Sequence and phosphorylation level determination of two donkey β‐caseins by mass spectrometry

Two coeluting components, with experimentally measured M_r values of 25529 and 24606 Da, were identified by reversed‐phase high‐performance liquid chromatography (RP‐HPLC) and mass spectrometric analysis in the dephosphorylated casein fraction of a milk sample collected from an individual donkey belonging to the Ragusano breed of the east of Sicily. By coupling enzymatic digestions, matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) and RP‐HPLC/nano‐electrospray ionization tandem mass spectrometry (nESI‐MS/MS) analysis, the two proteins were identified as donkey β‐CNs and their sequences characterized completely, using the two known β‐CNs from mare as references. The two donkey β‐CNs, showing a mass difference of 923 Da, differ by the presence of the domain E²⁷SITHINK³⁴ in the full‐length component (M_r 25529 Da). In comparison with the mare's β‐CNs used as reference, they present nine amino acid substitutions: L→S³⁷, R→H⁵², S→N⁸¹, P→V⁸⁴, L→V⁹¹, R→Q²⁰³, P→L/I²⁰⁶, L→F²¹⁰ and A→P²¹⁹. Together, these substitutions account for the increase of 18 Da in the M_r of the donkey β‐CNs with respect to the counterparts from the mare. The molecular mass determination by ESI‐MS for the phosphorylated proteins showed that the full‐length component was composed of highly multi‐phosphorylated isoforms with five to seven phosphate groups. By analogy with the homologous mare's β‐CNs, the full‐length (226 amino acids) β‐CN was termed variant A, whereas the shorter (218 amino acids) β‐CN was termed variant A^Δ5. Copyright © 2009 John Wiley & Sons, Ltd.     

Development and validation of a gas chromatography/mass spectrometry method for the assessment of genomic DNA methylation

A method for the determination of DNA global methylation, taken as the ratio (%) of 5‐methylcytosine (5mCyt) versus the sum of cytosine (Cyt) and 5mCyt, via gas chromatography/mass spectrometry (GC/MS), was developed and validated. DNA (2.5 µg) was hydrolyzed with aqueous formic acid 88%, spiked with cytosine‐2,4‐¹³C₂,¹⁵N₃ and 5‐methyl‐²H₃‐cytosine‐6‐²H₁ as internal standards, and derivatized with N‐methyl‐N‐(tert‐butyldimethylsilyl)trifluoroacetamide and 1% tert‐butyldimethylchlorosilane, in the presence of acetonitrile and pyridine. GC/MS, operating in single ion monitoring mode, separated and specifically detected all nucleobases as tert‐butyldimethylsilyl derivatives, without interferences, with the exception of guanosine. The method was linear throughout the range of clinical interest and had good sensitivity, with a limit of quantification of 3.2 pmol for Cyt and 0.056 pmol for 5mCyt, the latter corresponding to a methylation level of 0.41%. Intra‐ and inter‐day precision and accuracy were below 4.0% for both analytes and methylation. The matrix absolute effect, process efficiency and coefficient of variation ranged from 96.5 to 101.2%. The matrix relative effect was below 1%. The method was applied to the analysis of different human DNAs, including: nonmethylated DNA from PCR (methylation 0.00%), hypermethylated DNA prepared using M.SssI CpG methyltransferase (methylation 18.05%), DNA from peripheral blood leukocytes of healthy subjects (N = 6, median methylation 5.45%), DNA from bone marrow of leukemia patients (N = 5, 3.58%) and DNA from myeloma cell lines (N = 4, 2.74%). Copyright © 2009 John Wiley & Sons, Ltd.     

One-pot methodology for conversion of o-halogen nitrobenzenes to benzofuroxans

Reaction of o-halonitrobenzenes with sodium azide under reflux of DMF/H₂O gives benzofuroxans in one step in moderate to good yields. This is a faster methodology compared to the conventional procedure involving the preparation and subsequent pyrolysis of o-nitrophenyl azides. For comparison, the reaction was also performed under phase-transfer catalysis.     

A Flexible Pro‐porous Coordination Polymer: Non‐conventional Synthesis and Separation Properties Towards CO2/CH4 Mixtures

