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.     

A general approach toward the synthesis of C-nucleoside pyrazolo[1,5-a]-1,3,5-triazines and their 3',5'-bisphosphate C-nucleotide analogues as the first reported in vivo stable P2Y(1)-receptor antagonists

In our effort to identify potent purinergic P2Y(1) receptor antagonists as potent platelet aggregation inhibitors with enhanced metabolic stability, we developed an efficient route for the large-scale preparation of 2'-deoxy-C-nucleosides of pyrazolo[1,5-a]-1,3,5-triazine. The key strategic elements of this novel synthetic approach involved the following: (i) the use of a novel activating group, the N-methyl-N-phenylamino group, which was easily generated in high yield by treatment of the pyrazolo[1,5-a]-1,3,5-triazin-4-one (5) with phosphorus oxychloride and dimethylaniline under high pressure, (ii) a regio- and stereospecific palladium-mediated coupling reaction of the readily available unprotected glycal 1,4-anhydro-2-deoxy-D-erythro-pent-1-enitol (4b) and the 8-iodo derivative (16), and (iii) the stereoselective reduction of the ketone group of the furanosyl ring followed by the subsequent displacement of the N-methyl-N-phenylamino group upon treatment with methylamine. The beta configuration at the anomeric C-1' position of the glycal moieties was perfectly retained throughout this conversion. This procedure afforded 8-(2'-deoxy-beta-D-ribofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (21) and 8-(2'-deoxy-beta-D-xylofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (24) with an overall yield of 50% and 39%, respectively. Finally, the conversion of nucleosides 21 and 24 to the pyrazolotriazine C-nucleotides 3',5'-bisphosphate 2 and 3',5'-cyclophosphate 26 is also described herein and represents the first reported nucleotide derivatives within the pyrazolo[1,5-a]-1,3,5-triazine series. Preliminary biological testing has shown that compound 2 strongly inhibits ADP-induced human platelet aggregation and shape change and possesses significant efficacies 30 min after injection in rat, highlighting a strong P2Y(1)-receptor antagonist activity in vitro combined with a prolonged duration of action in vivo.     

A novel silver(i)-mediated DNA base pair

We have generated a novel silver(I)-mediated unnatural DNA base pair consisting of two 2,6-bis(ethylthiomethyl)pyridine nucleobases SPy. This metallo-base pair has a remarkably high pairing stability and selectivity which rivals that of the natural base pairs dA:dT and dC:dG. UV-melting experiments revealed that the dSPy:dSPy self-pair can replace natural base pairs at multiple sites and still form stable DNA duplexes.     

Aromatic ring synthesis by N-aminopyrrole diels-alder reaction. Total synthesis of juncusol

A total synthesis of the cytotoxic phytoalexin juncusol ($\text{1}$) is described.     

Solidification of semicrystalline polymers using a variable interface temperature model

Solidification of semicrystalline materials often occurs in significantly undercooled melts. The crystal growth process in such melts is convoluted due to the fact that the interface between the solid and liquid domains of the microscopic crystals is at an unknown temperature. However, it is possible to let the temperature of this interface be unspecified and solve the problem with a semianalytical method if the growth velocity is prescribed. Solutions for the temperature profiles in both solid and liquid phases are presented in this work, along with the interface temperature, for phase change processes controlled by the kinetics of crystallization rather than diffusion processes, which is typical for polymers. The method is used for one-dimensional problems in cartesian, cylindrical, and spherical geometries that correspond to commonly found microstructures. It is found that the temperature of the interface is significantly below the equilibrium melting point and a quasi steady-state regime is reached rapidly. Comparison with the classical Neumann's solution shows that the temperature profiles are similar but the position of the interface differs considerably. © 1996 John Wiley & Sons, Inc.     

Third-order Nonlinear Optical Properties of Octa-substituted Metal-free Phthalocyanine Thin Films

Third-order nonlinear optical susceptibility, χ⁽³⁾ of symmetrically octa-substituted metal-free phthalocyanine thin films measured by the third-harmonic generation technique are reported. The metal-free phthalocyanine has been found to show a χ⁽³⁾ (−3ω; ω,ω, ω) value as large as 7.73×10⁻¹² esu at 1.80 μm. The figure of merit, χ⁽³⁾/α, was estimated to be 4.17×10¹⁷ esu cm at 1.05 μm and 6.97×10¹⁶ esu cm at 1.65 μm. Both linear and third-order optical properties of liquid-crystalline metal-free phthalocyanines are discussed