Kinetic characterization of an extremely slow DNA binding equilibrium

We here exploit the recently reported thermodynamic preference for poly(dAdT)(2) over mixed-sequence calf thymus (ct) DNA of two binuclear ruthenium complexes, DeltaDelta-[mu-bidppz(bipy)4Ru2](4+) (B) and DeltaDelta-[mu-bidppz(phen)(4)Ru(2)](4+) (P), that bind to DNA by threading intercalation, to determine their intrinsic dissociation rates. After adding poly(dAdT)(2) as a sequestering agent to B or P bound to ct-DNA, the observed rate of change in luminescence upon binding to the polynucleotide reflects the rate of dissociation from the mixed sequence. The activation parameters for the threading and dissociation rate constants allow us for the first time to characterize the thermodynamics of the exceedingly slow threading intercalation equilibrium of B and P with ct-DNA. The equilibrium is found to be endothermic by 33 and 76 kJ/mol, respectively, and the largest part of the enthalpy difference between the complexes originates from the forward threading step. At physiological temperature (37 degrees C) B and P have dissociation half-lives of 18 and 38 h, respectively. This is to our knowledge the slowest dissociating noncovalently bound DNA-drug reported. SDS sequestration is the traditional method for determination of rate constants for cationic drugs dissociating from DNA. However, the rates may be severely overestimated for slowly dissociating molecules due to unwanted catalysis by the SDS monomers and micelles. Having determined the intrinsic dissociation rates with poly(dAdT)(2) as sequestering agent, we find that the catalytic effect of SDS on the dissociation rate may be up to a factor of 60, and that the catalysis is entropy driven. A simple kinetic model for the SDS concentration dependence of the apparent dissociation rate suggests an intermediate that involves both micelles and DNA-threaded complex.     

DHA-induced changes of supported lipid membrane morphology

Docosahexaenoic acid (DHA) is a polyunsaturated long fatty acid known to have fundamental effects on cell membrane function. Here, the effect of DHA on phosphocholine-supported lipid bilayers was measured using the quartz crystal microbalance with dissipation monitoring (QCM-D) technique. Above a concentration of 60 muM (i.e., near the critical micelle concentration), DHA had drastic effects on the viscoelastic properties of the supported membranes, suggesting a more complex process and structure than simple insertion of molecules in the bilayer. Fluorescence microscopy revealed the spontaneous formation of elongated out-growths from the bilayers, which were remarkable for their length ( approximately 100 mum) and extensive coverage of the surface. These results demonstrate the applicability of QCM-D as a method to screen for conditions where membrane remodeling occurs but also that complementary techniques are required to describe in more detail the changes in viscoelastic properties of the membrane. These results are highly relevant for the present rapid development in the field of model lipid membranes aiming toward increased knowledge about processes occurring at biological surfaces.     

A new mechanism of benzophenone photoreduction in photoinitiated crosslinking of polyethylene and its model compounds

The photolytic products and a new photoreduction mechanism of benzophenone (BP) as a photoinitiator in the photocrosslinking of polyethylene (PE) and its model compounds (MD) have been studied by means of fluorescence, ESR, ¹³C and ¹H NMR spectroscopy. The fluorescence spectra from the PE and MD systems demonstrate that the main photoreduction product of BP (PPB) is benzpinacol formed by the recombination of two diphenylhydroxymethyl (K^•) radical intermediates. The ESR spectrum obtained from the UV irradiation of the MD/BP system gives positive evidence of K^• radicals. Two new PPB products: an isomer of benzpinacol with quinoid structure, 1‐phenyl‐hydroxymethylene‐4‐diphenyl‐hydroxymethyl‐2,5‐cyclohexa‐diene and three kinds of α‐alkylbenzhydrols have been detected and identified for the first time by ¹³C and ¹H NMR spectroscopy from the MD systems. The latter could be formed by the reactions of K^• radicals with alkyl radicals produced by hydrogen abstraction of the excited triplet state ³(BP)* from polyethylene or its model compounds. These results provide new experimental evidence for elucidating the photoreduction mechanism of BP in the photoinitiated crosslinking of polyethylene. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 999–1005, 2000     

Amphiphilic graft copolymers - preparation and interfacial properties

Amphiphilic graft copolymers containing poly(ethylene oxide) (PEO) grafts have been prepared by various methods, for example, by coupling of reactive hydrophobic backbone polymers with end-functionalised PEO, by macromonomer copolymerisation, and by anionic graft polymerisation of EO onto polymer backbones carrying functional groups as initiator precursors. The graft copolymers are amphiphilic and were shown to accumulate at surfaces and interfaces in solution and in the solid state. Amphiphilic starch derivatives were prepared by reaction of amylose and starch with aliphatic α-epoxides.     

