ChipCheck--a program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays

Presented here is the program ChipCheck that allows the computation of total hybridization equilibria for hybridization experiments involving small oligonucleotide arrays. The calculation requires the free energies of binding for all pairs of probes and targets as well as total strand concentrations and probe molecule numbers. ChipCheck has been tested computationally on microarrays with up to 100 spots and 42 target strands (4200 binding equilibria). It arrives at solutions through iterations employing the multidimensional Newton method. While currently running in simulation mode only, an extension of the approach to the exhaustive analysis of chip results is being outlined and may be implemented in the future. The output displays the extent of correct and cross hybridization both graphically and numerically. In principle, calculating total hybridization equilibria allows for eliminating noise from DNA chip results and thus an improvement in sensitivity and accuracy.     

Biologically active metabolites from fungi, 17. 8-alpha-acetoxyverrol,a new member of the trichothecene sesquiterpenes

8-alpha-Acetoxyverrol (4), the first open chain example of the trichothecenes with oxygenation at C-8, was isolated from cultures of Aphanocladium spectabile. The compound doses the biosynthetic gap to the macrocyclic verrucarins.     

A physical model of laser-assisted blocking of blood flow: II. Pulse modulation of radiation

A method for the calculation of blocking of blood flow upon treatment of vessel pathologies by laser irradiation at a wavelength of 530 nm are considered. The model is based on the assumption that blood-vessel occlusion is a consequence of preceding photothermal coagulation of internal layers of the vessel wall. The irradiation regimes are determined that provide homogeneous and highly efficient coagulation of the vessel wall under irradiation of tissues by series of short radiation pulses.     

Bio-compatible in-tube solid-phase microextraction capillary for the direct extraction and high-performance liquid chromatographic determination of drugs in human serum

A restricted access material (RAM), alkyl-diol-silica (ADS), was used to prepare a highly bio-compatible solid-phase microextraction (SPME) capillary for the automated and direct in-tube extraction of several benzodiazepines from human serum. The bifunctionality of the ADS extraction phase prevented fouling of the capillary by protein adsorption while simultaneously trapping the analytes in the hydrophobic porous interior. This the first report of a restricted access material utilized as an extraction phase for in-tube SPME. The approach simplified the required apparatus in comparison to existing RAM column switching procedures, and more importantly eliminated the excessive use of extraction solvents. The biocompatibility of the ADS material also overcame the existing problems with in-tube SPME that requires an ultrafiltration or other deproteinization step prior to handling biological samples, therefore further minimizing the sample preparation requirements. The calculated oxazepam, temazepam, nordazepam and diazepam detection limits were 26, 29, 22 and 24 ng/ml in serum, respectively. The method was linear over the range of 50-50 000 ng/ml with an average linear coefficient (R2) value of 0.9998. The injection repeatability and intra-assay precision of the method were evaluated with five injections of a 10-microg/ml serum sample (spiked with all compounds), resulting in an average RSD<7%. The ADS extraction column was robust, providing many direct injections of biological fluids for the extraction and subsequent determination of benzodiazepines.     

Trifluoromethylation of [AuF3(SIMes)]: Preparation and Characterization of [Au(CF3)xF3−x(SIMes)] (x=1–3) Complexes

Trifluoromethylation of [AuF₃(SIMes)] with the Ruppert–Prakash reagent TMSCF₃ in the presence of CsF yields the product series [Au(CF₃)_xF_3−x(SIMes)] (x=1–3). The degree of trifluoromethylation is solvent dependent and the ratio of the species can be controlled by varying the stoichiometry of the reaction, as evidenced from the ¹⁹F NMR spectra of the corresponding reaction mixtures. The molecular structures in the solid state of trans-[Au(CF₃)F₂(SIMes)] and [Au(CF₃)₃(SIMes)] are presented, together with a selective route for the synthesis of the latter complex. Correlation of the calculated SIMes affinity with the carbene carbon chemical shift in the ¹³C NMR spectrum reveals that trans-[Au(CF₃)F₂(SIMes)] and [Au(CF₃)₃(SIMes)] nicely follow the trend in Lewis acidities of related organo gold(III) complexes. Furthermore, a new correlation between the Au−C_carbene bond length of the molecular structure in the solid state and the chemical shift of the carbene carbon in the ¹³C NMR spectrum is presented.     

On the formation of protonated acetic acid from ionized n-alkanoic acids in the gas phase

By means of collisional activation mass spectrometry and semi-empirical molecular orbital calculations (MNDO) it is shown that the [C₂H₅O₂]⁺ ions from metastable molecular ions of n-pentanoic and hexanoic acid have the structure of carbonyl protonated acetic acid [CH₃C(OH)₂]⁺. The MNDO calculated geometries of this ion and some other isomeric forms are given together with the ΔH_f⁰ values.