Structural analysis of base mispairing in DNA containing oxidative guanine lesion

Classical molecular dynamics methods were used to analyze the importance of 8-oxoguanine (8-oxoG) pairing with other DNA bases in order to determine the impact of oxidative guanine lesions on DNA structure. Six lesioned molecules, each containing 8-oxoG mispaired with one of the four normal bases on the the opposite strand at the center of 40-mer DNA, and one non-damaged DNA molecule, were simulated for 2 nanoseconds of real time. The 8-oxoG lesioned bases were found to incorporate opposite all normal bases. There are observed conformational and energetical differences among these parings. 8-oxoG in anti-form creates firm hydrogen bonds with cytosine and this bonding has a strong attractive electrostatic interaction energy similar to that of a native base pair-guanine to cytosine. Meanwhile, it does not form a stable base pair with purine bases (adenine and guanine) nor with the pyrimidine base thymine. On the other hand, the 8-oxoG in syn-form was found to pair with adenine.      

On the k-index of graphs

Given a graph, join every two vertices which are at a distance greater than a fixed integer k (>1)by a new path of length k. Thus a graph transformation is defined. The least number of iterations of this transformation such that the last iteration does not change the graph, is called the k-index of the original graph. In the present paper the graphs are classified according to their k-indices. The results are applied in the study of so-called tied graphs.     

Development of rapid and high‐throughput LC–MS/MS method for quantification of olprinone in rabbit plasma

A simple, highly sensitive and rapid method for quantification of olprinone (phosphodiesterase 3 inhibitor) in rabbit plasma using liquid chromatography–tandem mass spectrometry with electrospray was developed. An aliquot of 50 μL of plasma sample was cleaned up and extracted using Ostro? 96‐well plate followed by dilution. Chromatographic separation of olprinone and olprinone‐d3 was carried out on a CORTECS^® T3 column within 3 min. Detection was achieved using a triple quadrupole mass spectrometer employing electrospray ionization operated in positive ion multiple reaction monitoring mode using the transitions m/z 251.07 → m/z 155.06 and m/z 254.21 → m/z 158.10 for olprinone and olprinone‐d3, respectively. The method was validated according to US Food and Drug Administration guideline for bioanalytical methods, and showed excellent linearity in the range 10.0–2000.0 ng/mL with coefficient of determination >0.99. The intra‐ and inter‐day precisions (CV) were <5.1% and the accuracies were within the range 99.7–103.2% at all quality control concentrations. Furthermore, olprinone was stable under various stability conditions. The developed method was used for quantification of olprinone in rabbit plasma after its intravenous administration at the dose of 1 mg/kg in order to better understand the metabolism of olprinone in a rabbit model of lung injury.     

Polysubstituted 5‐Phenylazopyrimidines: Extremely Fast Non‐ionic Photochromic Oscillators

Photochromic systems with an ultrahigh rate of thermal relaxation are highly desirable for the development of new efficient photochromic oscillators. Based on DFT calculations, we designed a series of 5‐phenylazopyrimidines with strong push–pull character in silico and observed very low energy barriers for the thermal (Z)‐to‐(E) isomerization. The structure of the (Z)‐isomer of the slowest isomerizing derivative in the series was confirmed by NMR analysis with in situ irradiation at low temperature. The substituents can tune the lifetime of thermal back isomerization from hundreds of microseconds to several nanoseconds (8 orders of magnitude). The photoswitching parameters were extracted from transient absorption techniques and a dominant rotation mechanism of the (Z)‐to‐(E) thermal fading was proposed based on DFT calculations.     

Spectral properties of tetraanionic porphyrin in formamide colloids of layered double hydroxides

Formamide colloidal suspensions of layered double hydroxides (LDHs) with anionic dye, meso-tetrakis(4-sulfonatophenyl)porphine (TPPS) were prepared. Optical properties of these suspensions were investigated by means of absorption and fluorescence spectroscopies in the visible region. For more detailed characterization, second derivative curves of the spectra were calculated. The adsorption of the dye on LDH nanosheets led to partial molecular aggregation, reflected in significant changes of the dye optical properties. The Soret band in the absorption spectra was split into two peaks and decreased in intensity. Changes were observed also for the Q-bands. The molecular aggregation significantly quenched the emission of the dye. The low intensity emission from dye H-aggregates was identified at slightly longer wavelengths. The molecular aggregation increased with the dye/LDH ratio. At low dye loadings, the optical properties were very similar to the dye solution. The yields of the dye molecular aggregation increased with LDH surface charge.      