Isolation of Escherichia coli inner membranes by metal affinity two-phase partitioning

As reduction of sample complexity is a central issue in membrane proteomic research, the need for new pre-fractionation methods is significant. Here we present a method for fast and efficient enrichment of Escherichia coli inner membranes expressing a His-tagged integral membrane L-fucose-proton symporter (FucP). An enriched inner membrane fraction was obtained from a crude membrane mixture using affinity two-phase partitioning in combination with nickel-nitrilotriacetic acid (Ni-NTA) immobilized on agarose beads. Due to interaction between the beads and FucP, inner membranes were selectively partitioned to the bottom phase of a polymer/polymer aqueous two-phase system consisting of poly(ethylene glycol) (PEG) and dextran. The partitioning of membranes was monitored by assaying the activity of an inner membrane marker protein and measuring the total protein content in both phases. The enrichment of inner membrane proteins in the dextran phase was also investigated by proteomic methodology, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), trypsin digestion and liquid chromatography in combination with tandem mass spectrometry (LC-MS/MS). Using a high level of significance (99.95%) in the subsequent database search, 36 proteins assigned to the inner membrane were identified in the bottom phase, compared to 29 when using the standard sucrose gradient centrifugation method for inner membrane isolation. Furthermore, metal affinity two-phase partitioning was up to 10 times faster than sucrose gradient centrifugation. The separation conditions in these model experiments provide a basis for the selective isolation of E. coli membranes expressing His-tagged proteins and can therefore facilitate research on such membrane proteomes.     

Preparation and characterization of terraced surfaces of low-index faces of anatase, rutile, and brookite

Simple polishing and relatively low temperature annealing procedures for preparing atomically flat terraced surfaces of various single-crystal TiO2 polymorphs are described. Anatase (101), anatase (001), rutile (100), rutile (110), and brookite (111) surfaces could all be prepared with a terraced surface structure as revealed in AFM images. The rutile (100) and (110) and anatase (101) surfaces were also shown to produce acceptable LEED patterns immediately upon insertion into a UHV system without the usual sputter and anneal cycles.     

Validation of the extended Tanaka column characterization protocol by multivariate analysis of chromatographic retention of low‐molecular‐weight analytes on reversed phase columns using methanol and acetonitrile as organic modifiers

The validity of the extended Tanaka column characterization procedure against the retention behavior of 101 analytes of widely differing properties chromatographed on five differing stationary phase chemistries has been established using a chemometric technique called principal component analysis (PCA). It was concluded that the simple and conveniently determined column characterization parameters covered the same space in the PCA loading plot as the retention times for the 101 differing analytes. This confirms that the ten column characterization parameters of the extended Tanaka protocol encode the same information as the retention times of the 101 analytes. Significant selectivity differences were observed between stationary phases and the mobile‐phase modifiers – MeOH and MeCN. PCA contribution plots served as a convenient way to highlight specific selectivity differences between stationary phases. logD values exhibited a poor correlation with retention indicating that retention in RP‐LC is not solely dictated by the analyte's hydrophobicity. The use of MeOH was found to generate greater selectivity differences with the five stationary phases than when MeCN is used.     

Enantiospecific kinking of DNA by a partially intercalating metal complex

Opposite enantiomers of [Ru(phenanthroline)(3)](2+) affect the persistence length of DNA differently, a long speculated effect of helix kinking. Our molecular dynamics simulations confirm a substantial change of duplex secondary structure produced by wedge-intercalation of one but not the other enantiomer. This effect is exploited by several classes of DNA operative proteins.     

Analysis of parameter effects on chemical reaction coupled transport phenomena in SOFC anodes

Mass, heat and momentum transport processes are strongly coupled by internal chemical reforming reactions in planar design solid oxide fuel cell (SOFC) anodes. In this paper, a three-dimensional computational fluid dynamics approach is applied to simulate and analyze reforming reactions of methane and various transport processes in a duct relevant for SOFC anodes. The results show that the anode duct design and operating parameters, grouped as three characteristic ratios, are significant for the chemical reactions and further for multi-species distribution, fuel gas transport and heat transfer in the sub-domains of the anode.     

Some remarks on the perturbation and variation–perturbation calculations of the free energy for quantum systems

A generalization of the Gibbs–Bogoliubov inequality F ? F₀ + 〈H ? H₀〉₀ for the free energy F is studied which leads to a variation principle for this quantity that may be of importance in certain computational applications to quantum systems. This approach is coupled with a study of the perturbation expansion of the free energy for a canonical ensemble with H = H₀ + λV in the general case when H₀ and V do not commute. The second- and high-order derivatives of the free energy with respect to the perturbation parameter λ are calculated. From the second-order term is finally obtained a second-order correction to the previous variational minimum for the free energy.