Kinetics of comet formation in single‐cell gel electrophoresis: Loops and fragments

We investigated the mechanisms of DNA exit during single‐cell gel electrophoresis (the comet assay) by measuring the kinetics of the comet tail formation. In the neutral comet assay, the rate of DNA exit was found to be dependent on the topological state of DNA, which was influenced by either ethidium bromide or a low radiation dose. The results clearly show that the comet tail is formed by extended DNA loops: the loop extension, being reversible when the DNA torsional constraint remains in the loops, is favored when the constraint is relaxed. The kinetics of the comet formation in the case of a high radiation dose points out that accumulation of the single‐strand breaks causes DNA fragmentation. In contrast to the neutral comet assay, the alkaline comet assay is not related to the chromatin loops. Our results imply that the alkaline treatment induces detachment of the loops from the nuclear matrix, and the comet tail is formed by ssDNA fragments, the ends of which are pulled out from the comet head by electric force. We suggest that the kinetic approach can be considered as an important improvement of the comet assay.     

Purification of the specific immunoglobulin G1 by immobilized metal ion affinity chromatography using nickel complexes of chelating porous and nonporous polymeric sorbents based on poly(methacrylic esters). Effect of polymer structure

Ni2+ complexes of the chelating nonporous and porous bead sorbents based on methacrylic esters crosslinked with ethylene dimethacrylate were used in isolation of the horseradish peroxidase-specific immunoglobulin IgG1 from the crude mouse ascitic fluid by immobilized metal ion affinity chromatography (IMAC). Iminodiacetic and aspartic acids were attached to porous poly(glycidyl methacrylate) beads differing in size, morphology and chemical composition. Ethylenediaminetriacetic acid and quinolin-8-ol chelating groups were attached mainly to the surface hydroxyl groups in nonporous poly(diethylene glycol methacrylate) beads through spacers. The latter sorbents exhibited better kinetic characteristics than the former but a very low IgG1 sorption capacity. In a single-step IMAC procedure, the best efficiency in the specific IgG1 purification was obtained with porous sorbents (recovery 92%, purity 73%). Differences in IMAC separations are discussed from the point of view of morphology of polymer beads as well as of the type and concentration of chelating ligands.     

Substitution at C-4 in 3,5-disubstituted 4H-1,2,6-thiadiazin-4-ones

3,5-Diaryl-4H-1,2,6-thiadiazin-4-ones react with NaBH₄ to give the 3,5-diaryl-4H-1,2,6-thiadiazin-4-ols and with MeLi to give 4-methyl-3,5-diaryl-4H-1,2,6-thiadiazin-4-ols. The latter dehydrate with p-toluenesulfonic acid to give (3,5-diarylthiadiazin-4-ylidene)methanes. (3,5-Diphenyl-4H-1,2,6-thiadiazin-4-ylidene)methane 15 suffers mono bromination with NBS to give bromo(3,5-diphenyl-4H-1,2,6-thiadiazin-4-ylidene)methane 17. Dichloro- and dibromo(3,5-diphenyl-4H-1,2,6-thiadiazin-4-ylidene)methanes 18 and 19 are formed directly from the 3,5-diphenylthiadiazin-4-one 9 via the Appel reaction using Ph₃P and CCl₄ or CBr₄, respectively. 3,5-Diarylthiadiazin-4-ones treated with P₂S₅ give 3,5-diarylthiadiazine-4-thiones that react with tetracyanoethylene oxide to give the (thiadiazin-4-ylidene)malononitriles. Finally, the 3,5-diphenylthiadiazine-4-thione 20 reacts with ethyl diazoacetate to give ethyl 2-(3,5-diphenyl-4H-1,2,6-thiadiazin-4-ylidene)acetate 26. The above reactions show that a variety of substitutions at C-4 of 3,5-diaryl substituted 1,2,6-thiadiazin-4-ones can be achieved, which extends the potential applications of this heterocycle. All compounds are fully characterized and a brief comparison of their spectroscopic properties is given.     

