A device for extraction, manipulation and stretching of DNA from single human chromosomes

We describe the structure and operation of a micro/nanofluidic device in which individual metaphase chromosomes can be isolated and processed without being displaced during exchange of reagents. The change in chromosome morphology as a result of introducing protease into the device was observed by time-lapse imaging; pressure-driven flow was then used to shunt the chromosomal DNA package into a nanoslit. A long linear DNA strand (>1.3 Mbp) was seen to stretch out from the DNA package and along the length of the nanoslit. Delivery of DNA in its native metaphase chromosome package as well as the microfluidic environment prevented DNA from shearing and will be important for preparing ultra-long lengths of DNA for nanofluidic analysis.     

Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

Reliable predictions of relative binding free energies are essential in drug discovery, where chemists modify promising compounds with the aim of increasing binding affinity. Conventional Thermodynamic Integration (TI) approaches can estimate corresponding changes in binding free energies, but suffer from inadequate sampling due to ruggedness of the molecular energy surfaces. Here, we present an improved TI strategy for computing relative binding free energies of congeneric ligands. This strategy employs a specific, unphysical single-reference (SR) state and Hamiltonian replica exchange (HREX) to locally enhance sampling. We then apply this strategy to compute relative binding free energies of twelve ligands in the L99A mutant of T4 Lysozyme. Besides the ligands, our approach enhances hindered rotations of the important V111, as well as V87 and L118 sidechains. Concurrently, we devise practical strategies to monitor and improve HREX-SRTI efficiency. Overall, the HREX-SRTI results agree well (R(2) = 0.76, RMSE = 0.3 kcal/mol) with available experimental data. When optimized for efficiency, the HREX-SRTI precision matches that of experimental measurements.     

An automated multidimensional preparative gas chromatographic system for isolation and enrichment of trace amounts of xenon from ambient air

The monitoring of radioactive xenon isotopes is one of the principal methods for the detection of nuclear explosions in order to identify clandestine nuclear testing. In this work, a miniaturized, multiple-oven, six-column, preparative gas chromatograph was constructed in order to isolate trace quantities of radioactive xenon isotopes from ambient air, utilizing nitrogen as the carrier gas. The multidimensional chromatograph comprised preparative stainless steel columns packed with molecular sieves, activated carbon, and synthetic carbon adsorbents (e.g., Anasorb®-747 and Carbosphere®). A combination of purification techniques—ambient adsorption, thermal desorption, back-flushing, thermal focusing, and heart cutting—was selectively optimized to produce a well-defined xenon peak that facilitated reproducible heart cutting and accurate quantification. The chromatographic purification of a sample requires approximately 4 h and provides complete separation of xenon from potentially interfering components (such as water vapor, methane, carbon dioxide, and radon) with recovery and accuracy close to 100%. The preparative enrichment process isolates and concentrates a highly purified xenon gas fraction that is suitable for subsequent ultra-low-level γ-, ß/γ-spectroscopic or high-resolution mass spectrometric measurement (e.g., to monitor the gaseous fission products of nuclear explosions at remote locations). The Xenon Processing Unit is a free-standing, relatively lightweight, and transportable system that can be interfaced to a variety of sampling and detection systems. It has a relatively inexpensive, rugged, and compact modular (19-inch rack) design that provides easy access to all parts for maintenance and has a low power requirement.     

Organic redox couples and organic counter electrode for efficient organic dye-sensitized solar cells

A series of organic thiolate/disulfide redox couples have been synthesized and have been studied systematically in dye-sensitized solar cells (DSCs) on the basis of an organic dye (TH305). Photophysical, photoelectrochemical, and photovoltaic measurements were performed in order to get insights into the effects of different redox couples on the performance of DSCs. The polymeric, organic poly(3,4-ethylenedioxythiophene) (PEDOT) material has also been introduced as counter electrode in this kind of noniodine-containing DSCs showing a promising conversion efficiency of 6.0% under AM 1.5G, 100 mW·cm(-2) light illumination. Detailed studies using electrochemical impedance spectroscopy and linear-sweep voltammetry reveal that the reduction of disulfide species is more efficient on the PEDOT counter electrode surface than on the commonly used platinized conducting glass electrode. Both pure and solvated ionic-liquid electrolytes based on a thiolate anion have been studied in the DSCs. The pure and solvated ionic-liquid-based electrolytes containing an organic redox couple render efficiencies of 3.4% and 1.2% under 10 mW·cm(-2) light illumination, respectively.     

