New phosphorylating reagents for deoxyribonucleosides and oligonucleotides

New phosphorylating reagents 1 and 2 were prepared in three steps from 4-hydroxybenzaldehyde. They showed good efficiency in the solid phase synthesis of 5′-phosphate monoester nucleosides. End-phosphate DNA sequence synthesis demonstrated the efficiency of the new reagents (1 and 2) according to the general procedure of automated DNA synthesis. The oxidation of P(III) to P(V) and the removal of benzyl protecting groups were achieved in a single step by treatment with a 0.02 M I₂/pyridine/H₂O solution. Due to this one-pot treatment, it is possible to use the phosphorylating reagents (1 and 2) for the synthesis of base-sensitive ODNs. The reagents 1 and 2 are unique among phosphorylating reagents.     

Structural Inhomogeneity in Electrolyte Solutions: The Calcium Perchlorate–Water System

A new approach has been proposed to study the structure of aqueous electrolyte solutions. NIR, Raman and attenuated total reflectance, Fourier transform infra-red (ATR FTIR) spectra have been measured for aqueous calcium perchlorate solutions in the 0.22–4.3 mol·L^?1 (0.22–7.46 mol·kg^?1) concentration range at 25 °C. By the methods of principal component analysis (PCA) and multivariate curve resolution—alternating least squares (MCR-ALS) the number, spectra and concentration profiles have been determined for spectroscopically distinguishable forms of water and ClO ₄ ^? ion in solutions. The results have been analyzed using a phenomenological model, establishing thereby: concentration ranges for structural rearrangements of the solution, the nature of structural microirregularities and different states of the ClO ₄ ^? ion in the areas of domination of the natural water structure, and of cybotactic groups of calcium perchlorate hexa and tetra hydrates.     

Aminolysis of glycal-derived allyl epoxides and activated aziridines. Effects of the absence of coordination processes on the regio- and stereoselectivity

The addition of primary and secondary aliphatic amines to glycal-derived allyl epoxides is completely 1,2-regio- and anti-stereoselective, whereas mixtures of the corresponding anti-1,2- [3-N-(substituted-amino) glycals] and anti-1,4-addition products (N-glycosyl amines) are obtained with N-(mesyl)-aziridines. In this way, structural moieties, otherwise difficult to synthesize, are obtained by means of a very simple protocol. The regio- and stereoselectivity observed with epoxides is the consequence of an isomerization process, whereas the result obtained with aziridines is explained by the absence of an effective substrate-nucleophile (amine) coordination.     

One-pot amide synthesis from allyl or benzyl halides and amines by Pd-catalysed carbonylation

Amides can be prepared from allyl or benzyl halides and primary or secondary amines, using Pd(0) catalyst under CO pressure, in a one-pot synthesis. The reaction proceeds through the acyl palladium halide formation which undergoes an acylic nucleophilic substitution from the amine.     

Control of organoclay structure in hydrocarbon polymers

Two different kinds of organoclays were prepared by mixing a pristine montmorillonite and a double‐chain ammonium salt in many different thermoplastic or elastomeric polymers. Independently of the chemical nature of the considered polymers, the obtained organoclays presented a basal spacing of 4 or 6 nm, when the mixing occurred in the absence or in the presence of a small amount of stearic acid (SA), respectively. X‐ray diffraction and Fourier transform infrared measurements support the hypothesis that these two kinds of organoclays correspond to paraffin‐type tilted and perpendicular bi‐layer intercalates, respectively. The co‐intercalation of SA molecules with the double‐chain amphiphile is suggested, to explain the observed expansion of the clay interlayer distance. The obtained results suggest an easy way to control the organoclay structure in polymer composites. Moreover, the authors on the basis of these results propose a criticism to the extensive literature that systematically explains most d basal spacing increase observed for clays in polymer with the penetration of apolar polymer chains in the clay interlayer space. Copyright © 2010 John Wiley & Sons, Ltd.     

