Signal amplification and detection via a supramolecular allosteric catalyst

The design of a supramolecular allosteric catalyst system for catalytic signal amplification and detection is presented. The catalyst was switched "on" by the introduction of an analyte that also behaves as an allosteric activator. Concentrations of Cl- ions as low as 800 nM were catalytically amplified and detected. The signal was transduced via a pH-sensitive fluorescent probe and observed visually using a laboratory, handheld UV lamp and by spectrophotometry. Furthermore, the allosteric effect was quantified using gas chromatography for a range of Cl- concentrations. This three-part detection scheme involving analyte binding, allosteric catalyst activation, and signal transduction represents a new approach to small-molecule detection.     

Rational materials design of sorbent coatings for explosives: applications with chemical sensors

A series of chemoselective polymers had been designed and synthesized to enhance the sorption properties of polymer coated chemical sensors for polynitroaromatic analytes. To evaluate the effectiveness of the chemoselective coatings, a polynitroaromatic vapor test bed was utilized to challenge polymer coated surface acoustic wave (SAW) devices with different explosive vapors. Dinitrotoluene detection limits were determined to be in the <100 parts per trillion ranges. ATR-FTIR studies were used to determine the nature of the polymer-polynitroaromatic analyte interactions, and confirm the presence of hydrogen-bonding between polymer pendant groups and the nitro functional groups of polynitroaromatic explosive materials.     

Metal clips induce folding of a short unstructured peptide into an alpha-helix via turn conformations in water. Kinetic versus thermodynamic products

Short peptides corresponding to two to four alpha-helical turns of proteins are not thermodynamically stable helices in water. Unstructured octapeptide Ac-His1-Ala2-Ala3-His4-His5-Glu6-Leu7-His8-NH(2) (1) reacts with two [Pd((15)NH(2)(CH(2))(2)(15)NH(2))(NO(3))(2)] in water to form a kinetically stable intermediate, [[Pden](2)[(1,4)(5,8)-peptide]](2), in which two 19-membered metallocyclic rings stabilize two peptide turns. Slow subsequent folding to a thermodynamically more stable two-turn alpha-helix drives the equilibrium to [[Pden](2)[(1,5)(4,8)-peptide]] (3), featuring two 22-membered rings. This transformation from unstructured peptide via turns to an alpha-helix suggests that metal clips might be useful probes for investigating peptide folding.     

High-frequency (140-GHz) time domain EPR and ENDOR spectroscopy: the tyrosyl radical-diiron cofactor in ribonucleotide reductase from yeast

High-frequency pulsed EPR and ENDOR have been employed to characterize the tyrosyl radical (Y*)-diiron cofactor in the Y2-containing R2 subunit of ribonucleotide reductase (RNR) from yeast. The present work represents the first use of 140-GHz time domain EPR and ENDOR to examine this system and demonstrates the capabilities of the method to elucidate the electronic structure and the chemical environment of protein radicals. Low-temperature spin-echo-detected EPR spectra of yeast Y* reveal an EPR line shape typical of a tyrosyl radical; however, when compared with the EPR spectra of Y* from E. coli RNR, a substantial upfield shift of the g(1)-value is observed. The origin of the shift in g(1) was investigated by 140-GHz (1)H and (2)H pulsed ENDOR experiments of the Y2-containing subunit in protonated and D(2)O-exchanged buffer. (2)H ENDOR spectra and simulations provide unambiguous evidence for one strongly coupled (2)H arising from a bond between the radical and an exchangeable proton of an adjacent residue or a water molecule. Orientation-selective 140-GHz ENDOR spectra indicate the direction of the hydrogen bond with respect to the molecular symmetry axes and the bond length (1.81 A). Finally, we have performed saturation recovery experiments and observed enhanced spin lattice relaxation rates of the Y* above 10 K. At temperatures higher than 20 K, the relaxation rates are isotropic across the EPR line, a phenomenon that we attribute to isotropic exchange interaction between Y* and the first excited paramagnetic state of the diiron cluster adjacent to it. From the activation energy of the rates, we determine the exchange interaction between the two irons of the cluster, J(exc) = -85 cm(-)(1). The relaxation mechanism and the presence of the hydrogen bond are discussed in terms of the differences in the structure of the Y*-diiron cofactor in yeast Y2 and other class I R2s.     

Fine characterization of the ethylene and ethane sorption in poly(amide 12-block-tetramethylenoxide) copolymer/AgBF4 membranes

Ethylene/ethane sorption characteristics were determined for dry Pebax™ (poly(amide 12-block-tetramethylenoxide) copolymer)/AgBF₄ membranes by using an electronic microbalance. The membranes containing 0.7 and 22 wt.% AgBF₄ showed a dual-mode sorption isotherm. The ethane isotherms for all the membranes were of the Henry-type, which is the normal sorption for gases in rubbery polymers. The abnormal presence of Langmuir sorption sites only for ethylene in the rubbery copolymer, never reported sofar, is attributed to the silver-based specific complexation sites. The silver salt which dissolved in limited amounts in the rubbery copolymer had a much smaller Langmuir sorption capacity than the salt that crystallized in the copolymer. The sorption kinetics indicate that the crystallized salt did adsorb slowly ethylene according to a zeroth-order kinetics, but not ethane. The gas uptake kinetics resulting from a step of the pressure surrounding the copolymer exhibited one stage for ethane but two stages for ethylene. For the latter, there was first a fast Fickian sorption stage, then a drift of the zeroth-order sorption of ethylene on salt crystals, which contributes for a large part to the total uptake. The zeroth-order sorption suggests that the sorbed ethylene amount in the second-stage is independent of the crystal-surface coverage. The value of the Fickian diffusion coefficient calculated by fitting the kinetics with a solution of the second Fick’s law was 5 × 10⁻¹² m²/s for both ethylene (the first stage) and ethane, and is typical for small organic compounds in a rubbery material.     