Synthesis of asymmetric 3,5-diaryl-4H-1,2,6-thiadiazin-4-ones via Suzuki–Miyaura and Stille coupling reactions

Asymmetric 3,5-diaryl substituted 4H-1,2,6-thiadiazin-4-ones can be prepared from 3,5-dichloro-4H-1,2,6-thiadiazin-4-one (1) via a multi-step protocol: selective nucleophilic mono-chloro substitution gives either the mono-methoxy or benzyloxy substituted mono-chlorothiadiazinones that can be phenylated via Suzuki–Miyaura coupling. Subsequent BBr₃ mediated dealkylation gives 3-hydroxy-5-phenyl-4H-1,2,6-thiadiazin-4-one (9) that can be activated by a modified Finkelstein halodehydroxylation via the triflate, enabling further arylation reactions using Suzuki–Miyaura or Stille coupling chemistry.     

Interference-free determination of thallium in aqua regia leaches from rocks, soils and sediments by D(2)-ETAAS method using mixed palladium-citric acid-lithium chemical modifier

The mixture of palladium (chloride) with citric acid and lithium is proposed as a new chemical modifier for the elimination of interference occurred during the determination of Tl in aqua regia extracts from rocks, soils and sediments by electrothermal atomic absorption spectrometry using instrumentation with deuterium-lamp background correction (D₂-ETAAS). Palladium was preferred to rhodium and platinum as to analyte stabilization, citric acid served as an effective reducing agent facilitating formation of Pd-Tl stable covalent bonds playing an important role in the analyte stabilization. Citric acid in addition helps to remove most of interfering chloride at low temperature. The further addition of Li increased significantly the robustness of chemical modifier against strongly interfering ZnCl₂ matrix by binding free chlorine into a more stable LiCl molecule. In the presence of the proposed chemical modifier the temperature for the final step of pyrolysis was adjustable up to 1000 °C, without any noticeable loss of volatile Tl species and the interference of the rest chloride matrix was significantly reduced. The application of the modifier to direct determination of Tl in aqua regia extracts from rocks, soils and sediments has ensured the characteristic mass and LOD value for the original sample 13 pg and 0.043 μg g⁻¹, respectively (10-μL aliquots of sample) and has enabled the use of matrix-free standard solutions for attaining accurate analysis. The accuracy was verified by the analysis of certified reference samples and by the comparison of results with those found by an inductively coupled plasma orthogonal acceleration time-of-flight mass spectrometer (ICP-oa-TOFMS) method.     

Salicylaldoxime in manganese(III) carboxylate chemistry: Synthesis, structural characterization and physical studies of hexanuclear and polymeric complexes

The use of salicylaldehyde oxime (H₂salox) in manganese(III) carboxylate chemistry has yielded new members of the family of hexanuclear compounds presenting the [Mn₆(μ₃-O)₂(μ₂-OR)₂]¹²⁺ core, complexes [Mn^III₆(μ₃-O)₂(O₂CPh)₂(salox)₆(L₁)₂(L₂)₂] (L₁ = py, L₂ = H₂O (1); L₁ = Me₂CO, L₂ = H₂O (2); L₁ = L₂ = MeOH (3)). Addition of NaOMe to the acetonitrile reaction mixture, afforded the 1D complex [Mn^III₃Na(μ₃-O)(O₂CPh)₂(salox)₃(MeCN)]_n (4), whereas addition of NaClO₄ to the acetone reaction mixture afforded an analogous 1D complex [Mn^III₃Na(μ₃-O)(O₂CPh)₂(salox)₃(Me₂CO)]_n (5). The structures of 1–3 present the [Mn₆(μ₃-O)₂(μ₂-OR)₂]¹²⁺ core and can be described as two [Mn₃(μ₃-O)]⁷⁺ triangular subunits linked by two μ₂-oximato oxygen atoms of the salox²⁻ ligands, which show the less common μ₃-κ²O:κO′:κN coordination mode. The benzoato ligands are coordinated through the usual syn,syn-μ₂-κO:κO′ mode. The 1D polymeric structures of 4 and 5 consist of alternating [Mn₃(μ₃-O)]⁷⁺ subunits and Na⁺ atoms linked through two μ₃-κ²O:κO′:κN and one μ₄-κ²O:κ²O′:κN salox²⁻ ligands as well as one syn,anti-μ₂-κO:κO′ benzoato ligand. DC and AC magnetic susceptibility studies on 1 revealed the stabilization of an S = 4 ground state, and indications of single-molecule magnetism behavior, whereas the DC experimental data from polycrystalline sample of 5 are indicative of antiferromagnetic interactions within the [Mn₃] subunit. Solid state ¹H NMR data of 1 were used to probe the spin-lattice relaxation of the system.     

Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers

Product ion spectra produced by collision-induced dissociation (CID) in tandem mass spectrometry experiments can differ markedly between instruments. There have been a number of attempts to standardise the production of product ion spectra; however, a consensus on the most appropriate approach to the reproducible production of spectra has yet to be reached. We have previously reported the comparison of product ion spectra on a number of different types of instruments - a triple quadrupole, two ion traps and a Fourier transform ion cyclotron resonance mass spectrometer (Bristow AWT, Webb KS, Lubben AT, Halket JM. Rapid Commun. Mass Spectrom. 2004; 18: 1). The study showed that a high degree of reproducibility was achievable. The goal of this study was to improve the comparability and reproducibility of CID product ion mass spectra produced in different laboratories and using different instruments. This was carried out experimentally by defining a spectral calibration point on each mass spectrometer for product ion formation. The long-term goal is the development of a universal (instrument independent) product ion mass spectral library for the identification of unknowns.The spectra of 48 compounds have been recorded on eleven mass spectrometers: six ion traps, two triple quadrupoles, a hybrid triple quadrupole, and two quadrupole time-of-flight instruments. Initially, 4371 spectral comparisons were carried out using the data from eleven instruments and the degree of reproducibility was evaluated. A blind trial has also been carried out to assess the reproducibility of spectra obtained during LC/MS/MS.The results suggest a degree of reproducibility across all instrument types using the tuning point technique. The reproducibility of the product ion spectra is increased when comparing the tandem in time type instruments and the tandem in space instruments as two separate groups. This may allow the production of a more limited, yet useful, screening library for LC/MS/MS identification using instruments of the same type from different manufacturers.     

Evaluation of automated direct sample introduction with comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry for the screening analysis of dioxins in fish oil

An automated direct sample introduction technique coupled to comprehensive two-dimensional gas chromatography-time of flight mass spectrometry (DSI-GC x GC/TOF-MS) was applied for the development of a relatively fast and easy analytical screening method for 17 polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) and 4 non-ortho polychlorinated biphenyls (PCBs) in fish oil. Comparison of instrumental performance between DSI-GC x GC/TOF-MS and the traditional gas chromatographic high resolution mass spectrometric (GC-HRMS) method showed good agreement of results for standard solutions analyzed in blind fashion. Relatively high tolerance of the DSI technique for lipids in the final extracts enabled a streamlined sample preparation procedure that only required gel permeation chromatography (GPC) and solid-phase extraction (SPE) cleanup with graphitized carbon black. The sample size for the method was 2g of cod liver oil, which achieved limits of quantitation (LOQs) of 0.019-7.8 pg/g toxic equivalent quotients for the individual PCDD/Fs. Lower detection limits can be achieved by using larger sample size and scaling up the sample preparation procedure, but this adds to the labor, time, solvent consumption, and expense of the approach. However, the streamlined method yielded 0.94 pg/g and 2.3 pg/g LOQs for 2,3,7,8-tetrachloro dibenzofuran (TCDF) and 3,3',4,4',5-pentachloro biphenyl (CB126), which were sufficiently low for regulatory monitoring of 2g samples. Therefore, instead of congener specific analysis, this streamlined analytical screening method for TCDF and CB126 has the potential to monitor fish oil contaminated with dioxin and dioxin-like PCBs at or above current food safety limits. Acceptable recoveries for nearly all analytes at three different spiking levels in fish oil samples were achieved with good repeatability.