Novel deletion of the E3A ubiquitin protein ligase gene detected by multiplex ligation-dependent probe amplification in a patient with Angelman syndrome

Angelman syndrome (AS) is a severe neurobehavioural disorder caused by failure of expression of the maternal copy of the imprinted domain located on 15q11-q13. There are different mechanisms leading to AS: maternal microdeletion, uniparental disomy, defects in a putative imprinting centre, mutations of the E3 ubiquitin protein ligase (UBE3A) gene. However, some of suspected cases of AS are still scored negative to all the latter mutations. Recently, it has been shown that a proportion of negative cases bear large deletions overlapping one or more exons of the UBE3A gene. These deletions are difficult to detect by conventional gene-scanning methods due to the masking effect by the non-deleted allele. In this study, we have used for the first time multiplex ligation-dependent probe amplification (MLPA) and comparative multiplex dosage analysis (CMDA) to search for large deletions affecting the UBE3A gene. Using this approach, we identified a novel causative deletion involving exon 8 in an affected sibling. Based on our results, we propose the use of MLPA as a fast, accurate and inexpensive test to detect large deletions in the UBE3A gene in a small but significant percentage of AS patients.     

Novel and highly sensitive mixed-polymeric electrokinetic chromatography system for determination of contaminants and impurities of heparin samples

A mixed‐polymeric electrokinetic chromatography system has been developed for the simultaneous determination of a contaminant like oversulfated condroitin sulfate (OSCS) and impurities expressed as dermatan (Der) in heparin (Hep) samples. The EKC system consisted of 0.5% w/v polymeric β‐CD, 0.4% w/v tetronic^® 1107 and 400 mM tris‐phosphate buffer at pH 3.5. The optimized electrophoretic conditions included the use of an uncoated‐silica capillary of 50 cm of total length and 75 μm id, an applied voltage of ?7 kV, a temperature of 30°C and 200 nm UV‐detection. The highly sensitive method developed showed low values of LOD, 0.07% w/w (0.07 μg/mL) (OSCS) and 0.1% w/w (0.1 μg/mL) (Der), and values of LOQ 0.2% w/w (0.2 μg/mL) (OSCS) and 0.3% w/w (0.3 μg/mL) (Der) with a concentration level of Hep sample as low as 0.1 mg/mL. Additional parameters of validation such as specificity, linearity, accuracy, and robustness were evaluated according to international guidelines. Owing to its simplicity, high sensitivity, and reliability, the proposed method can be an advantageous alternative to the traditional methodologies for the analysis of Hep in raw material and specially in finished products because of the low amounts of Hep sample required.     

"Compression-only" behavior: a second-order nonlinear response of ultrasound contrast agent microbubbles

Oscillating phospholipid-coated ultrasound contrast agent microbubbles display a so-called "compression-only" behavior, where it is observed that the bubbles compress efficiently while their expansion is suppressed. Here, a theoretical understanding of the source of this nonlinear behavior is provided through a weakly nonlinear analysis of the shell buckling model proposed by Marmottant et al. [J. Acoust. Soc. Am. 118, 3499-3505 (2005)]. It is shown that the radial dynamics of the bubble can be considered as a superposition of a linear response at the fundamental driving frequency and a second-order nonlinear low-frequency response that describes the negative offset of the mean bubble radius. The analytical solution deduced from the weakly nonlinear analysis shows that the compression-only behavior results from a rapid change of the shell elasticity with bubble radius. In addition, the radial dynamics of single phospholipid-coated microbubbles was recorded as a function of both the amplitude and the frequency of the driving pressure pulse. The comparison between the experimental data and the theory shows that the magnitude of compression-only behavior is mainly determined by the initial phospholipids concentration on the bubble surface, which slightly varies from bubble to bubble.     

Initial state effects on J/ψ production at RHIC energy: from d+Au to Au+Au

We present a calculation of the cold nuclear matter effect on inclusive production of J/ψ in d+A and A+A collisions in the framework of the gluon saturation/CGC approach. Our model is based on the observation that the leading production mechanism involves odd number of inelastic interactions with the nuclei. Our numerical calculations are in good agreement with the experimental data in the case of d+Au collisions. However, in Au+Au collisions the cold nuclear matter effect is not suffcient to describe the data.     

An alternating extragradient method with non euclidean projections for saddle point problems

In this work we analyze a first order method especially tailored for smooth saddle point problems, based on an alternating extragradient scheme. The proposed method is based on three successive projection steps, which can be computed also with respect to non Euclidean metrics. The stepsize parameter can be adaptively computed, so that the method can be considered as a black-box algorithm for general smooth saddle point problems. We develop the global convergence analysis in the framework of non Euclidean proximal distance functions, under mild local Lipschitz conditions, proving also the \(\mathcal {O}(\frac{1}{k})\) rate of convergence on the primal–dual gap. Finally, we analyze the practical behavior of the method and its effectiveness on some applications arising from different fields.