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.     

Acetone powder from dormant seeds of Ricinus communis L

The influence of several factors on the hydrolytic activity of lipase, present in the acetone powder from dormant castor seeds (Ricinus communis) was evaluated. The enzyme showed a marked specificity for short-chain substrates. The best reaction conditions were an acid medium, Triton X-100 as the emulsifying agent and a temperature of 30 degrees C. The lipase activity of the acetone powder of different castor oil genotypes showed great variability and storage stability of up to 90%. The toxicology analysis of the acetone powder from genotype Nordestina BRS 149 showed a higher ricin (toxic component) content, a lower 2S albumin (allergenic compound) content, and similar allergenic potential compared with untreated seeds.     

Stereochemical aspects of the asymmetric synthesis of chiral α,β-dihydroxy phosphonates. Synthesis of α,β-dihydroxy phosphonic acids

Stereocontrol in the asymmetric phosphonylation of aldehydes via organophosphorous esters has been obtained starting from chiral aldehydes. The nature of the O-protecting group is crucial to obtain, in terms of diastereoselectivity and chemical yields, the best results. An ab initio molecular orbital study on 2-silyloxy propanal and MM2 studies on 2-alkoxy propanal show the existence of stable cyclic and acyclic conformers, which are presumably responsible for the high syn diastereoselectivity observed in the addition of non-metal carrying phosphites.