Dynamic behavior of DNA base pairs containing 8-oxoguanine

The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.     

Regioselective homogeneous hydrogenation of heteroaromatic nitrogen compounds by use of [RuH(CO)(NCMe)2(PPh3)2]BF4 as the precatalyst

Summary The complex [RuH(CO)(NCMe)₂(PPh₃)₂]BF₄ (1) is an efficient and regioselective catalyst precursor for the hydrogenation of polyaromatic nitrogen compounds such as quinoline (Q), isoquinoline (iQ), indole (ln), 5,6- and 7,8-benzoquinoline (BQ) and acridine (A) under relatively mild reaction conditions (125 °C, 4 atm H₂). The order of individual initial rates was: A > Q > 5,6-BQ > 7,8-BQ > ln > iQ, reflecting both steric and electronic effects. For the regioselective homogeneous hydrogenation of A to 9,10-dihydroacridine (DHA) catalysed by complex (1), a kinetic study was carried out; the experimentally determined rate law was r = k ₁ [Ru] [H₂]. These findings are consistent with a mechanism involving the hydrogenation of [RuH(CO)(A)(NCMe)(PPh₃)₂]BF₄ to yield DHA and the unsaturated species [RuH(CO)(NCMe)(PPh₃)₂]BF₄ in the rate-determining step.     

Fractionation of metals and metalloids by chemical bonding from particles accumulated by electrostatic precipitation in an Argentine thermal power plant

A study was undertaken to evaluate the distribution of Al, As, Cr, Cu, Fe, Mn, Ni, Pb, Ti, V and Zn in fly ashes collected in the electrostatic precipitator of a thermal power plant in San Nicolás (Argentina). Five samples were collected during one week of operation. For the fractionation, the scheme applied consisted in extracting the elements in four fractions namely (i) soluble and exchangeable elements; (ii) carbonates, oxides and reducible elements; (iii) bound to sulfidic metals; and (iv) residual elements. Metals and metalloids at μg g^− 1 level were determined in each fraction by inductively coupled plasma optical emission spectrometry (ICP OES). For validation, a standard reference material (SRM 1633 coal fly ash) from NIST was subjected to the same chemical sequential extraction procedure that the samples. X-ray diffraction powder (XRD) analysis and scanning electron microscopy (SEM) were used to characterize the major minerals present in the matrix. Total analyte concentration (in μg g^− 1) varied from 10.6 for Pb to 17,622 for Al. Minimum and maximum concentrations (in μg g^− 1) found in individual samples in the four fractions were: Al, 92.7–9668; As, < 0.3–143; Cr, 2.0–10.4; Cu, < 0.2–35.6; Fe, < 0.3–4992; Mn, < 0.1–128; Ni, < 0.3–139; Pb, < 0.5–9.1; Ti, < 0.3–2243; V, 17.0–112.9; and Zn, < 0.1–68.2. The leachability of the 11 elements under study proved to be different. Low percentages of Al (1%), V (7%) and Cr (8%) were detected in the most bioavailable fraction. Arsenic was found to be most abundant in the non-silicate phase, represented by the second and third fractions, while Cr, Fe, Ni, Pb and Zn were mostly associated to the residual fraction.     

Effect of pH on the interfacial adsorption activity of pulmonary surfactant

The effect of pH on the interfacial adsorption activity of pulmonary surfactant was examined. Measurements of the surface tension were made in a Wilhelmy-like surface microbalance specially designed to assay small volumes of hypophase in thermostatically controlled conditions. Alkaline pH caused a significant decrease of the surface activity of both pulmonary surfactant and a lipid extract from surfactant (LES) (containing all of the lipids and surfactant protein-B (SP-B) and surfactant protein-C (SP-C) hydrophobic surfactant proteins, but lacking surfactant protein-A). The pK calculated from the change of surface activity versus pH was 9.18±0.26 and 9.27±0.31 for pulmonary surfactant and LES, respectively. The results from this study support the idea that electrostatic interactions between basic residues of SP-B and SP-C and negatively charged surfactant phospholipids could be important for the interfacial adsorption activity of pulmonary surfactant.     

Trapping H- bound to the nitrogenase FeMo-cofactor active site during H2 evolution: characterization by ENDOR spectroscopy

We here show that the iron-molybdenum (FeMo)-cofactor of the nitrogenase alpha-70(Ile) molybdenum-iron (MoFe) protein variant accumulates a novel S = (1)/(2) state that can be trapped during the reduction of protons to H(2). (1,2)H-ENDOR measurements disclose the presence of two protons/hydrides (H(+/)(-)) whose hyperfine tensors have been determined from two-dimensional field-frequency (1)H ENDOR plots. The two H(+/)(-) have large isotropic hyperfine couplings, A(iso)( )() approximately 23 MHz, which shows they are bound to the cofactor. The favored analysis for these plots indicates that the two H(+/)(-) have the same principal values, which indicates that they are chemically equivalent. The tensors are further related to each other by a permutation of the tensor components, which indicates an underlying symmetry of binding relative to the cofactor. At present, no model for the structure of the iron-molybdenum (FeMo)-cofactor in the S = (1)/(2) state trapped during the reduction of H(+) can be shown unequivocally to satisfy all of the constraints generated by the ENDOR analysis. The data disfavors any model that involves protonation of sulfides, and thus suggests that the intermediate instead contains two chemically equivalent bound hydrides; it appears unlikely that these are terminal monohydrides.     

