Single DNA molecule stretching in sudden mixed shear and elongational microflows

High-throughput stretching and monitoring of single DNA molecules in continuous elongational flow offers compelling advantages for biotechnology applications such as DNA mapping. However, the polymer dynamics in common microfluidic implementations are typically complicated by shear interactions. These effects were investigated by observation of fluorescently labeled 185 kb bacterial artificial chromosomes in sudden mixed shear and elongational microflows generated in funneled microfluidic channels. The extension of individual free DNA molecules was studied as a function of accumulated fluid strain and strain rate. Under constant or gradually changing strain rate conditions, stretching by the sudden elongational component proceeded as previously described for an ideal elongational flow (T. T. Perkins, D. E. Smith and S. Chu, Science, 1997, 276, 2016): first, increased accumulated fluid strain and increased strain rate produced higher stretching efficiencies, despite the complications of shear interactions; and second, the results were consistent with unstretched molecules predominantly in hairpin conformations. More abrupt strain rate profiles did not deliver a uniform population of highly extended molecules, highlighting the importance of balance between shear and elongational components in the microfluidic environment for DNA stretching applications. DNA sizing with up to 10% resolution was demonstrated. Overall, the device delivered 1000 stretched DNA molecules per minute in a method compatible with diffraction-limited optical sequence motif mapping and without requiring laborious chemical modifications of the DNA or the chip surface. Thus, the method is especially well suited for genetic characterization of DNA mixtures such as in pathogen fingerprinting amidst high levels of background DNA.     

Comparison of the effectiveness of solid-phase and ultrasound-mediated liquid-liquid extractions to determine the volatile compounds of wine

Two ultrasound-assisted liquid–liquid extraction (LLE-I, LLE-II) methods were compared to a solid-phase extraction (SPE) protocol to assess their effectiveness for the analysis of up to 44 volatile compounds in a synthetic and several commercial white, red and “cream” wines produced in the southwest of Spain. Regardless of the extraction protocol used the highest recoveries corresponded to acids and terpene alcohols and the lowest to lactones and alcohols. In any case, it was concluded that one of the liquid–liquid extraction protocols evaluated led to higher recoveries for a greater number of odorants that could be implicated in the aroma of the wines than the solid-phase extraction. However, the SPE method also presented some advantages that should not be overlooked, like higher repeatability and throughput and lower solvent consumption.     

Gear effect—10 : Conformational aspects of the positive or negative buttressing effects of methyl groups: polymethylpyridines

The effect of the shape of a methyl group on reactivity, which cannot be accounted for by considering a methyl group as a spherical substituent with the appropriate van der Waals radius, was considered in kinetics of alkylalion of substituted pyridines and barriers to rotation and ground state conformations of an isopropyl group attached to a planar framework. The perturbation of a methyl group by an o-methyl group is accounted for by a unique conformational explanation which involves the polyhedral shape of the methyl group.     

Ru(TPP)CO]-Catalysed Intramolecular Benzylic CH Bond Amination, Affording Phenanthridine and Dihydrophenanthridine Derivatives

Shedding light on azides: [Ru(TPP)CO] (TPP=tetraphenyl porphyrin dianion), white light and O(2) were found to be a suitable catalyst combination to perform the annulation of several biaryl azides. The high chemoselectivity of the process allows the synthesis of phenanthridines and dihydrophenanthridines in good yield and purity.     

Water confined in MCM-41: a mode coupling theory analysis

In this paper we analyze molecular dynamics simulation results on supercooled water in a MCM-41 pore in order to test the mode coupling theory. A layer analysis must be performed for water in the pore in order to exclude the contribution of water bound to the strongly hydrophilic surface. Upon supercooling a range of temperatures is reached where the liquid follows the mode coupling theory. From the power law behavior of the relaxation times extracted from the Kohlrausch-William-Watts fit to the self-intermediate scattering function, we obtain the crossover temperature T(C) and the γ exponent of the theory. The time-temperature superposition principle is also satisfied. A fit to the von Schweidler law yields a coefficient b from which all the other parameters of the theory have been calculated. In particular, we obtained the same value of γ as extracted from the power law fit to the relaxation times, in agreement with the requirements of the theory. For very low temperatures, the mode coupling theory no longer holds as hopping processes intervene and water turns its behavior to that of a strong liquid.