Assignment of absolute configuration at phosphorus of P-chiral diastereomers of deoxyribonucleoside methanephosphonamidates by means of NMR spectroscopy

Recently, we have prepared a novel class of DNA analogues containing the [3′-NH-P(CH₃)(O)-O-5′] methanephosphonamidate linkage. Synthesis of such analogues requires preparation of the dinucleoside methanephosphonamidates N×N, where N is a 2′-deoxyribonucleoside moiety and × is the methanephosphonamidate linkage. Dimers T×T and C×T were obtained in a non-stereospecific manner giving rise to a pair of P-chiral diastereomers. Such diastereomers were effectively separated into fast and slow migrating ones by means of chromatographic methods (TLC). As described in our previous work (Nawrot et al. Nucleic Acids Res.1998, 26, 2650), the stereochemistry of the phosphorus chiral center of T×T fast migrating diastereomer is R_P and of T×T slow migrating diastereomer is S_P, as established by means of 2D ROESY experiments. Here we describe assignment of the absolute configuration at the phosphorus center of fast and slow migrating diastereomers of C×T dimer. The 2D ROESY sequence with phosphorus decoupling during acquisition used in these measurements allowed observation of the P-Me group as a singlet instead of a ¹H-³¹P-coupled doublet. The apparent advantage of this approach was a much better signal to noise ratio and improved resolution in the F1 dimension. For the fast migrating C×T diastereomer an R_P and for slow migrating C×T diastereomer an S_P configuration was assigned. Conformational analysis of both pairs of diastereomers T×T and C×T indicates significant differences in sugar ring puckering, which strongly depend on the nature of the nucleobase at the 5′-terminus of the dimer. The ribose rings of the 3′-amino-2′,3′-dideoxycytidine moiety of both diastereomers of C×T adopt predominantly a C3′-endo (North) conformation, while thymine-substituted ribofuranoses originating either from C×T or T×T dimers prefer a C2′-endo (South) conformation.     

Introduction of the HPLC method for the determination of quinolone residues in various muscle tissues

For use in veterinary sanitary control of foodstuffs and raw materials of animal origin in Slovenia, we developed a routine and confirmation analytical method for determining the residues of enrofloxacin, ciprofloxacin and flumequine in the muscle tissue of cattle, pigs and poultry. For the muscle tissue of freshwater fish, the determination of the flumequine residues was introduced. The results obtained through simultaneous determination of the residues of enrofloxacin, ciprofloxacin and flumequine showed that the values for the examined antibiotics were up to 600 times lower than the prescribed maximum residue levels (MRL). Another advantage of this method is that it covers a wide range of different fluoroquinolones.     

Determination of Cr(VI) in welding fumes by anion-exchange fast protein liquid chromatography with electrothermal atomic absorption spectrometric detection

The applicability of an anion-exchange fast protein liquid chromatographic-electrothermal atomic absorption spectrometric procedure (FPLC-ETAAS) was investigated for the determination of Cr(VI) in welding fumes after alkaline extraction of aerosols loaded on filters. Gas tungsten arc welding (GTAW) of stainless steel was applied. Samples of welding fumes were collected during regular welding on polycarbonate membrane filters of 8 microm and 0.4 microm pore size (inhalable and respirable aerosols). Alkaline extraction (2% NaOH-3% Na2CO3) of filters in a heated ultrasonic bath was applied to leach Cr from the airborne particulate matter. 0.5 cm3 of sample extract was then injected onto an anion-exchange FPLC column. Tris-HCl buffer (0.005 mol dm(-3), pH 8.0) and the same buffer with NaCl (0.5 mol dm(-3)) were employed in gradient elution (15 min, flow rate 1 cm3 min(-1)). The separated Cr species were determined "off line" by ETAAS in 0.5 cm3 fractions. Cr(VI) was reproducibly and quantitatively eluted from 12.0 to 13.0 min with a maximum peak at 12.5 min. Good repeatability of measurement (+/-3.0%) of alkaline extracts was obtained for Cr(VI). The LOD (3s) was found to be 0.035 microg m(-3) Cr(VI), when 2 m3 of aerosols were collected on the filter. Validation of the procedure was performed by spiking alkaline extracts and by the analysis of standard reference material CRM 545, Cr(VI) in welding dust loaded on a filter. The technique was successfully applied for the determination of Cr(VI) in welding fumes.     

