Determination of the turnover number of the restriction endonuclease EcoRI using evanescent wave technology

Binding and catalytic activity of the type II restriction endonuclease EcoRI on immobilized DNA has been observed in real time using three different evanescent wave biosensors and two different immobilization techniques. The method gives direct access to the turnover number (kcat) without the necessity for the determination of any concentration or activity. The combination of different evanescent wave techniques gives access to the catalytic mechanism and allows the determination of the rate limiting step.     

Preferred dimerization of tetra-tolyl- and tetra-tosylurea derivatives of flexible and rigidified calix[4]arenes

The dimerization of tetratolyl- and tetratosyl-urea derivatives 1 and 2, derived from a tetrapentoxy calix[4]arene in the cone conformation and of the corresponding tetra-urea derivatives 3 and 4, in which the cone conformation is rigidified by the two crown-3 tethers, have been studied. All six possible equimolar mixtures were examined by 1H NMR using CDCl3 and CD2Cl2 as solvents. While no heterodimers are found for the combinations 1/3 and 2/4 in either solvent, all remaining combinations lead to the (exclusive) formation of heterodimers in CD2Cl2. In CDCl3 heterodimers are only observed for the combinations of 3 with 2 or 4. These results are discussed in terms of entropic and enthalpic contributions and compared with MD-simulations in a box of chloroform solvent molecules.     

Importance of the diamine reactant in the production of polyphosphonamides by the interfacial technique

The stirred interfacial polycondensation of phenylphosphonic dichloride and 1,6-hexanediamine has been studied as a function of several reaction variables. The reaction is rapid, being completed in less than 1 min. When organic solvent is varied and reactant molar ratio is varied with an excess of the acid chloride, yield is constant. When reactant molar ratio is varied polymer yield increases with increase in amine concentration. When reactant concentration is increased yield increases. With the addition of a soluble salt in the aqueous phase yield is increased. The above indicates that the diffusion of the amine to the reaction zone is of primary importance in determining polymerization rate and that the diffusion of the acid chloride is relatively unimportant. Polymer yield was found to be dependent on the pH of the amine in the aqueous phase. The observed trend is related to the apparent solubility of the amine in the aqueous phase such that the greater the apparent solubility of the amine, the less the polymer yield. Polymer molecular weight is found to be independent of reaction variables tested. Polymer was also formed from the condensation of phenylphosphonic dichloride with p-phenylenediamine, H₂N-D-NH₂ (where D is a 36-carbon hydrocarbon chain), 1,3-di-4-piperidylpropane, and 4-aminomethylpiperidine; phenyl phosphorodichloridate with 1,6-hexanediamine; chloromethyl phosphonic dichloride with 1,6-hexanediamine.     

Counterion Exchange Selectivity in Detergent–Polymer Aggregates

In aqueous solution, the interaction between sodium dodecyl sulfate (SDS) and poly(ethylene glycol) (PEG) results in the formation of small aggregates or clusters of SDS attached to the PEG polymer chain. Selectivity coefficients for exchange of two monovalent (N-methyl-4-cyanopyridinium cation and Tl⁺) and two divalent (methylviologen cation and Cu²⁺) counterions at the surface of SDS–PEG clusters, determined employing photophysical techniques, are similar, but not identical, to those for exchange at the surface of SDS micelles in the absence of PEG. The principal factor affecting ion exchange selectivity in SDS–PEG clusters does not appear to be aggregate size or surface charge density but rather the presence of poly(oxyethylene) subunits at the aggregate surface.     

