Empirical energy functions for energy minimization and dynamics of nucleic acids

An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.     

Harmful azo colorants in leather. Determination based on their cleavage and extraction of corresponding carcinogenic aromatic amines using modern extraction techniques

This study concerns the possibilities of using microwave-assisted extraction (MAE) or supercritical fluid extraction (SFE) for detection of harmful azo colorants in leather. After degreasing of the leather sample with SFE there follows a reductive cleavage of the azo colorants to their corresponding aromatic amines in the MAE or SFE equipment. The aromatic amines are subsequently extracted using either MAE or SFE and then finally determined by liquid chromatography with diode-array detection. The results have been compared with recoveries obtained using the German DIN method 53316. This standard method, based on conventional solvent extraction, is used in several European countries. Overall much better recoveries were obtained using MAE or SFE. With both MAE and SFE the amine recoveries of spiked leather samples were generally above 50%. The average recoveries were 62% for MAE and 60% for SFE (solvent collection) compared to 24% with the DIN method. For genuine leather samples the recoveries decreased, especially for benzidine. In this case the average values for MAE, SFE and DIN were 54, 38 and 19%, respectively. The quantification limits in leather samples using MAE or SFE were below 1 mg/kg for all amines investigated. The within-laboratory precision was generally better than 10%, varying somewhat with the analyte considered. With the proposed methodology, the amount of hazardous organic solvents used could be decreased and the sample throughput increased with at least a factor of two with less manual handling compared to the DIN method.     

Standard additio--a way of improving quantification of banned azo dyes in leather

An analytical procedure based on supercritical-fluid extraction and microwave-assisted extraction was applied on six different real leather samples for the determination of banned azo dyes. Determination of the dyes was performed indirectly by measuring their corresponding harmful aromatic amines, formed after reduction. A comparative study between external standard calibration and standard addition using both the dyes as well as the corresponding amines showed that the latter quantification method provided the highest accuracy.     

Studies on dodecyl betainate in combination with its degradation products or with phosphatidyl choline-phase behavior and hemolytic activity

Surface active betaine esters contain a hydrolysable bond and give naturally occurring products (fatty alcohol and the amino acid betaine) on degradation. They are therefore interesting candidates for use as cationic surfactants in pharmaceutical applications. In this work the phase behavior of two systems of relevance for the utilization of dodecyl betainate as a pharmaceutical excipient is studied, namely dodecyl betainate/dodecanol/betaine hydrochloride/D2O and dodecyl betainate/phosphatidyl choline (PC)/ethanol/D2O. The techniques used for phase characterisation were 2H NMR measured on the solvent, small angle X-ray spectroscopy and optical microscopy. Dilute dodecyl betainate/PC dispersions were characterized using laser diffraction. It is shown that introduction of relatively small amounts of the hydrolysis products of dodecyl betainate, i.e., dodecanol and betaine (used in the form of betaine hydrochloride), has a strong effect on the phase behavior of the binary dodecyl betainate/D2O system. The degradation products change the average curvature of the surfactant film so that, instead of a hexagonal phase at concentrations above the micellar phase, a probably defective, lamellar phase seems to form. The dodecyl betainate/PC/ethanol/D2O system shows a large region of a highly swelling lamellar phase. Dispersions of dodecyl betainate/PC/ethanol in water can be prepared with low energy input; i.e., the preconcentrate can be regarded as a self-dispersing solution. Introduction of dodecyl betainate and its degradation products does not impair the ability of PC to form vesicles. Experiments for evaluating the toxicity of surface active betaine esters to erythrocytes were also performed. There are indications that the hemolytic activity of dodecyl betainate is lower than that of the stable surfactant tetradecyltrimethylammonium chloride, which has similar critical micelle concentration. A combination of dodecyl betainate and PC gives very low hemolytic activity.     

Hydrolyzable nonionic surfactants: stability and physicochemical properties of surfactants containing carbonate, ester, and amide bonds

A linear and a branched nonionic cleavable surfactants containing a carbonate bond have been prepared from tetra(ethylene glycol) and an alkylchloroformate. The stability of these carbonate surfactants was determined by investigating their hydrolysis and biodegradability characteristics. The hydrolysis was catalyzed by alkali or enzymes (esterase from porcine liver and lipases from Mucor miehei and Candida antarctica B) and was monitored using 1H NMR. It was found that the stability toward alkali was higher for a carbonate surfactant than for a corresponding surfactant with an ester as weak bond. Biodegradation tests resulted in more than 60% degradation after 28 days for both carbonate surfactants. Physicochemical properties, such as critical micelle concentration (CMC), cloud point, area per molecule, and surface tension at the CMC, were determined and compared to those obtained from similar surfactants containing ester, amide, or ether bonds. It was found that the carbonate linkage is hydrophobic and that the oxycarbonyl part of the carbonate group is equivalent, in a formal sense, to an extra methylene group in the alkyl chain of the surfactant.     

