tetrakis(3,5-lutidine)dicopper(II) has been prepared and characterized by X-ray crystallographic and spectroscopic methods. The dimeric molecule, which possesses a crystallographic inversion center, contains two(1,1) bridging azido ligands. Each copper(II) atom in the cyclic Cu₂N₂ unit is further coordinated by two oxygen atoms from two(0,0-nitrato) bridges at Cu-O distances of 2.465(3) and 2.568(3) Å and two nitrogen atoms from the lutidine molecules [Cu-N=2.003(3) and 2.012(3) Å] to give a distorted tetragonal bipyramid. Both azido ligands are linear [N-N-N angle=179.0(4) and asymmetric N-N=1.207(4) and N-N=1.135(5) Å]. The azido bridges produce a rather short Cu Cu distance of 3.013(2) Å. Infrared and electronic data are presented and discussed.     

Self-inclusion properties of C60-linked calix[5]arene

C₆₀-linked calix[5]arenes were synthesized and their intramolecular binding properties were investigated. The self-inclusion ratio of the C₆₀ moiety was determined by using UV-vis spectroscopy, and the ratio depends on chain length, temperature, and solvent. Influence of temperature and solvent was explained by the thermodynamic data of the intramolecular complex formation process.     

A conductance study of the association of alkali cations with 1,13-dibenzo-24-crown-8 in acetonitrile

A conductance study concerning the association of Na⁺, K⁺, Rb⁺, and Cs⁺ with 1,13-dibenzo-24-crown-8 in acetonitrile has been carried out at 35, 30, 25, 20, and 15°C. The observed molar conductivities were found to decrease significantly for mole ratios less than unity. A model involving 11 stoichiometry has been used to analyze the conductivity data. The stability constant, K, and the molar conductivity _C for each 11 complex were determined from the conductivity data by using a nonlinear least squares curve fitting procedure. The binding sequence, based on the value of log K at 25°C, is found to be Rb⁺>Cs⁺>K⁺>Na⁺. Values of H^o and S^o are reported and their significance is discussed.     

Preparation and characterization of Mg(II)-, Ca(II) and Cd(II) complexes of 1,2-ethanediol and water

Mixed ligand complexes of different compositions were prepared with water, sulfate ion and 1,2-ethanediol as ligand. IR spectra and the thermoanalytical curves of the complexes were recorded. Oxygen atoms bound by one or two coordinate bonds to the metal ion, or by hydrogen-bonds in the crystal, were observed. As for the water molecule, 1,2-ethanediol molecules of crystal and monohydrate type were found, depending on the type of binding of the oxygen atoms.This revised version was published online in November 2005 with corrections to the Cover Date.     

PPh3催化Mannich反应机理的密度泛函研究

通过密度泛函理论研究了PPh3催化苯胺、苯甲醛和乙酰乙酸乙酯三组分Mannich反应的机理.计算结果表明该机理主要分3个步骤进行:PPh3催化乙酰乙酸乙酯发生酮式-烯醇式互变异构得到烯醇;烯醇辅助苯胺和苯甲醛缩合并脱水生成亚胺;亚胺和烯醇通过加成反应生成β-氨基羰基化合物.通过详细的机理研究,发现烯醇从亚胺的背面进攻其亲电C原子的过渡态的相对能量更低,容易得到反式的产物,对实验观察到的非对映选择性进行了合理的解释.     

Dual chemosensing properties of new anthraquinone-based receptors toward fluoride ions

Novel colorimetric receptors 1-[(2-hydroxy-5-bromo-benzylidene)-amino]-anthraquinone, 1-[(2-hydroxy-5-methyl-benzylidene)-amino]-anthraquinone, and 1-[(2-hydroxy-5-nitro-benzylidene)-amino]-anthraquinone have been synthesized as fluoride ion sensors. A color change was observed visually (naked-eye) upon addition of fluoride ions in organic solvents to solutions of the receptors.     

Novel separation method for highly sensitive speciation of cancerostatic platinum compounds by HPLC–ICP–MS

A high-performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC–ICP–MS) method is presented for analysis of cisplatin, monoaquacisplatin, diaquacisplatin, carboplatin, and oxaliplatin in biological and environmental samples. Chromatographic separation was achieved on pentafluorophenylpropyl-functionalized silica gel. For cisplatin, carboplatin, and oxaliplatin limits of detection of 0.09, 0.10, and 0.15 g L^–1, respectively, were calculated at m/z 194, using aqueous standard solutions. (3 L injection volume). The method was utilized for model experiments studying the stability of carboplatin and oxaliplatin at different chloride concentrations simulating wastewater and surface water conditions. It was found that a high fraction of carboplatin is stable in ultrapure water and in solutions containing 1.5 mol L^–1 Cl^–, whereas oxaliplatin degradation was increased by increasing the chloride concentration. In order to support the assessment of oxaliplatin eco-toxicology, the method was tested for speciation of patient urine. The urine sample contained more than 17 different reaction products, which demonstrates the extensive biotransformation of the compound. In a second step of the study the method was successfully evaluated for monitoring cancerostatic platinum compounds in hospital waste water.