Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase

High fidelity polymerases are efficient catalysts of phosphodiester bond formation during DNA replication or repair. We interpret molecular dynamics simulations of a polymerase bound to its substrate DNA and incoming nucleotide using a quasiharmonic model to study the effect of external forces applied to the bound DNA on the kinetics of phosphoryl transfer. The origin of the force dependence is shown to be an intriguing coupling between slow, delocalized polymerase-DNA modes and fast catalytic site motions. Using noncognate DNA substrates we show that the force dependence is context specific.     

Simultaneous determination of novel β-lactamase inhibitor WCK 4234 and Meropenem in dog plasma by LC–MS/MS and its application to preclinical pharmacokinetic study

A precise and accurate liquid chromatography–tandem mass spectrometric (LC–MS/MS) bioanalytical method has been developed and validated for the simultaneous quantification of WCK 4234 and meropenem (MEM) in dog plasma. Protein precipitation using acetonitrile was employed as a sample preparation approach. Cefepime was used as an internal standard. The developed method was selective, sensitive (limit of quantification, 0.075 μg/ml for both drugs), accurate (recovery > 90%), precise (CV < 10%) and linear (r² ≥ 0.99, concentration range 0.075–120 μg/ml for both analytes). The developed method was successfully applied for the determination of both drugs in plasma to assess the pharmacokinetics in beagle dogs. WCK 4234 + MEM in a 1:1 ratio at 15 + 15 and 30 + 30 mg/kg doses were administered by the intravenous route. The mean plasma concentration and area under the concentration–time curve of WCK 4234 ranged from 38.3 to 77.4 μg/ml and from 47.8 to 77.1 μg h/ml, respectively, and the values for MEM ranged from 52.2 to 115.3 μg/ml and 70.5 to 133.6 μg h/ml respectively. The elimination half-life of WCK 4234 and MEM was around 0.8 h.     

Boron-Containing Lipids and Liposomes: New Conjugates of Cholesterol with Polyhedral Boron Hydrides

A series of boron-containing lipids were prepared by reactions of cyclic oxonium derivatives of polyhedron boranes and metallacarboranes (closo-dodecaborate anion, cobalt and iron bis(dicarbollides)) with amine and carboxylic acids which are derived from cholesterol. Stable liposomal formulations, on the basis of synthesized boron-containing lipids, hydrogenated soybean l -α-phosphatidylcholine and (HSPC) 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (DSPE-PEG) as excipients, were prepared and then characterized by dynamic light scattering (DLS) that revealed the formation of particles to be smaller than 200 nm in diameter. The resulting liposomal formulations showed moderate to excellent loading and entrapment efficiency, thus justifying the design of the compounds to fit in the lipid bilayer and ensuring ease of in vivo use for future application. The liposomal formulations based on cobalt and iron bis(dicarbollide)-based lipids were found to be nontoxic against both human breast normal epithelial cells MCF-10A and human breast cancer cells MCF-7.     

Exergy and exergo-environmental analysis of a 660 MW supercritical coal-fired power plant

Journal of Thermal Analysis and Calorimetry - This paper presents the exergy and exergo-environmental analysis of the 660&nbsp;MW supercritical coal-fired unit situated in western India. The...     

Thin and surface adhesive ferroelectric poly(vinylidene fluoride) films with β phase‐inducing amino modified porous silica nanofillers

We report an efficient route for ferroelectric polar β phase generation in poly(vinylidene fluoride) (PVDF) through incorporation of amine functionalized, porous silica (MCM‐41 and fumed silica) based nanofillers. These porous highly functionalized surfaces exhibit the efficient secondary interaction with polymer chain via hydrogen bonding. Structural analysis through FTIR, XRD, and TEM confirm high degree of ferroelectric polar β phase generation of PVDF through incorporation of amino modified porous silica nanofillers. Optimized loading (5 wt %) of amine functionalized, porous silica in PVDF matrix enhances relative intensity of β phase up to 75%. Disappearance of spherulite structure of PVDF with amino modified porous silica nanofillers, as confirmed through POM, TEM, SEM and AFM studies also supports the above conclusion. The P‐E hysteresis loop at sweep voltage of ±50 V of a thin PVDF‐amino modified porous nanofiller film shows excellent ferroelectric property with nearly saturated high remnant polarization 2.8 µC.cm^?2 owing to its large proportion of β PVDF, whereas, a nonpolar pure PVDF thin film shows unsaturated hysteresis loop with 0.6 µC.cm^?2 remnant polarization. PVDF films with the nanofillers exhibit strong adhesive strength over different metallic substrates making them have edge over PVDF in various thin film applications. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2401–2411     

meso- and β-Pyrrole-Linked Chlorin-Bacteriochlorin Dyads for Promoting Far-Red FRET and Singlet Oxygen Production

