Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism

The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling. The experimental spectra were unambiguously assigned to the quadruplex DNA arrangement, and several IR and VCD bands related to this structural motif were determined. Involvement of MD in the modeling was essential for realistic simulation of the spectra. The VCD signal was found to be more sensitive to dynamical structural variations than the IR signal. The combination of the spectroscopic techniques with multiscale simulations provides extended information about nucleic acid conformations and their dynamics.     

The electrodeless discharge lamp: a prospective tool for photochemistry: Part 3. The microwave photochemistry reactor

A simple and original microwave photochemical reactor is described in detail. It consists of an electrodeless discharge lamp placed into the reaction vessel in a modified domestic microwave oven. The microwave field generates ultraviolet radiation by the lamp at the same time when it interacts with the reaction mixture. The construction, experimental set-ups, applications, and safety precautions are discussed.     

Polyacrylonitrile molecular weight effect on the structural and magnetic properties of metal–carbon nanomaterial

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Determination of the LOQ in real-time PCR by receiver operating characteristic curve analysis: application to qPCR assays for Fusarium verticillioides and F. proliferatum

Real-time PCR (qPCR) is the principal technique for the quantification of pathogen biomass in host tissue, yet no generic methods exist for the determination of the limit of quantification (LOQ) and the limit of detection (LOD) in qPCR. We suggest using the Youden index in the context of the receiver operating characteristic (ROC) curve analysis for this purpose. The LOQ was defined as the amount of target DNA that maximizes the sum of sensitivity and specificity. The LOD was defined as the lowest amount of target DNA that was amplified with a false-negative rate below a given threshold. We applied this concept to qPCR assays for Fusarium verticillioides and Fusarium proliferatum DNA in maize kernels. Spiked matrix and field samples characterized by melting curve analysis of PCR products were used as the source of true positives and true negatives. On the basis of the analysis of sensitivity and specificity of the assays, we estimated the LOQ values as 0.11 pg of DNA for spiked matrix and 0.62 pg of DNA for field samples for F. verticillioides. The LOQ values for F. proliferatum were 0.03 pg for spiked matrix and 0.24 pg for field samples. The mean LOQ values correspond to approximately eight genomes for F. verticillioides and three genomes for F. proliferatum. We demonstrated that the ROC analysis concept, developed for qualitative diagnostics, can be used for the determination of performance parameters of quantitative PCR.     

Fast choice of separation conditions for analyses by capillary zone electrophoresis using an information system Xemic

An information system Xemic applicable in analytical chemistry is described and its use in capillary electrophoresis for searching suitable separation conditions is demonstrated. This system is capable to provide suitable separation conditions even for analytes for which no electrophoretic experiments have been published so far. The system works with a database of components of anionic character the analyses of which have been performed, published in reviewed scientific journals, and included into a database created by an expert. Moreover, the system learned to search also in abstracts or complete scientific articles to find articles dealing with the determination of a substance in a given sample matrix. When no experiments have been published so far for a defined substance in a specific matrix, Xemic shows the separation conditions for determination of the substance regardless of the matrix. When no response can be found for the analyte of interest at all, the system Xemic works like an expert in the field and searches chemically similar substances and offers a series of substances the physicochemical properties of which are close to the followed analyte with respect to the behavior in the electric field, and shows working conditions for their analysis. Thus, the analyst puts only the order in the form of a given analyte in a given matrix and obtains a recommendation of a separation system that should enable to perform a successful separation. The system is not rigid and enables the operator to change the importance of individual attributes used in similarity search so as to obtain a broader or narrower group of similar components. With a certain probability the analyte of interest can be successfully analyzed under separation conditions that suited for the analysis of the most similar substances in the given matrix.     

Raman and FTIR spectroscopic characterization of electrochemically synthesized poly(triphenylamine), PTPA

Triphenylamine was electrochemically polymerized in a mixture of toluene and acetonitrile with different electrolyte salts. The poly(triphenylamine) (PTPA) films are insoluble in polar solvents and show high stability and no degradation or loss in electrochemical properties when stored in a laboratory atmosphere. The PTPA films were characterized in situ by FTIR external reflection spectroscopy and by Raman spectroscopy. Electronic Publication     

On the complexation of some univalent cations with 1,3-alternate-25,27-bis(1-octyloxy)calix[4]arene-crown-6 in nitrobenzene saturated with water

From extraction experiments and γ-activity measurements, the exchange extraction constants corresponding to the general equilibrium M⁺ (aq) + 1·Cs⁺ (nb) ? 1·M⁺ (nb) + Cs⁺ (aq) taking place in the two-phase water–nitrobenzene system (M⁺ = Ag⁺, K⁺, Rb⁺, Tl⁺; 1 = 1,3-alternate-25,27-bis(1-octyloxy)calix[4]arene-crown-6; aq is aqueous phase, nb is nitrobenzene phase) were determined. Moreover, the stability constants of the 1·M⁺ complexes in water-saturated nitrobenzene were calculated; they were found to increase in the series of K⁺ < Rb⁺ < Ag⁺ < Tl⁺.