End-labeled free-solution electrophoresis of DNA

DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.     

Synthesis of nanosized TiO2/SiO2 particles using microwave processes and their photocatalytic activity on the decomposition of orange II

The nanosized titania and TiO₂/SiO₂ particles were prepared by the microwave-hydrothermal method. The effect of physical properties TTIP/TEOS ratio and calcination temperature has been investigated. The major phase of the pure TiO₂ particle is of the anatase structure, and a rutile peak was observed above 800°C. In TiO₂/SiO₂ particles, however, no significant rutile phase was observed, although the calcination temperature was 900°C. No peaks for the silica crystal phase were observed at either silica/titania ratio. The crystallite size of TiO₂/SiO₂ particles decreases as compared to pure TiO₂ at high calcination temperatures. The TiO₂/SiO₂ particles show higher activity on the photocatalytic decomposition of orange II as compared to pure TiO₂ particles.     

Photodissociation tandem mass spectrometry at 266 nm of an aliphatic peptide derivatized with phenyl isothiocyanate and 4-sulfophenyl isothiocyanate

Photodissociation (PD) tandem mass spectra have been obtained at 266 nm for the protonated molecules of a tryptic peptide, ASHLGLAR, and of its phenyl isothiocyanate and 4-sulfophenyl isothiocyanate derivatives, generated by matrix-assisted laser desorption/ionization. Derivatization with the aromatic chromophores greatly reduced the intensity of the laser required for efficient PD. Major fragment ions observed in the three spectra are quite similar. General features of the PD tandem mass spectra and their potential utility for analytical purposes are discussed.     

Microfluidics: from dynamic lattices to periodic arrays of polymer disks

We used coupling of flow and geometric confinement to assemble emulsion droplets in two-dimensional gliding lattices with a high degree of order and symmetry. Highly monodisperse discoid droplets with circular shapes were generated in a microfluidic flow-focusing device. Originally, close-packed lattices formed from these circular discoid droplets. Progressive confinement led to the gradual deformation of the circular disks: first, they elongated in the direction parallel to the direction of flow and then transformed into hexagons. Assembly driven by the combination of flow and confinement also allowed for the formation of lattices from droplets with a bimodal size distribution. We used photopolymerization of the monomer droplets to trap the lattice structure in the solid state and produce highly periodic arrays of solid polymer disks.     

Nuclear quadrupole hyperfine structure in the microwave spectrum of HCl-N2O: electric field gradient perturbation of N2O by HCl

The microwave spectra of six isotopomers of HCl-N(2)O have been obtained in the 7-19 GHz region with a pulsed molecular beam, Fourier transform microwave spectrometer. The nuclear quadrupole hyperfine structure due to all quadrupolar nuclei is resolved and the spectra are analyzed using the Watson S-reduced Hamiltonian with the inclusion of nuclear quadrupole coupling interactions. The spectroscopic constants determined include rotational constants, quartic and sextic centrifugal distortion constants, and nuclear quadrupole coupling constants for each quadrupolar nucleus. Due to correlations of the structural parameters, the effective structure of the complex cannot be obtained by fitting to the spectroscopic constants of the six isotopomers. Instead, the parameters for each isotopomer are calculated from the A and C rotational constants and the chlorine nuclear quadrupole coupling constant along the a-axis, chi(aa). There are two possible structures; the one in which hydrogen of HCl interacts with the more electronegative oxygen of N(2)O is taken to represent the complex. The two subunits are approximately slipped parallel. For H (35)Cl-(14)N(2)O, the distance between the central nitrogen and chlorine is 3.5153 A and the N(2)O and HCl subunits form angles of 72.30 degrees and 119.44 degrees with this N-Cl axis, respectively. The chlorine and oxygen atoms occupy the opposite, obtuse vertices of the quadrilateral formed by O, central N, Cl, and H. Nuclear quadrupole coupling constants show that while the electric field gradient of the HCl subunit remains essentially unchanged upon complexation, there is electronic rearrangement about the two nitrogen nuclei in N(2)O.     

