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).     

Modified nucleosides in human serum.

Methylated purines and pyrimidines derived from the degradation of transfer ribonucleic acid have been shown to be excreted in abnormal amounts in the urine of patients with cancer. Recent technology developed by Gehrke and Kuo has allowed the separation and quantification of modified nucleosides in serum using reversed-phase high-performance liquid chromatography with diode-array measurement. Serum levels of ten modified nucleosides were measured in 37 normal healthy adults to establish normal values and to correlate activity with age and sex. In addition, serum levels of patients with several malignancies were measured to determine activity in these diseases. Levels of modified nucleosides in normal individuals were consistently reproducible and showed no significant variation among males versus females or with age. Patients with malignant diseases showed consistent elevations and these were highest in patients with more advanced disease. The evidence of no significant differences in the mean levels of modified nucleosides in serum with age or sex in normal adults and elevations in patients with malignancies demonstrate the potential value of modified nucleosides as cancer biomarkers.     

Chemoproteomic profiling of kinases in live cells using electrophilic sulfonyl triazole probes

Sulfonyl-triazoles are a new class of electrophiles that mediate covalent reaction with tyrosine residues on proteins through sulfur-triazole exchange (SuTEx) chemistry. Recent studies demonstrate the broad utility and tunability of SuTEx chemistry for chemical proteomics and protein ligand discovery. Here, we present a strategy for mapping protein interaction networks of structurally complex binding elements using functionalized SuTEx probes. We show that the triazole leaving group (LG) can serve as a releasable linker for embedding hydrophobic fragments to direct molecular recognition while permitting efficient proteome-wide identification of binding sites in live cells. We synthesized a series of SuTEx probes functionalized with a lipid kinase fragment binder for discovery of ligandable tyrosines residing in catalytic and regulatory domains of protein and metabolic kinases in live cells. We performed competition studies with kinase inhibitors and substrates to demonstrate that probe binding is occurring in an activity-dependent manner. Our functional studies led to discovery of probe-modified sites within the C2 domain that were important for downregulation of protein kinase C-alpha in response to phorbol ester activation. Our proof of concept studies highlight the triazole LG of SuTEx probes as a traceless linker for locating protein binding sites targeted by complex recognition elements in live cells.

Sulfonyl-triazole probes modified with a kinase recognition element are developed for live cell activity-based profiling to identify tyrosine sites located in catalytic and regulatory domains that are important for kinase function.     

Photoreactivation of cyclobutane dimers and (6-4) photoproducts in the epidermis of the marsupial, Monodelphis domestica

Radioimmunoassays were used to investigate the repair of cyclobutane pyrimidine dimers and pyrimidine (6-4)pyrimidone photoproducts ((6-4] photoproducts) in the epidermis of the South American opossum, Monodelphis domestica. In the absence of photoreactivating light, both types of photodamage were excised with similar kinetics, 50% of the damage remaining 8 h after UV irradiation in vivo. Exposure of UV-irradiated skin to photoreactivating light resulted in removal of most of the cyclobutane dimers and an enhanced rate of (6-4) photoproduct repair. Photoenhanced excision repair of non-dimer damage increases the range of biologically effective lesions removed by in vivo photoreactivation.     

EXCISION OF CYCLOBUTANE DIMERS IN GENOMIC AND EPISOMAL DNA IN HUMAN CELLS

Abstract Direct determination has been made of cyclobutyl pyrimidine dimer induction and excision repair in an episomal SV40 DNA population in vivo . Maintaining SV40-transformed human (GM637) cells in confluent culture results in amplification of a mutant SV40 episome to high copy number. T4 endonuclease V was used to quantify the induction and repair of cyclobutane dimers in the SV40 episome and genomic DNA of the same cells. Differences in both parameters were observed cyclobutane dimers were induced at 1.5–2-fold greater frequency in episomal DNA and excised at a reduced rate compared to genomic DNA in the host cells.     

An annulene-fused cyclopentadienide. A photochromic cyclopentadienodimethyldihydropyrene where the fused cyclopentadienide group resembles benzene in its effect on the dihydropyrene-metacyclophanediene valence isomerization

The synthesis of the green cyclopentadiene-fused dimethyldihydropyrene 12 was achieved in 36% yield in 7 steps from the parent dihydropyrene 3. Reaction of 12 with KH or LiCH(2)SiMe(3) gave the [14]annulene-fused cyclopentadienide anion quantitatively. In the (1)H NMR spectra, the internal methyl protons of 12 at delta -3.9, change dramatically on formation of anion 5, becoming deshielded to delta -1.82. This is caused by the reduction in diatropicity of the [14]annulene ring on fusion to the 6pi-cyclopentadienide ring. The anion is also a photochromic switch. Irradiation of the closed form 5 with visible light opens it to the open form 5', which reverts to the closed form 5 either with UV light or thermally. The switching behavior is between that of the parent 3/3' and the benzannelated system 4/4' and suggests that in its effect on the photoswitching, cyclopentadienide is behaving chemically similar to benzene.     

Synthesis of digitoxigenin by remote functionalization

Treatment of a 21-hydroxy-20-keto steroid with the mixed anhydride of trifluoroacetic acid—diethylphosphonoacetic acid leads directly to cardenolides by an intramolecular Horner-Emmons reaction. Photolysis of 3β-acetoxy-5β,14α-card-20(22)-enolide and iodobenzenedichloride in benzene solution then yields 3β-acetoxy-5β-carda-14,20(22)-dienolide (β-anhydrodigitoxigenin acetate).     