The novel coordination polymers [Cu(Hoxonic)(H₂O)]_n ( 1 ) and [Cu(Hoxonic)(bpy)_0.5]_n ? 1.5 n H₂O ( 2?H₂O ) (H₃oxonic: 4,6‐dihydroxy‐1,3,5‐triazine‐2‐carboxylic acid; bpy: 4,4′‐bipyridine) have been isolated and structurally characterised by ab initio X‐ray powder diffraction. The dense phase 1 contains 1D zig‐zag chains in which Hoxonic dianions bridge square‐pyramidal copper(II) ions, apically coordinated by water molecules. On the contrary, 2?H₂O , prepared by solution and solventless methods, is based on 2D layers of octahedral copper(II) ions bridged by Hoxonic ligands, further pillared by bpy spacers. The resulting pro‐porous 3D network possesses small hydrated cavities. The reactivity, thermal, magnetic and adsorptive properties of these materials have been investigated. Notably, the adsorption studies on 2 show that this material possesses unusual adsorption behaviour. Indeed, guest uptake is facilitated by increasing the thermal energy of both the guest and the framework. Thus, neither N₂ at 77 K nor CO₂ at 195 K are incorporated, and CH₄ is only minimally adsorbed at 273 K and high pressures (0.5 mmol g^?1 at 2500 kPa). By contrast, CO₂ is readily incorporated at 273 K (up to 2.5 mmol g^?1 at 2500 kPa). The selectivity of 2 towards CO₂ over CH₄ has been investigated by means of variable‐temperature zero coverage adsorption experiments and measurement of breakthrough curves of CO₂/CH₄ mixtures. The results show the highly selective incorporation of CO₂ in 2 , which can be rationalised on the basis of the framework flexibility and polar nature of its voids.     

Non-centrosymmetric tetrameric assemblies of tetramethylammonium halides with uranyl salophen complexes in the solid state

Ditopic salophen-UO(2) receptors 1-4 and 7 co-crystallize with tetramethylammonium (TMA) chloride and fluoride salts producing good quality crystals amenable for X-ray diffraction characterization. The arrangement of the receptor and salt units in the crystal lattice is such that tetrameric ball-shaped assemblies are formed, where an inner cluster of four TMA cations are surrounded by an outer shell of four UO(2)-bound anions. These elaborate architectures, which occur in all cases, regardless of a certain degree of structural modification on the receptors, lead to lattices that belong to non-centrosymmetric (NCS) space groups. Interestingly, the tetragonal symmetry of the tetrameric ball-shaped assemblies is either retained (I4?) or lost (R3c and I4?3d) at the lattice level, without compromising the NCS nature of the crystal lattices. The principal X-ray investigation on TMAX (X = Cl/F) co-crystals, that is, 1-(TMA)Cl, 2-(TMA)Cl, 3-(TMA)Cl, 4-(TMA)Cl, 7-(TMA)Cl, and 7-(TMA)F, is accompanied by NMR and electrospray ionization (ESI) mass spectrometry studies to gather additional insight on the modality of formation of the solid state structures observed. The important role of cation-π interactions in the receptor-salt recognition process is renewed and strengthened by comparison with NMR titration data with a novel reference compound, the salophen-UO(2) complex 8. Given the importance of NCS and polar crystalline solids in the development of functional materials, this study shows that this property can be introduced into elaborate host-guest systems, as those which assemble in the architectures described here, thus expanding its field of applicability.     

Photo-induced pyridine substitution in cis-[Ru(bpy)(2)(py)(2)]Cl(2): a snapshot by time-resolved X-ray solution scattering

Determination of transient structures in light-induced processes is a challenging goal for time-resolved techniques. Such techniques are becoming successful in detecting ultrafast structural changes in molecules and do not require the presence of probe-like groups. Here, we demonstrate that TR-WAXS (Time-Resolved Wide Angle X-ray Scattering) can be successfully employed to study the photochemistry of cis-[Ru(bpy)(2)(py)(2)]Cl(2), a mononuclear ruthenium complex of interest in the field of photoactivatable anticancer agents. TR-WAXS is able to detect the release of a pyridine ligand and the coordination of a solvent molecule on a faster timescale than 800 ns of laser excitation. The direct measurement of the photodissociation of pyridine is a major advance in the field of time-resolved techniques allowing detection, for the first time, of the release of a multiatomic ligand formed by low Z atoms. These data demonstrate that TR-WAXS is a powerful technique for studying rapid ligand substitution processes involving photoactive metal complexes of biological interest.     

Pulse shape analysis to reduce the background of BEGe detectors

A simple technique for pulse shape discrimination in HPGe-detectors of the so-called BEGe type, based on just one parameter obtained from one signal read out, is presented here. This technique allows discriminating between pulses generated when the deposited energy is located within a small region of about 1 mm³ from the pulses generated when the energy is deposited at different locations several mm or cm apart. Two possible applications using this technique are: (i) experiments that look for neutrinoless double β decay in ⁷⁶Ge, such as GERDA; (ii) γ spectrometry measurements where the Compton continuum can be reduced and the efficiency for cascading γ-rays can remain high. With this active background reduction technique a Compton suppression factor of about 3 was obtained. The detector response may be influenced by the detector size. The detector used for this study had a diameter of 6 cm, a thickness of 2.6 cm and a relative efficiency of 19%. The results obtained with this detector were consistent with the results obtained by Budjá? et al. [J Instrum 4:10, 2009] with a 50% relative efficiency BEGe detector.