A series of chlorin-bacteriochlorin dyads (derived from naturally occurring chlorophyll-a and bacteriochlorophyll-a), covalently connected either through the meso-aryl or β-pyrrole position (position-3) via an ester linkage have been synthesized and characterized as a new class of far-red emitting fluorescence resonance energy transfer (FRET) imaging, and heavy atom-lacking singlet oxygen-producing agents. From systematic absorption, fluorescence, electrochemical, and computational studies, the role of chlorin as an energy donor and bacteriochlorin as an energy acceptor in these wide-band-capturing dyads was established. Efficiency of FRET evaluated from spectral overlap was found to be 95 and 98 % for the meso-linked and β-pyrrole-linked dyads, respectively. Furthermore, evidence for the occurrence of FRET from singlet-excited chlorin to bacteriochlorin was secured from studies involving femtosecond transient absorption studies in toluene. The measured FRET rate constants, k_FRET, were in the order of 10¹¹ s⁻¹, suggesting the occurrence of ultrafast energy transfer in these dyads. Nanosecond transient absorption studies confirmed relaxation of the energy transfer product, ¹BChl*, to its triplet state, ³Bchl*. The ³Bchl* thus generated was capable of producing singlet oxygen with quantum yields comparable to their monomeric entities. The occurrence of efficient FRET emitting in the far-red region and the ability to produce singlet oxygen make the present series of dyads useful for photonic, imaging and therapy applications.     

Electroosmosis modulated peristaltic biorheological flow through an asymmetric microchannel: mathematical model

A theoretical study is presented of peristaltic hydrodynamics of an aqueous electrolytic non-Newtonian Jeffrey bio-rheological fluid through an asymmetric microchannel under an applied axial electric field. An analytical approach is adopted to obtain the closed form solution for velocity, volumetric flow, pressure difference and stream function. The analysis is also restricted under the low Reynolds number assumption (Stokes flow) and lubrication theory approximations (large wavelength). Small ionic Peclét number and Debye–Hückel linearization (i.e. wall zeta potential ≤ 25 mV) are also considered to simplify the Nernst–Planck and Poisson–Boltzmann equations. Streamline plots are also presented for the different electro-osmotic parameter, varying magnitudes of the electric field (both aiding and opposing cases) and for different values of the ratio of relaxation to retardation time parameter. Comparisons are also included between the Newtonian and general non-Newtonian Jeffrey fluid cases. The results presented here may be of fundamental interest towards designing lab-on-a-chip devices for flow mixing, cell manipulation, micro-scale pumps etc. Trapping is shown to be more sensitive to an electric field (aiding, opposing and neutral) rather than the electro-osmotic parameter and viscoelastic relaxation to retardation ratio parameter. The results may also help towards the design of organ-on-a-chip like devices for better drug design.     

An efficient and sustainable protocol for oxidation of alcohols to carbonyl compounds

A simple and extremely efficient protocol is developed for oxidation of alcohols to carbonyl compounds at room temperature by using green solvent lactic acid and green oxidant H₂O₂. This protocol provides high conversion under catalyst free conditions. The easy work up procedure allows high selectivity and good to excellent yields of carbonyl compounds with purity. We have performed wide range of substrates in present study with primary focus on reusability of lactic acid.     

The sugar conformation governs (6-4) photoproduct formation at the dinucleotide level

The LNA dinucleotide mimic of TpT whose two-sugar puckers are locked in the C3'-endo conformation selectively produces the corresponding cyclobutane pyrimidine dimer under 254 nm irradiation. In the natural series (TpT) the sugar puckers are in a major C2'-endo sugar conformation and the (6-4) photoproduct is also produced. Consequently, this study demonstrates that the C2'-endo conformation of the sugar pucker is necessary for (6-4) photoproduct formation.     

Adhesion induced mesoscale instability patterns in thin PDMS-metal bilayers

We show that the surface of a thin elastomer-metal (aluminum) hybrid bilayer becomes spontaneously patterned when brought in adhesive contact with a rigid surface. The self-organized surface patterns show three distinct morphological phases-columns, labyrinths, and holes-depending on the area of contact. The characteristic wavelength of these patterns is found to be 2.94+/-0.20 times the total film thickness, independent of the morphological phase and the surface properties of the contacting surface. Interestingly, the metal films 60-120 nm thick showed the same scaling, but the bilayers with thicker metal films were completely stable. This observation demonstrates for the first time a "hard" transition to the instability as the elastic stiffness of the film is varied. We also report a protocol for alignment of the instability patterns and for transferring the metal patterns to another surface.