Influence of substituents on the anharmonicity of nus(OH) vibration in phenol derivatives explored by experimental and theoretical approach

Very good reproducibility of the first five vibrational transitions of phenol in the gas phase by the MP2/ 6-31G potential for O-H bond stretching was found. The vibrational levels were calculated by a program for variational solving of the time-independent Schr?dinger equation in one dimension. Relative intensities of particular transitions were determined on the basis of the function of the dipole moment. The substituent effects on the nu(s)(OH) transitions and on the intensity of these transitions, as well as on the structure of eleven phenols, was analyzed as a function of the pK(a) values.     

15NH4+ ion movement inside d(G4T4G4)2 G-quadruplex is accelerated in the presence of smaller Na+ ions

2D NMR studies demonstrate that the residence lifetime of 15NH4+ ions within the bimolecular G-quadruplex adopted by d(G4T4G4) is reduced from 270 ms in the presence of ammonium ions alone to 36 ms in the presence of Na+ ions.     

Total metal concentrations in serum of dialysis patients and fractionation of Cu, Rb, Al, Fe and Zn in spent continuous ambulatory peritoneal dialysis fluids

Total metal concentrations were determined in the serum of 12 continuous ambulatory peritoneal dialysis (CAPD) patients and in fresh and spent CAPD fluids by electrothermal and flame atomic absorption spectrometry (ETAAS, FAAS). Concentrations of Cu in serum of CAPD patients ranged from 720 to 1780 ng cm⁻³, Rb from 128 to 346 ng cm⁻³, Al from 10 to 72 ng cm⁻³, Fe from 800 to 2300 ng cm⁻³ and Zn from 659 to 1310 ng cm⁻³. The accuracy of the analytical procedure was checked by the analysis of the reference material Seronom™, Trace Elements in Serum. Good agreement between the certified and determined values was obtained for Al, Cu, Fe and Zn. The data on the total metal concentrations in CAPD fluids indicated that during CAPD fluid exchange the losses of Cu from 5.0 to 35 ng cm⁻³, of Rb from 50 to 110 ng cm⁻³ and of Al from 3.0 to 14.0 ng cm⁻³ occurred through the peritoneal membrane. Although fresh CAPD fluids contained traces of Fe (3.0-5.0 ng cm⁻³), the transfer of this element took place through the peritoneal membrane into spent CAPD fluid (13.0-38.0 ng cm⁻³). Zn concentrations were in general lower in spent (20.0-80 ng cm⁻³) than in fresh CAPD fluids (∼100 ng cm⁻³). To follow the mechanisms of the transfer of trace elements through the peritoneal membrane of CAPD patients, fractionation of metals was carried out in spent CAPD fluids by size exclusion chromatography with UV and AAS detection, applying Superdex HR 10/30 column. The chromatographic run was followed at 278 nm and separated metal species also determined ‘off line’ in 1 cm³ fractions by ETAAS or FAAS. From the UV chromatograms and AAS analysis of trace elements in the separated fractions it was demonstrated that Cu, Al, Fe and Zn were bound to proteins and only partially to low molecular weight (LMW) species, while Rb was associated exclusively with LMW species. For characterisation of the high molecular weight (HMW) binding proteins, fractions containing trace elements were subjected to SDS-PAGE electrophoresis. Al and Fe were presumably bound to transferrin, but due to its low concentration in spent CAPD fluids, it was not possible to confirm its presence in the separated fractions. About 10% of Al and 15% of Fe corresponded to LMW species. A fraction of HMW proteins of Cu in spent CAPD fluids was most probably bound to albumin and Zn to albumin and globulins. About 50% of Cu and Zn existed in LMW proteins, while Zn was also found partially in ionic form.     

Hemiortho esters and hydrotrioxides as the primary products in the low-temperature ozonation of cyclic acetals: an experimental and theoretical investigation