The use of discharge lamps as directly modulated atom reservoirs for selective line modulation in atomic emission spectrometry

A simple method is described for selectively modulating the atomic or ionic resonance lines emitted by an excitation source. A modified discharge lamp with a cylindrical hollow cathode is used to generate a modulated atom cloud. The emission from the excitation source is then imaged through the modulated atom cloud within the cylindrical cathode lamp, to yield a selectively modulated signal. The ability of the system to reduce spectral interferences in inductively-coupled plasma emission spectrometry is assessed and discussed.     

Isomer-specific spectroscopy and conformational isomerization energetics of o-, m-, and p-ethynylstyrenes

The infrared and ultraviolet spectroscopy of o-, m-, and p-ethynylstyrene isomers (oES, mES, and pES) were studied by a combination of methods, including resonance-enhanced two-photon ionization (R2PI), UV-UV hole-burning spectroscopy (UVHB), resonant ion-dip infrared spectroscopy (RIDIRS), and rotationally resolved fluorescence excitation spectroscopy. In addition, the newly developed method of stimulated emission pumping-population transfer spectroscopy (SEP-PTS) was used to determine the energy threshold to conformational isomerization in m-ethynylstyrene. The S(1) <-- S(0) origin transitions of oES and pES occur at 32 369 and 33 407 cm(-1), respectively. In mES, the cis and trans conformations are calculated to be close in energy. In the R2PI spectrum of mES, the two most prominent peaks (32672 and 32926 cm(-1)) were confirmed by UVHB spectroscopy to be S(1) <-- S(0) origins of these two conformers. The red-shifted conformer was identified as the cis structure by least-squares fitting of the rotationally resolved fluorescence excitation spectrum of the origin band. There are also two possible conformations in oES, but transitions due to only one were observed experimentally, as confirmed by UVHB spectroscopy. Density functional theory calculations (B3LYP/6-31+G) predict that the cis-ortho conformer, in which the substituents point toward each other, is about 8 kJ/mol higher in energy than the trans-ortho isomer, and should only be about 5% of the room temperature population of oES. Ground-state infrared spectra in the C-H stretch region (3000-3300 cm(-1)) of each isomer were obtained with RIDIRS. In all three structural isomers, the acetylenic C-H stretch fundamental was split by Fermi resonance. Infrared spectra were also recorded in the excited electronic state, using a UV-IR-UV version of RIDIR spectroscopy. In all three isomers the acetylenic C-H stretch fundamental was unshifted from the ground state, but no Fermi resonance was seen. The first observed and last unobserved transitions in the SEP-PT spectrum were used to place lower and upper bounds on the barrier to cis --> trans isomerization in m-ethynylstyrene of 990-1070 cm(-1). Arguments are given for the lack of a kinetic shift in the measurement. The analogous trans --> cis barrier is in the same range (989-1065 cm(-1)), indicating that the relative energies of the zero-point levels of the two isomers are (E(ZPL)(cis) - E(ZPL)(trans))= -75 to +81 cm(-1). Both the barrier heights and relative energies of the minima are close to those determined by DFT (Becke3LYP/6-31+G) calculations.     

Simple methods for the direct assembly, functionalization, and patterning of acid-terminated monolayers on Si111

This article describes mild methods to directly assemble, functionalize, and pattern monolayers of undecylenic acid on hydrogen-terminated Si(111). These monolayers were assembled under very mild conditions from a neat solution of undecylenic acid containing 0.1 mol % 4-(decanoate)-2,2,6,6-tetramethylpiperidinooxy at room temperature without the need for UV light. Because of these mild conditions, monolayers exposing carboxylic acids could be assembled in one step without the need to protect the acid prior to its assembly. The monolayers were extensively characterized by horizontal attenuated total reflection infrared spectroscopy, X-ray photoelectron spectroscopy (XPS), and contact angle goniometry. The monolayers bonded to the silicon surface preferentially through the olefin with no detectable bonds between the carboxylic acids and silicon. The crystallinity of the monolayer was studied by infrared spectroscopy through the antisymmetric--v(a)(CH(2))--and symmetric--v(s)(CH(2))--stretches for methylene. Because it is important for future applications to assemble functional surfaces, methods to react the acid-terminated monolayers with trifluoroacetic anhydride and triethylamine to yield a symmetric anhydride on the monolayer were studied. These anhydrides were reacted with a variety of milligram-quantity amines to yield amide-terminated surfaces. This method was general, and a variety of amines could be bonded to the monolayer. The stabilities of these monolayers upon exposure to ambient conditions and under a variety of solvents were described. Because patterned monolayers have found wide applications, we have developed methods to pattern 1-octadecylamine and poly(ethylenimine) on the micrometer scale using soft lithography. In addition, polymer brushes of polynorbornene with thicknesses from 32 to 150 nm were grown from monolayers patterned with the Grubbs' catalyst. The patterned surfaces were imaged by scanning electron microscopy, scanning probe microscopy, and ellipsometry to determine the thicknesses of the patterns and the fidelity of the method.