Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family

Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.     

Polyphenolics with Strong Antioxidant Activity from Acacia nilotica Ameliorate Some Biochemical Signs of Arsenic-Induced Neurotoxicity and Oxidative Stress in Mice

Neurotoxicity is a serious health problem of patients chronically exposed to arsenic. There is no specific treatment of this problem. Oxidative stress has been implicated in the pathological process of neurotoxicity. Polyphenolics have proven antioxidant activity, thereby offering protection against oxidative stress. In this study, we have isolated the polyphenolics from Acacia nilotica and investigated its effect against arsenic-induced neurotoxicity and oxidative stress in mice. Acacia nilotica polyphenolics prepared from column chromatography of the crude methanol extract using diaion resin contained a phenolic content of 452.185 ± 7.879 mg gallic acid equivalent/gm of sample and flavonoid content of 200.075 ± 0.755 mg catechin equivalent/gm of sample. The polyphenolics exhibited potent antioxidant activity with respect to free radical scavenging ability, total antioxidant activity and inhibition of lipid peroxidation. Administration of arsenic in mice showed a reduction of acetylcholinesterase activity in the brain which was counteracted by Acacia nilotica polyphenolics. Similarly, elevation of lipid peroxidation and depletion of glutathione in the brain of mice was effectively restored to normal level by Acacia nilotica polyphenolics. Gallic acid methyl ester, catechin and catechin-7-gallate were identified in the polyphenolics as the major active compounds. These results suggest that Acacia nilotica polyphenolics due to its strong antioxidant potential might be effective in the management of arsenic induced neurotoxicity.     

Inclusion of Carboxyl Function Inside of Cucurbiturils and its Use in Molecular Switches

We have prepared organic guest molecules in which two pyridinium rings are connected through an aromatic/aliphatic bridge bearing a carboxyl group. The supramolecular interactions between these guests and macrocyclic hosts cucurbit[7]uril ( CB7 ) and cucurbit[8]uril ( CB8 ) has been studied. We have demonstrated that the binding modes of the complexes depend on the type of central bridge present in the guest molecules and the size of the macrocycle. We have also showed that the binding mode between cucurbiturils and guests with aromatic bridges is pH independent. On the other hand, a guest containing an aliphatic bridge and CB7 formed a pseudorotaxane, which behaved as a pH‐driven molecular switch.     

Transfer measurements for the Ti+Ni systems at near barrier energies

Large enhancements have been observed in the sub-barrier fusion cross sections for Ti+Ni systems in our previous studies. Coupled channel calculations incorporating couplings to 2⁺ and 3⁻ states failed to explain these enhancements completely. A possibilty of transfer channels contributing to the residual enhancements had been suggested. In order to investigate the role of relevant transfer channels, measurements of one- and two-nucleon transfer were carried out for ^46,48Ti+⁶¹Ni systems. The present paper gives the results of these studies.     

Chromatographic behaviour of selected steroids and their inclusion complexes with beta-cyclodextrin on octadecylsilica stationary phases with different carbon loads

Retention and separation studies of selected estrogens, progestogens and their inclusion complexes with beta-cyclodextrin were conducted using two C18 HPLC columns with different carbon loads. The difference in carbon load between investigated octadecylsilica packing materials was about 50%. The mobile phases were composed of a 30% v/v acetonitrile-water mixture without and with addition of beta-cyclodextrin at a concentration of 12 mM. The experimental data revealed that retention of the steroids was significantly reduced on the column with the lower carbon load. Moreover, it was found that this column offers better separation power and shorter analysis time at the temperatures studied. However, the calculated values of the retention factor ratios (k0(mMCD))/k(12mMCD)) of the steroids were similar for both columns investigated. This observation suggests that the stationary phase structure appears to have little effect on the formation of host-guest complexes if the complexation process is localised to the chromatographic mobile phase. From a practical point of view, when the mobile phase is modified with beta-cyclodextrin, the separation of the steroids is strongly influenced by temperature. The best chromatographic conditions were determined for the separation of multicomponent samples on the column with lower carbon load. A possible retention mechanism for components of interest in the presence of macrocyclic additives is discussed.     

A host-guest optical sensor for aliphatic amines based on lipophilic cyclodextrin

A host-guest optical sensor for the determination of aliphatic amines as exemplified by octylamine is proposed. It is based on the reversible fluorescence enhancement of heptakis(2,6-di-O-isobutyl)-β-cyclodextrin(DOB-β-CD) hosting tetraphenylporphyrin (TPP) immobilized in poly(vinyl chloride) (PVC) membrane by aliphatic amine extracted from aqueous phase into membrane phase. The optimum membrane contained 1.15 wt % TPP, 6.15 wt % DOB-β-CD as sensing reagent and other membrane materials. The fluorescence enhancement of the membrane resulted from the formation of a stable three-component complex among DOB-β-CD, TPP, and aliphatic amines. With the optimum conditions described, the fluorescence response of the sensor to octylamine shows a good correlation with the theoretically derived equation in the range 1.0 × 10^–6 to 8.0 × 10^–4 mol/L. The response characteristics including reversibility, response time, reproducibility and lifetime and selectivity of this optical device are also discussed in detail. This sensor has also been applied for the determination of octylamine in water samples containing interferents with satisfactory recovery.     