Low-temperature ozonation (-78 degrees C) of 1,3-dioxolanes 1a-1f and 1,3-dioxanes 1g and h in acetone-d6, methyl acetate, and tert-butyl methyl ether produced both the corresponding hemiortho esters (2a-h, ROH) and acetal hydrotrioxides (3a-h, ROOOH) in molar ratios ROH/ROOOH ranging from 0.5 to 23. Both types of intermediates were fully characterized by 1H, 13C, and 17O NMR spectroscopy. DFT calculations suggest that ozone abstracts a hydride ion from 1 to form an ion pair, R+ -OOOH, which subsequently collapses to either the corresponding hemiortho ester (ROH) or the acetal hydrotrioxide (ROOOH). Hemiortho esters decomposed quantitatively into the corresponding hydroxy esters. Experimentally obtained activation parameters for the decomposition of 2a (E(a) = 13.5 +/- 1.0 kcal/mol, log A = 8.3 +/- 1.0) are in accord with a highly oriented transition state involving, according to B3LYP calculations (deltaH(a)(298) = 13.2 kcal/mol), two molecules of water as a bifunctional catalyst. This mechanism is also supported by the magnitude of the solvent isotope effect for the decomposition of 2e, i.e., k(H2O)/k(D2O) = 4.6 +/- 1.2. Besides the hydroxy esters and oxygen (3O2/1O2), dihydrogen trioxide (HOOOH) was formed in the decomposition of most of the acetal hydrotrioxides (ROOOH) investigated. The activation parameters for the decomposition of the hydrotrioxides 3a-e in various solvents were E(a) = 20 +/- 2 kcal/mol, log A = 13.5 +/- 1.5. Several mechanistic possibilities for the decomposition of ROOOH were tested by experiment and theory. The formation of the hydroxy esters and oxygen could be explained by the intramolecular transfer of the proton to form the hydroxy ester. The assistance of water in the decomposition of ROOOH to form the hydroxy esters, either directly or via hemiortho esters, was also investigated. According to DFT calculations, the formation of a hydroxy ester via hemiortho ester is energetically more favorable (deltaH(a)(298) = 14.5 kcal/mol), again due to the catalytic effect of two water molecules. HOOOH generation requires the involvement of water in the decomposition of ROOOH where the direct formation out of ROOOH is energetically preferred. The energy for a reaction between two molecules of water and singlet oxygen (delta1O2) is too high to occur in solution.     

Conformational analysis of oleandomycin and its 8-methylene-9-oxime derivative by NMR and molecular modelling

Conformations of the 14-membered macrolide antibiotic oleandomycin and its 8-methylene-9-oxime derivative were determined in various solvents. The experimental NMR data--coupling constants and NOE contacts--were compared with the results of molecular modelling--molecular mechanics calculations and molecular dynamics simulations. The conformational changes, on the right-hand side of the 14-membered ring, affected mostly the 3JH2,H3 values and NOE crosspeaks H3 or H4 to H11. Oleandomycin was found to be present predominantly in the C3-C5 folded-in conformations in DMSO-d6 solution, whereas in buffered D2O, acetone-d6 and CDCl3, there was a mixture of folded-in and folded-out conformational families. The predominant conformation of the 8-methylene-oleandomycin-9-oxime derivative in solution was a folded-out one although different amounts of folded-in conformation were also present depending on the solvent. Oleandrose and desosamine sugar moieties adopted the usual and expected chair conformation. The conformation around the glycosidic bonds, governing the relative orientation of sugars vs. the lactone ring, showed a certain flexibility within two conformationally close families. We believe that by combining the experimental NMR data and the molecular modelling techniques, as reported in this paper, we have made significant progress in understanding the conformational behaviour and properties of macrolides. Our belief is based on our own current studies on oleandomycins as well as on the previously reported results and best practices concerning other macrolides. A rational for macrolide conformational studies and advances in methodology has been suggested accordingly.     

Invariant and Almost-Invariant Subspaces for Pairs of Idempotents

It is known that every bounded operator on an infinite dimensional separable Hilbert space \({\mathcal{H}}\) has an invariant subspace if and only if each pair of idempotents on \({\mathcal{H}}\) has a common invariant subspace. We show that the same equivalence holds for operators and pairs of idempotents that are essentially selfadjoint. We also show that each pair of idempotents on \({\mathcal{H}}\) has a common almost-invariant half-space.     

Reversible pH Switch of Two‐Quartet G‐Quadruplexes Formed by Human Telomere

A four‐repeat human telomere DNA sequence without the 3′‐end guanine, d[TAGGG(TTAGGG)₂TTAGG] (htel1‐ΔG23) has been found to adopt two distinct two G‐quartet antiparallel basket‐type G‐quadruplexes, TD and KDH⁺ in presence of KCl. NMR, CD, and UV spectroscopy have demonstrated that topology of KDH⁺ form is distinctive with unique protonated T18?A20⁺?G5 base triple and other capping structural elements that provide novel insight into structural polymorphism and heterogeneity of G‐quadruplexes in general. Specific stacking interactions amongst two G‐quartets flanking base triples and base pairs in TD and KDH⁺ forms are reflected in 10 K higher thermal stability of KDH⁺. Populations of TD and KDH⁺ forms are controlled by pH. The (de)protonation of A20 is the key for pH driven structural transformation of htel1‐ΔG23. Reversibility offers possibilities for its utilization as a conformational switch within different compartments of living cell enabling specific ligand and protein interactions.