Mössbauer and molecular orbital study of the myoglobin-CO complex

Experimental Mössbauer spectra of the Fe⁵⁷-enriched CO complex of sperm whale myoglobin (MbCO) at T= 4.2 K with and without applied magnetic field (H⊥γ) were measured to derive the sign of the electric field gradient (EFG), the quadrupole splitting ΔE _Q, and the isomer shift δ of the heme iron. We find a positive EFG, δE _Q = 0.363 mm/sec, and δ + 0.266 mm/sec. Molecular orbital calculations were carried out to obtain theoretical estimates of EFG and ΔE _Q for several steric arrangements of the CO ligand relative to the heme group. Our results are most consistent with the conclusion that the iron is situated in the heme plane, and that a bent geometry with a Fe-C-O angle of about 135 ° is more favorable than a more symmetric structure with a linear Fe-C-O geometry.     

Theoretical evidence for the singlet diradical character of square planar nickel complexes containing two o-semiquinonato type ligands

Density functional theory and complete active space self-consistent field computations are applied to elucidate the singlet diradical character of square planar, diamagnetic nickel complexes that contain two bidentate ligands derived from o-catecholates, o-phenylenediamines, o-benzodithiolates, o-aminophenolates, and o-aminothiophenolates. In the density functional framework, the singlet diradical character is discussed within the broken symmetry formalism. The singlet-triplet energy gaps, the energy gained from symmetry breaking, the spin distribution in the lowest triplet state, and the form of the magnetic orbitals are applied as indicators for the singlet diradical character. Moreover, a new index for the diradical character is proposed that is based on symmetry breaking. All symmetry breaking criteria show that the complexes obtained from o-catecholates and o-benzodithiolates have the largest and the smallest singlet diradical character, respectively. The singlet diradical character should be intermediate for the complexes derived from o-phenylenediamines, o-aminophenolates, and o-aminothiophenolates. The diradical character of all complexes suggests the presence of Ni(II) central atoms. This is also indicated by the d-populations computed by means of the natural population analysis.     

Bead injection for surface enhanced Raman spectroscopy: automated on-line monitoring of substrate generation and application in quantitative analysis

The technique of bead injection has been adapted for surface enhanced Raman scattering (SERS) to substantially improve precision, long term stability and sensitivity of SERS detection in analytical chemistry. For this purpose a fully automated flow system comprising a dedicated flow-cell has been developed and tested. With the developed flow-cell, which contains two inlet and two outlet channels, it is possible to retain, perfuse and discharge minute amounts of polymer beads while monitoring all steps by Raman spectroscopy. First, beads carrying cation exchanger moieties were retained in the flow-cell and subsequently perfused with a silver nitrate and a hydroxylamine solution using one inlet of the flow cell. By this sequence homogeneous SERS active silver layers were formed on the beads. The uniformity of the achieved silver layer was studied by secondary electron microscopy. For measurement, the analyte was then introduced from the second inlet channel such that the interaction between the activated SERS beads and analyte occurred in close proximity and within the focus of the laser excitation beam. Due to the complete computer control of all experimental steps, including bead entrapment, SERS layer generation, sample introduction and final bead removal, highly reproducible conditions for SERS were achieved. The method was developed using 9-aminoacridine as a test molecule. Quantitative studies were carried out for 9-aminoacridine and acridine showing linear calibrations from 1-100 nmol l(-1) and 50-1,000 nmol l(-1), respectively, using a sample volume of 200 microl each. Typical relative standard deviations were 4.7% for 9-aminoacrine and 5.8% for acridine.     

The role of molecular shape in bilayer elasticity and phase behavior

A previously developed molecular level model for lipid bilayers [G. Brannigan and F. L. H. Brown, J. Chem. Phys. 120, 1059 (2004)] is extended to allow for variations in lipid length and simulations under constant surface tension conditions. The dependence of membrane elasticity on bilayer thickness is obtained by adjusting lipid length at constant temperature and surface tension. Additionally, bilayer fluidity at various lipid lengths is quantified by analysis of a length versus temperature phase diagram at vanishing tension. Regions of solid, gel-like (hexatic) and fluid bilayer behavior are established by identification of phase boundaries. The main melting transition is found to be density driven; the melting temperature scales inversely with lipid length since thermal expansion increases with lipid aspect ratio.