Rapid PCR in a continuous flow device

Continuous flow polymerase chain reaction (CFPCR) devices are compact reactors suitable for microfabrication and the rapid amplification of target DNAs. For a given reactor design, the amplification time can be reduced simply by increasing the flow velocity through the isothermal zones of the device; for flow velocities near the design value, the PCR cocktail reaches thermal equilibrium at each zone quickly, so that near ideal temperature profiles can be obtained. However, at high flow velocities there are penalties of an increased pressure drop and a reduced residence time in each temperature zone for the DNA/reagent mixture, that potentially affect amplification efficiency. This study was carried out to evaluate the thermal and biochemical effects of high flow velocities in a spiral, 20 cycle CFPCR device. Finite element analysis (FEA) was used to determine the steady-state temperature distribution along the micro-channel and the temperature of the DNA/reagent mixture in each temperature zone as a function of linear velocity. The critical transition was between the denaturation (95 degrees C) and renaturation (55 degrees C-68 degrees C) zones; above 6 mm s(-1) the fluid in a passively-cooled channel could not be reduced to the desired temperature and the duration of the temperature transition between zones increased with increased velocity. The amplification performance of the CFPCR as a function of linear velocity was assessed using 500 and 997 base pair (bp) fragments from lambda-DNA. Amplifications at velocities ranging from 1 mm s(-1) to 20 mm s(-1) were investigated. The 500 bp fragment could be observed in a total reaction time of 1.7 min (5.2 s cycle(-1)) and the 997 bp fragment could be detected in 3.2 min (9.7 s cycle(-1)). The longer amplification time required for detection of the 997 bp fragment was due to the device being operated at its enzyme kinetic limit (i.e., Taq polymerase deoxynucleotide incorporation rate).     

Nucleophilic catalysis with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) for the esterification of carboxylic acids with dimethyl carbonate

1,8-Diazabicyclo[5.4.0]undec-7-ene (DBU) is an effective nucleophilic catalyst for carboxylic acid esterification with dimethyl carbonate (DMC). The reaction pathway of this new class of nucleophilic catalysis has been studied. A plausible, multistep mechanism is proposed, which involves an initial N-acylation of DBU with DMC to form a carbamate intermediate. Subsequent O-alkylation of the carboxylate with this intermediate generates the corresponding methyl ester in excellent yield. In the absence of DBU or in the presence of other bases, such as ammonium hydroxide or N-methylmorpholine, the same reaction affords no desired product. This method is particularly valuable for the synthesis of methyl esters that contain acid-sensitive functionality.     

Chemistry of the phenoxathiins and isosterically related heterocycles. XXXI. Synthesis of the 1,3-diazaphenoxathiin ring system and the relationship of the 13C-NMR chemical shift of the C-10a resonances to the molecular dihedral angle determined by X-Ray diffraction: A further investigation

Synthesis of the 1,3-diazaphenoxathiin ring system and the confirmation of its structure by ¹³C-nmr spectroscopy and X-ray crystallography are reported. Implications of the ¹³C-nmr chemical shift of the C-10a resonance and its relationship to the molecular dihedral angle are presented. The molecule crystallizes in the Pbca space group and was found to have a dihedral angle of 165.5(9)°, the structure refining to a final R-factor of T = 0.0427.     

A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums

The five-site transferable interaction potential (TIP5P) for water is most accurate at reproducing experimental data when used with a simple spherical cutoff for the long-ranged electrostatic interactions. When used with other methods for treating long-ranged interactions, the model is considerably less accurate. With small modifications, a new TIP5P-like potential can be made which is very accurate for liquid water when used with Ewald sums, a more physical and increasingly more commonly used method for treating long-ranged electrostatic interactions. The new model demonstrates a density maximum near 4 degrees C, like the TIP5P model, and otherwise is similar to the TIP5P model for thermodynamic, dielectric, and dynamical properties of liquid water over a range of temperatures and densities. An analysis of this and other commonly used water models reveals how the quadrupole moment of a model can influence the dielectric response of liquid water.     

Highly substituted pyridines via tethered imine-enamine (TIE) methodology

A tethered imine-enamine methodology has been developed for the direct conversion of 1,2,4-triazines into highly substituted pyridines via the inverse electron demand Diels-Alder reaction which avoids the need for a discrete aromatisation step. This TIE methodology has also been applied in one pot reaction cascades involving 1,2,4-triazines and utilising MnO(2)-mediated tandem oxidation processes (TOPs).     

Simultaneous differential pulse-polarographic determination of CS2 and COS gases and its application in the analysis of dithiocarbamate fungicide residues in foods

The differential pulse-polarographic (DPP) determination of both CS₂ and COS gases, after their absorption in a methanolic piperidine reagent and the subsequent application of this technique to the residue analysis of dithiocarbamate fungicides is described. Rectilinear calibration curves for both CS₂ and COS in the respective regions of 1.5–9.2 and 2.1–12.6 μmol/l were obtained. The DPP method has been successfully applied to the determination of thiram residues on apples after a hot acid hydrolysis of the fruits.     

Effect of ether versus ester tethering on Heck cyclizations

Ether tethers allow Heck cyclizations to proceed in high yields. Ester tethers lead to low yields. Styrene trapping experiments indicate that ester reactions form viable organopalladium intermediates that cannot cyclize efficiently.     

Determination of arsenic, selenium, and antimony in cloud water by inductively coupled plasma mass spectrometry

The capability of inductively coupled plasma mass spectrometry in determining trace levels of As, Se, and Sb in cloud water was evaluated. Preliminary studies focused on identifying and eliminating potential interferences in the cloud water matrix, the choice of appropriate internal standards, and system optimization. The detection limits for As, Se, and Sb were 20, 100, 20 pg/mL using pneumatic nebulization, and 5, 25, 5 pg/mL, respectively, using ultrasonic nebulization with a precision of better than 5% RSD. The accuracy was demonstrated by the analysis of a NIST commercial reference material, SRM 1643d. In all cases, the results from ICP-MS analysis agreed within 4% of the certified values. Comparative analysis of cloud water samples obtained from a site downwind from large pollution sources (Whiteface Mountain, New York) and Changlagali Pakistan, a rural mountain peak, was carried out by hydride generation atomic absorption (HGAA) spectrometry. There was excellent agreement between the ICP-MS and HGAA results. Received: 31 July 1997 / Revised: 28 October 1997 / Accepted: 31 October 1997     

Boron-containing nucleosides. 1. Synthesis of the novel heterocycle 2-benzyl-1,4-dihydro-1-hydroxythieno[3,2-c][1,5,2]diazaborin-3(2H)-one: A thieno-fused 4-borauracil

The synthesis of the novel boron-containing nucleobase 2-benzyl-1,4-dihydro-1-hydroxythieno[3,2-c]-[1,5,2]diazaborin-3(2H)-one ( 8 ), a thieno-fused 4-borauracil, is described. Compound 8 was prepared in three steps starting from 2-thiophenecarbonyl chloride ( 4 ). A multinuclear and multisolvent nmr study of 8 indicates that the boron atom maintains a trigonal geometry in the solvents used.     

Regio- and stereoselective oxetane formation via paterno-buchi photocycloaddition

Carbonyl 2 + 2 photoaddition occurs selectively to the alkene moiety of 3-(4-methyl-3-pentenoxy)pyridine. Photolysis of alkene containing pyridines in acetophenone gives rise to an oxetane which is obtained with extremely high diastereoselectivity as shown by analysis of the major 2 + 2 photoproduct. A second photoproduct, 2,3-dihydroxy-2,3-diphenylbutane, is obtained as a result of acetophenone coupling.