Investigation of the quantitative properties of the quadrupole orthogonal acceleration time-of-flight mass spectrometer with electrospray ionisation using 3,4-methylenedioxymethamphetamine

This paper describes the investigation of the potential of a quadrupole orthogonal acceleration time-of-flight mass spectrometer (Q-TOF) equipped with an atmospheric pressure ionisation interface for quantitative measurements of small molecules separated by reversed phase liquid chromatography. To this end, the detection limits and linear dynamic range in particular were studied in an LC/MS/MS experiment using 3,4-methylenedioxymethamphetamine standards and 3,4-methylenedioxyethylamphetamine for internal standardisation. In a second phase, the experiment was repeated with real biological extracts (whole blood, serum, and vitreous humour). A calibration for 3,4-methylenedioxymethamphetamine and its metabolite 3,4-methylenedioxyamphetamine was prepared in each of these matrices again using 3,4-methylenedioxyethylamphetamine as internal standard. The resulting quantitative data were compared with those obtained by liquid chromatography with fluorescence detection for the same extracts. The Q-TOF results revealed excellent sensitivity and a linear dynamic range of nearly four decades (2-10 000 pg on-column, r(2) = 0.9998, 1/x weighting). Furthermore, all the calibration curves prepared in biological material were superimposable, LC/MS/MS and LC-fluorescence, and the quantitative results for actual samples compared very favourably. It was concluded that the Q-TOF achieves a linear dynamic range for quantitative LC/MS/MS work exceeding that of fluorescence detection and at much better absolute sensitivity. Copyright 1999 John Wiley & Sons, Ltd.     

Effect of spatial heterogeneity on level of rejuvenation in Ni80P20 metallic glass

Understanding the relation between spatial heterogeneity and structural rejuvenation is one of the hottest topics in the field of metallic glasses (MGs). In this work, molecular dynamics (MD) simulation is implemented to discover the effects of initial spatial heterogeneity on the level of rejuvenation in the Ni$_{80}$P$_{20 }$MGs. For this purpose, the samples are prepared with cooling rates of $10^{10}$ K/s-$10^{12}$ K/s to make glassy alloys with different atomic configurations. Firstly, it is found that the increase in the cooling rate leads the Gaussian-type shear modulus distribution to widen, indicating the aggregations in both elastically soft and hard regions. After the primary evaluations, the elastostatic loading is also used to transform structural rejuvenation into the atomic configurations. The results indicate that the sample with intermediate structural heterogeneity prepared with 10$^{11}$ K/s exhibits the maximum structural rejuvenation which is due to the fact that the atomic configuration in an intermediate structure contains more potential sites for generating the maximum atomic rearrangement and loosely packed regions under an external excitation. The features of atomic rearrangement and structural changes under the rejuvenation process are discussed in detail.     

A study of some parameters relevant to the response of harwell PMMA dosimeters to gamma and electron irradiation

The effects on the radiation response of Harwell polymethylmethacrylate (PMMA) dosimeters of dose-rate, radiation type, temperature during irradiation and post-irradiation storage, and post-irradiation stability, are of importance to the operators of commercial irradiation facilities.

This paper describes recent studies of the effects of some of these parameters on the radiation response of Harwell Red 4034, Amber 3042, and Gammachrome YR Perspex dosimeters, and provides data on batch to batch variation and shelf-life.     

Determination of steroids in human plasma using temperature-dependent inclusion chromatography for metabolomic investigations

Clinical and metabolomic investigations of complex human fluids require cost-effective methodologies that can rapidly assess the steroid hormone milieu of individual samples. The efficiency of quantification of many steroids is limited using immunoassays as these methods can only measure a single component of biological samples and are dependent upon the specificity of the antiserum used in the protocol. In this study, we optimised the solid-phase extraction protocol for the extraction of a range of steroids of varied polarity from estetrol to progesterone from human plasma. The final SPE procedure for efficient extraction of steroids was a washing mixture of 5 ml of 30% methanol and an elution solvent of 2 ml of 100% methanol using 0.5 g C-18 cartridges. This protocol resulted in a high recovery rate, ranging from 85.2 to 99.9% for both the internal standard (7,8-dimethoxyflavone) and steroids of interest. We also improved the separation methodology of our previous work using temperature dependent inclusion chromatography with a mobile phase composition of 35% acetonitrile and 12 mM of beta-cyclodextrin at 29 degrees C. Under these conditions most of the fluid components including estetrol were detected in the first 10 min with progesterone appearing at 43 min. This method is simplistic, inexpensive and reproducible with the capabilities of accurate quantification of steroids. Therefore it could have numerous clinical and metabolomic applications.