Silacarboxylic acids as efficient carbon monoxide releasing molecules: synthesis and application in palladium-catalyzed carbonylation reactions

Silacarboxylic acids have been demonstrated to be easy to handle, air-stable carbon monoxide precursors. Different silacarboxylic acids were synthesized from the corresponding chlorosilanes and carbon dioxide, and their decarbonylation, upon treatment with an array of activators, was evaluated. The release of CO from crystalline MePh(2)SiCO(2)H proved to be highly efficient, and it was successfully applied in a selection of palladium-catalyzed carbonylative couplings using near-stoichiometric quantities of carbon monoxide precursor. Finally, the synthesis of MePh(2)Si(13)CO(2)H and its application in carbonyl labeling of two bioactive compounds was demonstrated.     

Kinetics of ligand binding to membrane receptors from equilibrium fluctuation analysis of single binding events

Equilibrium fluctuation analysis of single binding events has been used to extract binding kinetics of ligand interactions with cell-membrane bound receptors. Time-dependent total internal reflection fluorescence (TIRF) imaging was used to extract residence-time statistics of fluorescently stained liposomes derived directly from cell membranes upon their binding to surface-immobilized antibody fragments. The dissociation rate constants for two pharmaceutical relevant antibodies directed against different B-cell expressed membrane proteins was clearly discriminated, and the affinity of the interaction could be determined by inhibiting the interaction with increasing concentrations of soluble antibodies. The single-molecule sensitivity made the analysis possible without overexpressed membrane proteins, which makes the assay attractive in early drug-screening applications.     

Mechanistic studies on the water-oxidizing reaction of homogeneous manganese-based catalysts: isolation and characterization of a suggested catalytic intermediate

The synthesis, isolation, and characterization of two high-valent manganese dimers with isomeric ligands are reported. The complexes are synthesized and crystallized from solutions of low-valent precursors exposed to tert-butyl hydroperoxide. The crystal structures display centrosymmetric complexes consisting of Mn(2)(IV,IV)(μ-O)(2) cores, with one ligand coordinating to each manganese. The ligands coordinate with the diaminoethane backbone, the carboxylate, and one of the two pyridines, while the second pyridine is noncoordinating. The activity of these complexes, under water oxidation conditions, is discussed in light of a proposed mechanism for water oxidation, in which this type of complexes have been suggested as a key intermediate.     

X-ray Raman scattering provides evidence for interfacial acetonitrile-water dipole interactions in aqueous solutions

Aqueous solutions of acetonitrile (MeCN) have been studied with oxygen K-edge x-ray Raman scattering (XRS) which is found to be sensitive to the interaction between water and MeCN. The changes in the XRS spectra can be attributed to water directly interacting with MeCN and are reproduced by density functional theory calculations on small clusters of water and MeCN. The dominant structural arrangement features dipole interaction instead of H-bonds between the two species as revealed by the XRS spectra combined with spectrum calculations. Small-angle x-ray scattering shows the largest heterogeneity for a MeCN to water ratio of 0.4 in agreement with earlier small-angle neutron scattering data.     

The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements

X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl(2), and AlCl(3) with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na(+) weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg(2+) and Al(3+), on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg(2+) and Al(3+) form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg(2+) and Al(3+) have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg(2+) and Al(3+) is, respectively, ～61% and ～71% higher than in bulk water.