An improved liquid chromatography/tandem mass spectrometry method for the determination of 8-oxo-7,8-dihydro-2'-deoxyguanosine in DNA samples using immunoaffinity column purification

The analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) represents an important biomarker of oxidative stress. A sensitive method for the detection of 8-oxodG in DNA samples has been developed that utilizes immunoaffinity column purification of 8-oxodG followed by liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) multiple reaction monitoring (MRM) mode analysis. An internal standard of stable-isotopically labelled 8-oxodG containing [(15)N(5)] was added prior to the enzymatic digestion of DNA to deoxynucleosides, which was then subjected to immunoaffinity column purification followed by microbore positive ion LC/MS/MS MRM. The 8-oxo-7,8-dihydroguanine (8-oxoG) base product ion at m/z 168 was monitored following cleavage of the glycosidic bond of the 8-oxodG [M+H](+) ion at m/z 284. Similar determinations were made for [(15)N(5)]8-oxodG by monitoring the [(15)N(5)]8-oxoG base product ion at m/z 173 formed from the [M+H](+) ion at m/z 289. The introduction of the immunoaffinity column purification step into the method represents a significant improvement for the accurate determination of 8-oxodG since all artefactual peaks that are observed following the direct injection of digested DNA onto the LC/MS/MS system are removed. The identity of these artefactual peaks has been confirmed to be 2'-deoxyguanosine (dG), thymidine (dT) and 2'-deoxyadenosine (dA). The presence of these artefactual peaks in MRM mode analysis can be explained as a consequence of a concentration effect due to their considerably higher relative abundance in DNA compared to 8-oxodG. The highest signal intensity was observed for the artefactual peak for dA due to the fact that the adenine base formed an adduct with methanol, which is a constituent of the mobile phase. The resulting [M+H](+) ion at m/z 284 (dA m/z 252 + CH(3)OH m/z 32) gave rise to a product ion at m/z 168 following the loss of deoxyribose in MRM mode analysis. Control calf thymus DNA was digested to deoxynucleosides and unmodfied deoxynucleosides were removed by immunoaffinity column purification; the enriched 8-oxodG was determined by LC/MS/MS MRM. The level of 8-oxodG in control calf thymus DNA was determined to be 28.8 +/- 1.2 8-oxodG per 10(6) unmodified nucleotides (n = 5) using 5 microg of digested DNA. The limit of detection of the microbore LC/MS/MS MRM for 8-oxodG was determined to be 25 fmol on-column with a signal-to-noise ratio of 3.5.     

Detection of monobromamine, monochloramine and dichloramine using selected ion flow tube mass spectrometry and their relevance as breath markers

We report a fast, sensitive, real-time method to measure monobromamine, monochloramine and dichloramine using selected ion flow tube mass spectrometry (SIFT-MS). Relative rate coefficients and product distributions are reported for the reagent ions H3O+ and O2 +. Rapid reactions with the haloamines were observed with H3O+ and O2 + but no fast reaction was found with NO+. A slow reaction between NO+ and dichloramine was observed. We demonstrate the feasibility of determining these compounds in a single human breath for which the limit of detection is approaching 10 parts per billion (ppb). We also report preliminary measurements of these compounds in the breath of individuals where the concentrations of bromamine and chloramine ranged from 10 to 150 ppb.     

Dynamics of Inflationary Universes with Positive Spatial Curvature

If the spatial curvature of the universe is positive, then the curvature term will always dominate at early enough times in a slow-rolling inflationary epoch. This enhances inflationary effects and hence puts limits on the possible number of e-foldings that can have occurred, independently of what happened before inflation began and in particular without regard for what may have happened in the Planck era. We use a simple multi-stage model to examine this limit as a function of the present density parameter ₀ and the epoch when inflation ends.     

The reactions of ozone with methyl and ethyl nitrites

The reactions of O₃ with CH₃ONO and C₂H₅ONO were studied using infrared absorption spectroscopy in a static reactor at temperatures between 298 and 352K. Both reactions followed simple second-order kinetics forming the corresponding nitrate: The rate coefficients are given by .     