Gas-phase derivatization of [C3H5]+ ions using tandem mass spectrometry methods A13C labelling study

The study of specifically ¹³C-labelled precursors sheds further light on the gas-phase chemistry of allyl and 2-propenyl cations. It is demonstrated that both species are formed from allyl and 2-propenyl bromide upon 70 eV electron impact ionization without skeletal reorganization. Gas-phase derivatization of the [C₃ H₅]⁺ ions with benzene facilitates, as suggested and observed earlier, the distinction of the two isomers using collision-induced dissociation of the Wheland complexes (or isomers thereof). The ¹³C labelling data clearly demonstrate that 64% of allyl cations survive the derivatization while 36% isomerize to 2-phenylpropyl cations; the latter are also formed via the reaction of 2-propenyl cation with benzene, protonation of α-methylstyrene and water loss from protonated 2-phenyl-2-propanol, respectively. Unimolecular loss of C₂H₄ from protonated allylbenzene proceeds via two competing reaction channels: one involves heterolysis of 1-phenylpropyl cations (～30%); the major pathway (～70%), however, involves decomposition via propylene benzenium ions.     

Theoretical and experimental reevaluation of the basicity of lambda3-phosphinine

We have investigated the basicity of phosphinine (C5H5P, phosphabenzene) in reevaluating its proton affinity (PA) and gas-phase basicity (GB) and the pK(a) value of its protonated form. As a necessary step, we have first determined its gas-phase proton affinity. Using both mass spectrometric and quantum chemical methods, we have obtained the values PA(C5H5P) = 195.8 +/- 1.0 kcal mol(-1) and GB(298)(C5H5P) = 188.1 +/- 1.0 kcal mol(-1), in good agreement with previous results. We then derived a value of pK(a)(C5H6P+) = -16.1 +/- 1.0 in aqueous solution using three different approaches: the latter markedly differs from the currently available value of -10. The reason for such a discrepancy in the pK(a) of protonated phosphinine in solution is discussed. In the theoretical determination of PAs, evaluation of the basis set superposition error (BSSE) showed that this effect is quite small, being 0.1-0.2 kcal mol(-1) for phosphinine, when a density functional theory (DFT) method in conjunction with a large basis set were used.     

1H and 13C NMR characterization of hemiamidal isoniazid-NAD(H) adducts as possible inhibitors of InhA reductase of Mycobacterium tuberculosis

Isoniazid (INH) is easily oxidized with manganese(III) pyrophosphate, a chemical model of the KatG protein involved in activation of INH inside the bacteria Mycobacterium tuberculosis. Performed in the presence of NAD(+), this oxidation generates a family of isomeric INH-NAD(H) adducts, which have been shown to be effective inhibitors of InhA, an enzyme essential in mycolic acid biosynthesis. In this work, we fully characterized by (1)H and (13)C NMR spectroscopy four main species of INH-NAD(H) adducts that coexist in solution. Two of them are open diastereoisomers consisting of the covalent attachment of the isonicotinoyl radical at position four of the nicotinamide coenzyme. The other two result from a cyclization involving the amide group from the nicotinamide and the carbonyl group from the isonicotinoyl radical to give diastereoisomeric hemiamidals. Although an INH-NAD(H) adduct with a 4S configuration has been characterized within the active site of InhA from Xray crystallography and this bound adduct interpreted as an open form (Rozwarski et al., Science 1998, 279, 98-102), it is legitimate to raise the question about the effective active form(s), open or cyclic, of INH-NAD(H) adduct(s). Is there a single active form or are several forms able to inhibit the InhA activity with different levels of inhibitory potency?     

Synthesis of coumarins by ring-closing metathesis using Grubbs’ catalyst

A novel generally applicable synthesis of coumarins from phenolic substrates utilizing ring-closing metathesis is described. This sequence involves O-allylation of phenols followed by ortho-Claisen rearrangement, subsequent based-induced isomerization affording 2-(1-propenyl)phenols, acylation with acryloyl chloride, and finally ring-closing metathesis (RCM) with Grubbs’ second generation catalyst.     

Removal of PCR inhibitors using dielectrophoresis as a selective filter in a microsystem

Diagnostic PCR has been used to analyse a wide range of biological materials. Conventional PCR consists of several steps such as sample preparation, template purification, and PCR amplification. PCR is often inhibited by contamination of DNA templates. To increase the sensitivity of the PCR, the removal of PCR inhibitors in sample preparation steps is essential and several methods have been published. The methods are either chemical or based on filtering. Conventional ways of filtering include mechanical filters or washing e.g. by centrifugation. Another way of filtering is the use of electric fields. It has been shown that a cell will experience a force when an inhomogeneous electric field is applied. The effect is called dielectrophoresis (DEP). The resulting force depends on the difference between the internal properties of the cell and the surrounding fluid. DEP has been applied to manipulate cells in many microstructures. In this study, we used DEP as a selective filter for holding cells in a microsystem while the PCR inhibitors were flushed out of the system. Haemoglobin and heparin - natural components of blood - were selected as PCR inhibitors, since the inhibitory effects of these components to PCR have been well documented. The usefulness of DEP in a microsystem to withhold baker's yeast (Saccharomyces cerevisiae) cells while the PCR inhibitors haemoglobin and heparin are removed will be presented and factors that influence the effect of DEP in the microsystem will be discussed. This is the first time dielectrophoresis has been used as a selective filter for removing PCR inhibitors in a microsystem.