Microcalorimetrics studies of the thermodynamics and binding mechanism between L-tyrosinamide and aptamer

In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.     

Mass spectrometry of heterocyclic compounds VIII–electron-impact-induced fragmentation of 1,2-diphenyl-pyrazolidine-3,5-dione and some 4-substituted derivatives

The mass spectra of 1,2-diphenyl-pyrazolidine-3,5-dione and twenty-one 4-substituted derivatives are reported. Their fragmentation patterns have been studied by deuterium labelling, exact mass measurements, metastable studies by the defocusing technique and low energy spectra. Hydrogen rearrangements from the 4-position of the heterocycle and/or from the ß-position of the 4-substituent groups, lead to the main primary fragment ions [C₁₂H₁₁N₂]⁺ (m/e 183) as shown by the metastables. The 4,4-d₂ derivative shows an appreciable isotope effect even for molecular ions decomposing in the ion source. By comparison with the metastable abundances of competitive reactions, the molecular ions (m/e 252) of the 4-unsubstituted compound appear to be structurally different from the corresponding m/e 252 fragment ions formed from 4-derivatives by the loss of 4-substituent with H rearrangement. If only vinylic or aromatic hydrogen atoms are present, primary cleavage of the heterocyclic ring occurs with loss of OH·, C₃O₂ and C₃HO₂. Important rearrangements leading to elimination of C₆H₆N and C₆H₇N are typical for unsaturated substituents on position four having allylic hydrogen atoms. Fragment ions, identical to molecular ions of some compounds discussed here, are obtained by electron-impact and/or thermal decompostion of some complex compounds containing more than one 1,2-diphenyl-pyrazolidine-3,5-dione system. The [C₆H₅N₂]⁺ (m/e 105) and [C₆H₅]⁺ (m/e 77) ions are common fragments of all the title compounds. Any hydrogen scrambling reactions between phenyl and heterocycle or 4-substituent groups can be excluded.     

Synthesis,spectroscopic and magnetic characterization of some iron(III)-nucleotide compounds

Summary Magnetic moments and⁵⁷Fe M?ssbauer spectra at various temperatures of polycrystalline samples of some Fe^III-nucleotide compounds are described and have been characterized by u.v.-visible and fluorescence spectroscopy. Conclusions regarding the binding of iron(III) to nucleic acids are discussed.     

Decolorization of Naphthol Blue Black using the Horseradish Peroxidase

This study evaluates the potential of the enzyme horseradish peroxidase in the decolorization of one common industrial azo dye, naphthol blue black. Studies are carried out to understand the process parameters such as pH, temperature and reaction time. The enzymatic decolorization of the dye was examined by UV-Vis spectrophotometer and LC-MS measurements. Temperature and pH conditions were optimized for obtaining high azo-dye decolorization. Azo-dye removal at a pH range 4-6 was found to be the highest for all temperatures. After 5 minutes of treatment, the color removal of dye was ca. 80-90%. The LC-MS and spectrophotometric analyses indicated that the decolorization of the azo dye with enzyme was due to the reduction of the azo bonds. This study verifies the viability of the use of the horseradish peroxidase in the decolorization of naphthol blue black.     

Photocatalytic efficiency of nanocrystalline zeolite TS-1 for the degradation of methyl orange

The photocatalytic properties of nanocrystalline TS-1 were confirmed via the degradation of an aqueous solution of the model compound methyl orange (MO). The light intensity and quantum yield were measured by ferrioxalate actinometry and the values are 1.7 × 10⁻⁵ einstein l⁻¹ s⁻¹ and 0.71, respectively. The experimental parameters such as catalyst loading, pH and initial concentration of MO were optimized at 1.5 g/L, 10 and 300 μM, in order. The results showed that the dye molecules are completely degraded to CO₂, H₂O and simple inorganic ions.     

Heterodiene syntheses—XIX: Correlation of the kinetic data with lumo energies in the reaction between 1-aryl-4-benzylidene-5-pyrazolones and isopropyl vinyl ether

The kinetics of the reaction between 1-p-substituted phenyl-4-benzylidene-5-pyrazolones and isopropyl vinyl ether have been studied by quantitative spectroscopic analysis and liquid chromatography. The rate increases with the electron attracting character of the substituents and a correlation is obtained with σ- constants. The polarographic one-electron half-wave reduction potentials E^red_{$\text{1}\text{2}$}, which represent an experimental measure for the relative energy of the lowest unoccupied molecular orbital (LUMO), were measured. Good correlations were obtained between these and the kinetic data, thus demonstrating the frontier-controlled character of the cycloaddition and the dominant interaction between the LUMO of the pyrazolone and the highest occupied molecular orbital (HOMO) of the vinyl ether.     

The stokes-kirchhoff relation in chemically reacting fluids

A generalized Kirchhoff-Stokes equation for the sound attenuation coefficient is derived from irreversible thermodynamics. The discrepancy between the experimental value of the absorption coefficient and the value calculated from the generalized equation is analyzed. In particular, the so-called effective bulk viscosity and the transport coefficient which links a chemical reaction to the viscous processes are emphasized. An experimental example illustrating the general situation is also given.     

Ion chemistry of α-diazoketones. 1. A collissional activation study of 1-diazo-3-phenoxypropan-2-one upon elecgtron impact

The gaseous ionic products of 1-diazo-3-phenoxypropan-2-one upon electron impact show that cyclization reactions, which have counterparts in condensed-phase chemistry, occur in competition with a mass spectral Wolff type rearrangement.     

Relationship between radial diffusion of copper ions released from a metal disk and cytotoxic effects. Comparison with results obtained using extracts

The extended use of metallic biomaterials yields to increasing sources of metal ions within the human body and may result in inflammation of the surrounding tissues, cell damage, and cancer. The aim of this study was to investigate the relationship between the radial diffusion of metal ions released from a metal disk by the corrosion process and the toxic effect on a cell line that grew around it. Results obtained with the metal disks (direct contact) were compared with assays made with extracts obtained from the dissolution of a metallic sample ex situ and then added to the cell culture to elucidate the cause of apparent inconsistencies in previous reports. The change of copper concentration due to corrosion and transient diffusion of copper ions from the copper disks into the cell line was evaluated according to Fick's 2nd law. Surviving cells distribution was interpreted considering the radial and time-dependence of copper concentration. We concluded that the toxic effect on those cells close to metallic biomaterials may be underestimated when only the extract methodology is employed for cytotoxic tests or when during the experiments with disks the presence of concentration gradients and the non-homogeneous distribution of dead cells are disregarded.