Characterisation of the surface Lewis acid-base properties of poly(butylene terephthalate) by inverse gas chromatography

Two modes of high-speed counter-current chromatography (HSCCC) were applied to separate 3- and 4-sulfophthalic acid from a mixture. Conventional HSCCC was useful for the separation of up to several hundred milligram quantities of these positional isomers, while pH-zone-refining CCC was implemented successfully to separations at the multigram level. The conventional HSCCC separations were performed with a standard J-type HSCCC system that has a superior resolution but a lower level of retention of the stationary phase of the biphasic solvent system used (acidified n-butanol-water). The pH-zone-refining CCC separations were performed with an X-type HSCCC system (a cross-axis system) that has a higher capability for retention of the stationary phase. The purified positional isomers (over 99% pure as determined by HPLC) were characterized by 1H NMR and negative ion electrospray ionization mass spectrometry.     

A sensitive, rapid and specific determination of midazolam in human plasma and saliva by liquid chromatography/electrospray mass spectrometry

A rapid, sensitive and selective liquid chromatography/electrospray mass spectrometry (LC/ES-MS) method was developed for the quantitative determination of the anaesthetic benzodiazepine midazolam (MID) in human saliva and plasma from patients undergoing anesthesia procedures. Biological samples spiked with diazepam-d5, the internal standard, were extracted into diethyl ether. Compounds were separated on a Xterra RP18 column using a mobile phase of acetonitrile/formic acid 0.1% at a flow rate of 0.25 mL/min under a linear gradient. Column effluents were analyzed using MS with an ES source in the positive ionization mode. Calibration curves were linear in the concentration ranges of 1-250 and 0.2-25 ng/mL in plasma and saliva, respectively. The limits of detection were 0.5 ng/mL in plasma and 0.1 ng/mL in saliva, using a 0.5-mL sample volume. The recoveries of the spiked samples were above 65%. The method was applied to ten real samples from patients undergoing midazolam treatment.     

31P{1H}-n.m.r. as a tool for identification of ruthenium isomers containing PPh3 or 1,4-bis(diphenylphosphino)butane ligands. X-ray structures of the cis-{RuCl2(PPh3)2 [4,4′-(-X)2-2,2′-bipy]} complexes [X=-H, -Me, -SMe and (-Cl, -Me)]

A series of cis-{RuCl₂(PPh₃)₂[4,4-(X)₂-2,2-bipy]} [cis-chlorines; X=-H, -Me, -SMe, and (-Cl,-Me)] complexes have had their structures determined by single crystal X-ray diffraction. The geometry of these complexes, also determined in CH₂Cl₂ solution by ³¹P{¹H}-n.m.r. spectroscopy, showed that the chemical shifts for the phosphorus atoms are slightly dependent on the pKa of the 4,4-(-X)₂-2,2-bipy ligands.     

Lanthanum chromites partially substituted by calcium,strontium and barium synthesized by urea combustion

Because of their electrical, magnetic and catalytic properties rare earth and transition metal mixed oxides are important compounds. Lanthanum chromites have been extensively used as solid oxide fuel cell (SOFC) interconnect materials. In this work, lanthanum chromites partially substituted by alkaline earth metals were synthesized by the urea combustion process. TG and DSC techniques were used to evaluate the presence of the organic material in the powder after reaction on the hot plate. The powders were calcinated at 900°C and characterized by XRD and SEM. The results show that the particles have nanometric dimensions and the perovskite structure was formed.     

Asymmetric synthesis of 2H-azirines derived from phosphine oxides using solid-supported amines. Ring opening of azirines with carboxylic acids

A simple and efficient asymmetric synthesis of 2H-azirine-2-phosphine oxides 3 is described. The key step is a solid-phase bound achiral or chiral amine-mediated Neber reaction of beta-ketoxime tosylates derived from phosphine oxides 1. Reaction of 2H-azirines 3 and 11 with carboxylic acids 4 gives phosphorylated ketamides 5 and 12. Ring closure of ketamides 5 and 12 with triphenylphosphine and hexachloroethane in the presence of triethylamine leads to the formation of phosphorylated oxazoles 8 and 13.