Electrochemical investigation of NaOH—Na<Subscript>2</Subscript>O—Na<Subscript>2</Subscript>O2—H<Subscript>2</Subscript>O—NaH melt by EMF measurements and cyclic voltammetry

Thermodynamic activity of sodium oxide and oxidation potential in NaOH—Na₂O—Na₂O₂—H₂O—NaH melt at the temperature of 400°C was investigated. Galvanic cell for the potentiometric measurements consisted either of a sodium electrode formed by β and β″-alumina semi-closed tube filled with liquid sodium or a platinum wire and of an oxygen electrode made from ZrO₂ (Y₂O₃) solid electrolyte with the Bi—Bi₂O3 reference mixture. The number of exchanged electrons determined from the electromotive force measurements was in good agreement with the assumed reactions. The activity coefficient of sodium oxide was lower than one. Voltammetric measurements were carried out with a sodium reference electrode and a nickel auxiliary electrode. Behaviour of platinum, gold, silver and nickel as working electrodes was studied. The experiments were carried out in nitrogen atmosphere. Several types of zirconia semi-closed tubes were tested for long-term measurements under the process conditions.     

Ruthenation of duplex and single-stranded d(CGGCCG) by organometallic anticancer complexes

We have studied the interaction of the organometallic anticancer ruthenium(II) complexes [(eta(6)-p-cymene)Ru(en)Cl][PF(6)] (1) and [(eta(6)-biphenyl)Ru(en)Cl][PF(6)] (2) (en=ethylenediamine) with the single-stranded (ss) DNA hexamer d(CGGCCG) (I) and the duplex d(CGGCCG)(2) (II) by HPLC, ESI-MS, and one- and two-dimensional (1)H and (15)N NMR spectroscopy. For ss-DNA, all three G's are readily ruthenated with [(eta(6)-arene)Ru(en)](2+), but for duplex DNA there is preferential ruthenation of G3 and G6, and no binding to G2 was detected. For monoruthenated duplexes, N7 ruthenation of G is accompanied by strong hydrogen bonding between G-O6 and en-NH for the p-cymene adducts. Intercalation of the non-coordinated phenyl ring between G3 and C4 or G6 and C5 was detected in the biphenyl adducts of mono- and diruthenated duplexes, together with weakening of the G-O6NH-en hydrogen bonding. The arene ligand plays a major role in distorting the duplex either through steric interactions (p-cymene) or through intercalation (biphenyl).     

Bayesian analysis of heterogeneity in the distribution of binding properties of immobilized surface sites

Once a homogeneous ensemble of a protein ligand is taken from solution and immobilized to a surface, for many reasons the resulting ensemble of surface binding sites to soluble analytes may be heterogeneous. For example, this can be due to the intrinsic surface roughness causing variations in the local microenvironment, nonuniform density distribution of polymeric linkers, or nonuniform chemical attachment producing different protein orientations and conformations. We previously described a computational method for determining the distribution of affinity and rate constants of surface sites from analysis of experimental surface binding data. It fully exploits the high signal/noise ratio and reproducibility provided by optical biosensor technology, such as surface plasmon resonance. Since the computational analysis is ill conditioned, the previous approach used a regularization strategy assuming a priori all binding parameters to be equally likely, resulting in the broadest possible parameter distribution consistent with the experimental data. We now extended this method in a Bayesian approach to incorporate the opposite assumption, i.e., that the surface sites a priori are expected to be uniform (as one would expect in free solution). This results in a distribution of binding parameters as close to monodispersity as possible given the experimental data. Using several model protein systems immobilized on a carboxymethyl dextran surface and probed with surface plasmon resonance, we show microheterogeneity of the surface sites in addition to broad populations of significantly altered affinity. The distributions obtained are highly reproducible. Immobilization conditions and the total surface density of immobilized sites can have a substantial impact on the functional distribution of the binding sites.