Efficient Automated Solid‐Phase Synthesis of DNA and RNA 5′‐Triphosphates

A fast, high‐yielding and reliable method for the synthesis of DNA‐ and RNA 5′‐triphosphates is reported. After synthesizing DNA or RNA oligonucleotides by automated oligonucleotide synthesis, 5‐chloro‐saligenyl‐N,N‐diisopropylphosphoramidite was coupled to the 5′‐end. Oxidation of the formed 5′‐phosphite using the same oxidizing reagent used in standard oligonucleotide synthesis led to 5′‐cycloSal‐oligonucleotides. Reaction of the support‐bonded 5′‐cycloSal‐oligonucleotide with pyrophosphate yielded the corresponding 5′‐triphosphates. The 5′‐triphosphorylated DNA and RNA oligonucleotides were obtained after cleavage from the support in high purity and excellent yields. The whole reaction sequence was adapted to be used on a standard oligonucleotide synthesizer.     

Preparation of Bragg mirrors on silica optical fibers and inner walls of silica capillaries by employing the sol–gel method,and titanium and silicon alkoxides

Journal of Sol-Gel Science and Technology - The paper presents results on sol–gel preparation and characterization of multilayered coatings, Bragg mirrors, on silica slides, silica fibers,...     

Multi-objective Geometry Optimization of a Gas Cyclone Using Triple-Fidelity Co-Kriging Surrogate Models

Cyclone separators are widely used in a variety of industrial applications. A low-mass loading gas cyclone is characterized by two performance parameters, namely the Euler and Stokes numbers. These parameters are highly sensitive to the geometrical design parameters defining the cyclone. Optimizing the cyclone geometry therefore is a complex problem. Testing a large number of cyclone geometries is impractical due to time constraints. Experimental data and even computational fluid dynamics simulations are time-consuming to perform, with a single simulation or experiment taking several weeks. Simpler analytical models are therefore often used to expedite the design process. However, this comes at the cost of model accuracy. Existing techniques used for cyclone shape optimization in literature do not take multiple fidelities into account. This work combines cheap-to-evaluate well-known mathematical models of cyclones, available data from computational fluid dynamics simulations and experimental data to build a triple-fidelity recursive co-Kriging model. This model can be used as a surrogate with a multi-objective optimization algorithm to identify a Pareto set of a finite number of solutions. The proposed scheme is applied to optimize the cyclone geometry, parametrized by seven design variables.     

Multifrequency electron paramagnetic resonance characterization of PpoA, a CYP450 fusion protein that catalyzes fatty acid dioxygenation

PpoA is a fungal dioxygenase that produces hydroxylated fatty acids involved in the regulation of the life cycle and secondary metabolism of Aspergillus nidulans . It was recently proposed that this novel enzyme employs two different heme domains to catalyze two separate reactions: within a heme peroxidase domain, linoleic acid is oxidized to (8R)-hydroperoxyoctadecadienoic acid [(8R)-HPODE]; in the second reaction step (8R)-HPODE is isomerized within a P450 heme thiolate domain to 5,8-dihydroxyoctadecadienoic acid. In the present study, pulsed EPR methods were applied to find spectroscopic evidence for the reaction mechanism, thought to involve paramagnetic intermediates. We observe EPR resonances of two distinct heme centers with g-values typical for Fe(III) S = (5)/(2) high-spin (HS) and Fe(III) S = (1)/(2) low-spin (LS) hemes. (14)N ENDOR spectroscopy on the S = (5)/(2) signal reveals resonances consistent with an axial histidine ligation. Reaction of PpoA with the substrate leads to the formation of an amino acid radical on the early millisecond time scale concomitant to a substantial reduction of the S = (5)/(2) heme signal. High-frequency EPR (95- and 180-GHz) unambiguously identifies the new radical as a tyrosyl, based on g-values and hyperfine couplings from spectral simulations. The radical displays enhanced T(1)-spin-lattice relaxation due to the proximity of the heme centers. Further, EPR distance measurements revealed that the radical is distributed among the monomeric subunits of the tetrameric enzyme at a distance of approximately 5 nm. The identification of three active paramagnetic centers involved in the reaction of PpoA supports the previously proposed reaction mechanism based on radical chemistry.     

Analysis of selenomethylselenocysteine and selenomethionine by LC-ESI-MS/MS with diethyl ethoxymethylenemalonate derivatization

A simple method to identify and determine Selenomethionine (SeMet) and Selenomethylselenocysteine (Se-MeSeCys) with diethyl ethoxymethylenemalonate (DEEMM) derivatization and LC-ESI-MS/MS determination was developed. Separation of SeMet and Se-MeSeCys was achieved in 15.3 minutes. The calibration graph was linear in the range of 0.32 pmol to 49 pmol for SeMet and 0.34 pmol to 40 pmol for Se-MeSeCys. To prevent oxidation of SeMet, 2-mercaptoethanol was introduced to the calibration solutions. Detection limits were 0.1 pmol, which are comparable to LC-ICP-MS analysis. The developed method therefore offers an alternative to LC-ICP-MS offering similar sensitivity and additionally allows identification. The method was used to determine Se-MeSeCys and SeMet in onion samples.     