Termolecular ion-molecule reactions in Titan's atmosphere. IV. A search made at up to 1 micron in pure hydrocarbons

The results of a study of ion-molecule reactions occurring in pure methane, acetylene, ethylene, ethane, propyne, propene, propane, and diacetylene at pressures up to 40 microns of pressure are reported. A variety of experimental methods are used: The standard double resonance in an ICR, for determination of the precursor ions and the modulated double resonance ejection in an ICR, for the determination of the daughter ions. The FA-SIFT technique was used for validation and examination of termolecular reactions with rate coefficients that are less than 10(-26) cm(6) s(-1). An extensive database of reaction kinetics already exists for many of these reactions. The main point of this study was the determination of the accuracy of this database and to search for any missing reactions and reaction channels that may have been omitted from earlier investigations. A specific objective of this work was to extend the study to the highest pressures possible to find out if there were any important termolecular reaction channels occurring. A new approach was used here. In the pure hydrocarbon gases the mass spectra were followed as a function of the pressure changes of the gas. An initial guess was first made using the current literature as a source of the reaction kinetics that were expected. A model of the ion abundances was produced from the solution of the partial differential equations in terms of reaction rate coefficients and initial abundances. The experimental data was fitted to the model for all of the pressures by a least squares minimization to the reaction rate coefficients and initial abundances. The reaction rate coefficients obtained from the model were then compared to the literature values. Several new channels and reactions were discovered when the modeled fits were compared to the actual data. This is all explained in the text and the implications of these results are discussed for the Titan atmosphere.     

Quadrant analysis of persistent spatial velocity perturbations over square-bar roughness

We explore a new application of the quadrant method in the context of the double-averaged Navier–Stokes equations for studying open channel flow near rough beds. Quadrant analysis is applied to spatial disturbances of time-averaged velocity components, using the experimental data from flow over two-dimensional regular transverse square-bar roughness. The spatial velocity disturbances change periodically performing a full cycle over a single roughness element, so that the quadrant diagrams are regular closed orbits. A colour code is used to produce a quadrant map of the flow cross-section, which reveals contributions from each quadrant to the time-averaged momentum transfer.     

High-power synchronously pumped AgGaS(2) optical parametric oscillator

Greater than 2 W of average power was generated in the infrared region by a AgGaS(2) optical parametric oscillator (OPO). A Q -switched mode-locked laser was used to pump the OPO synchronously. Tunability from 1.4 to 1.9mum and a maximum output power of 750 mW at 1.44mum were achieved with a standing-wave cavity. Redesigning the cavity into a ring configuration allowed the depleted pump, signal, and idler beams to be extracted efficiently through separate mirrors. This design generated signal and idler beams of high spatial quality at respective power levels of 1.5 and 620 mW at a pulse repetition rate of 2 kHz.     

Mechanism of enzymatic fluorination in Streptomyces cattleya

Recently a fluorination enzyme was identified and isolated from Streptomyces cattleya, as the first committed step on the metabolic pathway to the fluorinated metabolites, fluoroacetate and 4-fluorothreonine. This enzyme, 5'-fluoro-5'-deoxy adenosine synthetase (FDAS), has been shown to catalyze C-F bond formation by nucleophilic attack of fluoride ion to S-adenosyl-l-methionine (SAM) with the concomitant displacement of l-methionine to generate 5'-fluoro-5'-deoxy adenosine (5'-FDA). Although the structures of FDAS bound to both SAM and products have been solved, the molecular mechanism remained to be elucidated. We now report site-directed mutagenesis studies, structural analyses, and isothermal calorimetry (ITC) experiments. The data establish the key residues required for catalysis and the order of substrate binding. Fluoride ion is not readily distinguished from water by protein X-ray crystallography; however, using chloride ion (also a substrate) with a mutant of low activity has enabled the halide ion to be located in nonproductive co-complexes with SAH and SAM. The kinetic data suggest the positively charged sulfur of SAM is a key requirement in stabilizing the transition state. We propose a molecular mechanism for FDAS in which fluoride weakly associates with the enzyme exchanging two water molecules for protein ligation. The binding of SAM expels remaining water associated with fluoride ion and traps the ion in a pocket positioned to react with SAM, generating l-methionine and 5'-FDA. l-methionine then dissociates from the enzyme followed by 5'-FDA.