Reduction of the IgE-binding ability and maintenance of immunogenicity of gamma-irradiated Dermatophagoides farinae

House dust mites, Dermatophagoides farinae (DF) and Dermatophagoides pteronyssinus, are major allergens in the most common indoor allergen and are important risk factor for asthma. The modified antigen has been studied to treat allergic disorder. This study was carried out to measure possibility of modified allergen using gamma irradiation to treat allergy such as asthma. DF solutions (2 mg/ml) as target allergen were irradiated with Co-60 at 50 and 100 kGy. Conformational alternation of irradiated DF was observed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Levels of anti-irradiated DF mouse IgGs (sub-isotypes) against intact DF were measured similar to that of anti-intact DF IgGs. The binding abilities of house dust mite-allergic patients’ IgE were reduced depending on radiation dose, and irradiation could inhibit the binding ability of patients’ IgE more than 40%. This study has shown that the binding ability of IgE was reduced by conformational alteration by irradiation and the irradiated DF had epitopes capable to induce immunogeniciy.     

Pt‐Nanoparticle Incorporated Carbon Paste Electrode for the Determination of Cu(II) Ion by Anodic Stripping Voltammetry

Pt‐nanoparticles were synthesized and introduced into a carbon paste electrode (CPE), and the resulting modified electrode was applied to the anodic stripping voltammetry of copper(II) ions. The synthesized Pt‐nanoparticles were characterized by cyclic voltammetry, scanning electron microscopy and X‐ray photoelectron spectroscopy techniques to confirm the purity and the size of the prepared Pt‐nanoparticles (ca. 20 nm). This incorporated material seems to act as catalysts with preconcentration sites for copper(II) species that enhances the sensitivity of Cu(II) ions to Cu(I) species at a deposition potential of ?0.6 V in an aqueous solution. The experimental conditions, such as, the electrode composition, pH of the solution, pre‐concentration time, were optimized for the determination of Cu(II) ion using as‐prepared electrode. The sensitivity changes on the different binder materials and the presence of surfactants in the test solution. The interference effect of the coexisted metals were also investigated. In the presence of surfactants, especially TritonX‐100, the Cu(II) detection limit was lowered to 3.9×10^?9 M. However, the Pt‐nanoparticle modified CPE begins to degrade when the period of deposition exceeds to 10 min. Linear response for copper(II) was found in the concentration range between 3.9×10^?8 M and 1.6×10^?6 M, with an estimated detection limit of 1.6×10^?8 M (1.0 ppb) and relative standard deviation was 4.2% (n=5).     

Theoretical studies on the mechanism of acid-promoted hydrolysis of N-formylaziridine in comparison with formamide

[reaction: see text] We present an ab initio study of the acid-promoted hydrolysis reaction mechanism of N-formylaziridine in comparison with formamide. Since the rate of amide hydrolysis reactions depends on the formation of the tetrahedral intermediate, we focused our attention mainly on the reactant complex, the tetrahedral intermediate, and the transition state connecting these two stationary points. Geometries were optimized using the density functional theory, and the energetics were refined using ab initio theory including electron correlation. Solvent effects were investigated by using polarizable continuum method calculations. The proton-transfer reaction between the O-protonated and N-protonated amides was investigated. In acidic media, despite that the N-protonated species is more stable than the O-protonated one, it is predicted that both N-protonated and O-protonated pathways compete in the hydrolysis reaction of N-formylaziridine.     

Tuning chirality of single-wall carbon nanotubes by selective etching with carbon dioxide

CO2 molecule chemisorbs selectively on the zigzag tube edge without an activation barrier, whereas it physisorbs on the armchair edge of nanotubes. In addition, carbon nanotubes can be etched by an adsorbed oxygen atom of CO2 molecule. From our results, we suggest a selective etching mechanism for tuning the chirality of the mass-produced carbon nanotubes.