Kinetics of the Formation of Nano-Sized Platinum Particles in Water-in-Oil Microemulsions

The association between low-charge-density polyelectrolytes adsorbed onto negatively charged surfaces (mica and silica) and an anionic surfactant, sodium dodecyl sulfate (SDS), has been investigated using surface force measurements, ellipsometry, and XPS. All three techniques show that the polyelectrolyte desorbs when the SDS concentration is high enough. The XPS study indicates that desorption starts at a SDS concentration of ca. 0.1 unit of cmc (8x10(-4) M) and that the desorption proceeds progressively as the SDS concentration is increased. Surface force measurements show that for the polyelectrolyte studied here, having 1% of the segments charged, the desorption proceeds without any swelling of the adsorbed layer. This behavior differs from that observed when polyelectrolytes of greater charge density are used. Copyright 2001 Academic Press.     

Automated magnetic preparation of DNA templates for solid phase sequencing.

An integrated protocol for solid-phase DNA sequencing using a robotic work station is described involving magnetic separation of DNA and analysis of the sequencing product by electrophoresis with automated detection of the fluorescently labeled fragments. The method, which is based on magnetic beads in combination with streptavidin-biotin technology, can be used for sequencing both genomic and plasmid DNA. The DNA template is obtained by the polymerase chain reaction (PCR). Protocols to prepare five and ten immobilized samples is described, giving 10 and 20 single-stranded templates, respectively. The magnetic purification steps are performed in a microtiter plate and this allows for an integrated scheme involving a subsequent procedure for automated primer annealing and sequencing reactions. Here, the procedure is examplified by direct genomic sequencing of DNA in blood sample from a human immunodeficiency virus (HIV)-infected patient and a cloned human antibody DNA fragment using fluorescently labeled sequencing primers.     

THE REPAIR OF DNA STRAND BREAKS IN HUMAN LYMPHOCYTES EXPOSED TO NEAR UV-RADIATION (UVA) AND FAR UV-RADIATION (UVC)

Abstract— UVA irradiation of human lymphocytes induces DNA strand breaks and a portion of these breaks are closed at a slower rate than X-ray induced DNA strand breaks and the strand breaks generated during repair of UVC induced DNA lesions. In addition, the yield of DNA strand breaks in lymphocytes pretreated with UVA radiation and given a subsequent exposure with UVC radiation is higher and shows a slower decrease with increasing repair time in comparison with the expected yield based on additivity between UVA and UVC induced DNA strand breaks. This indicates that UVA delays the closure of the intermediate strand breaks formed in the repair process of UVC induced DNA lesions.     

Method for differential detection and identification of components in protein mixtures analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

We demonstrate that the semi-quantitative information in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra of tryptically digested protein mixtures can, via a systematic statistical approach, be utilized for the identification of a protein present in different concentrations in two samples. Multiple mass spectra were acquired from a series of tryptically digested test samples in which the concentration of one protein was varied and the concentrations of three other proteins were held constant. The mass spectra were subjected to soft independent modeling of class analogy (SIMCA) analysis assuming that spectra originating from two different samples belonged to different data classes. The SIMCA analysis yielded information on which individual m/z values discriminate between two classes. Protein identification by proteolytic peptide mass fingerprinting was performed with different numbers of mass values in the fingerprint according to the discriminatory information, beginning with the mass corresponding to the best discrimination, followed by the best together with the second best, etc. By using the Probity algorithm, which computes the statistical significance of each identification result, we demonstrate that the first protein identified at a desired significance level (0.001) is the protein that was present in a different concentration in the two samples. Differential analysis of expression is often performed by comparing 2D-gel-spot intensities followed by mass spectrometric identification of the respective protein in each spot that differs. The method presented here has the potential to allow identification of the protein component that differs in cases where a gel-spot is poorly resolved and contains several proteins.     

Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling

We present results showing the importance of appropriate treatment of atomic masses in molecular dynamics (MD)-based single topology free-energy perturbations (FEPs) on small molecule systems. The reversibility of gas phase simulations is significantly improved by scaling the atomic mass of mutated atoms with the lambda variable normally used for the scaling of energy terms. Because this effect is less pronounced for solvated systems, it will not cancel in estimates of the relative hydration free energy difference. The advantage of mass scaling is demonstrated by a null mutation of ethane to ethane and the calculation of the relative hydration free energy difference between ethane and n-propane. Furthermore, it is found that the simulation time necessary for converged MD/FEPs is prohibitively large for relative hydration free energy calculations on cyclic alkanes. Therefore, we explore an alternative free energy pathway including strongly constrained conformations to improve convergence in FEP simulations of flexible molecules.