Guanidiniocarbonyl-pyrrole-aryl conjugates as nucleic acid sensors: switch of binding mode and spectroscopic responses by introducing additional binding sites into the linker

Two novel guanidiniocarbonyl pyrrole-pyrene conjugates 3 and 4 as spectroscopic probes for ds-polynucleotides were synthesized and their interaction with different ds-DNAs/RNAs studied. Compared to a previously reported first set of conjugates (1 and 2) the significant extension and increased rigidity of the central part of the structure resulted in a switch of DNA binding mode from intercalative (previously studied derivatives 1 and 2 with a nonbinding and flexible linker) to minor groove binding of the two novel guanidiniocarbonyl-pyrrole-pyrene conjugates 3 and 4. These two compounds interact strongly with ds-DNAs, but only weakly with ds-RNA. The newly incorporated heterocyclic moieties within the central part of the structure of 3 and 4 were able to control by steric and hydrogen-bonding effects the alignment of the molecules within various, structurally different forms of DNA minor grooves, whereby even small differences in the position of the attached pyrene within the groove were reflected in different fluorimetric responses. In addition, 3 and 4 revealed intriguing in vitro selectivity among various human tumour cell lines.     

Equilibrium acidities of superacids

In this paper, we report the most comprehensive equilibrium superacidity scale that is available to date. Contrary to most of the past works, this scale is set up in a medium of constant composition and the obtained acidity values characterize the acidities of molecules rather than acidities of media. The current scale is thus complementary to the well-known H(0) scale in the information that it provides. The solvent used is 1,2-dichloroethane (DCE). DCE has very weak basic properties (but sufficiently high polarity) and is an appropriate solvent for measuring acidities of very strong acids of diverse chemical nature. DCE acidities of well-known superacids (CF(3)SO(2)OH, (CF(3)SO(2))(2)NH, cyanocarbon acids, etc.) as well as common mineral acids (H(2)SO(4), HI, HBr, etc.) are reported. Acidities of altogether 62 acids have been determined from 176 interlinked relative acidity measurements. The scale spans 15 orders of magnitude (from picric acid to 1,1,2,3,3-pentacyanopropene) and is expected to be a useful tool in design, use, and further acidity measurements of superacidic molecules.     

Towards a unified view of fluids

It has traditionally been believed that, unlike normal fluids whose structural properties are determined primarily by the intermolecular short-range repulsive interactions, the properties of polar and associating fluids are strongly affected by the long-range Coulombic interactions. In the course of investigations to determine the primary driving forces governing the behaviour of various (non-simple) fluids, and hence to gain a deeper understanding of the molecular mechanisms leading to the development of theoretically based simple models and theory, extensive and systematic computer simulations have been performed on typical quadrupolar (carbon dioxide), dipolar (acetone and acetonitrile), and associating (hydrogen fluoride, methanol, and water) fluids using the available realistic effective pair potentials and their variants involving forces of different ranges. In addition to the main structural characteristics (one- and two-dimensional site–site correlation functions, local g factors, and radial slices through the full pair correlation function), the dielectric constants and the thermodynamic properties (internal energy and pressure) of both the homogeneous liquid and supercritical fluid phases, and vapor–liquid equilibria have also been considered. Furthermore, in the case of water, the diffusion coefficient and viscosity have also been considered along with water at the interface. All the obtained results lead to the unambiguous conclusion that the structure, defined in terms of the complete set of site–site correlation functions, for both polar and associating pure fluids is governed by the same molecular mechanism as for normal fluids, i.e. by the short-range interactions (which, however, may be both repulsive and attractive), whereas the long-range part of the electrostatic forces, regardless of their strength, plays only a marginal role and may be treated as a perturbation only. The consequences of these findings for theory and applications are also discussed.     

From realistic to simple models of fluids. III. Primitive models of carbon dioxide,hydrogen sulphide and acetone,and their properties

Recently developed methodology to construct primitive models of associating fluids as direct descendants of complex realistic intermolecular potential functions [L. Vl?ek, I. Nezbeda. Molec. Phys., 102, 485 (2004).] is extended to polar fluids and applied to three substances of practical importance: quadrupolar carbon dioxide, and dipolar hydrogen sulphide and acetone. It is shown that the structural properties (in terms of the site–site correlation functions) of the primitive models of polar fluids reproduce very well those of their parent realistic models but, nonetheless, they perform worse than in the case of associating fluids. A number of thermodynamic properties of the developed models obtained by computer simulations is also reported (for their later use in theoretical investigation) and discussed.     

The Role of Alkali Cation Intercalates on the Electrochemical Characteristics of Nb2CTX MXene for Energy Storage

The intercalation of cations into layered-structure electrode materials has long been studied in depth for energy storage applications. In particular, Li⁺-, Na⁺-, and K⁺-based cation transport in energy storage devices such as batteries and electrochemical capacitors is closely related to the capacitance behavior. We have exploited different sizes of cations from aqueous salt electrolytes intercalating into a layered Nb₂CT_x electrode in a supercapacitor for the first time. As a result, we have demonstrated that capacitive performance was dependent on cation intercalation behavior. The interlayer spacing expansion of the electrode material can be observed in Li₂SO₄, Na₂SO₄, and K₂SO₄ electrolytes with d-spacing. Additionally, our results showed that the Nb₂CT_x electrode exhibited higher electrochemical performance in the presence of Li₂SO₄ than in that of Na₂SO₄ and K₂SO₄. This is partly because the smaller-sized Li⁺ transports quickly and intercalates between the layers of Nb₂CT_x easily. Poor ion transport in the Na₂SO₄ electrolyte limited the electrode capacitance and presented the lowest electrochemical performance, although the cation radius follows Li⁺>Na⁺>K⁺. Our experimental studies provide direct evidence for the intercalation mechanism of Li⁺, Na⁺, and K⁺ on the 2D layered Nb₂CT_x electrode, which provides a new path for exploring the relationship between intercalated cations and other MXene electrodes.