An N,N′-diaryl urea based conjugated polymer model system

An N,N′-diphenyl urea was designed as a model system for aggregation phenomenon in poly(phenyleneethynylenes) (PPEs). The unmethylated N,N′-diphenyl urea adopts an open, unfolded conformation in which the two diphenyl acetylene fluorophores are far enough away, mimicking the unaggregated state. Dimethylation forces the aromatic surfaces together into π-π contact, mimicking the aggregated state of PPEs. Analogous to bulk PPEs, this model system shows dramatic differences in quantum yield between the folded and unfolded states, with the unfolded urea having greater than 400-fold higher fluorescence quantum yield than its folded equivalent.     

Characterization of reaction products formed during thin-layer chromatographic detection of thiocarbamate herbicides

The reaction between thiocarbamate herbicides and 2,6-dichlorobenzoquinone-N-chloroimine or 2,6-dibromobenzoquinone-N-chloroimine is suitable for the detection of these herbicides on thin-layer plates with high sensitivity. The reactions were followed by infrared, nuclear magnetic resonance and mass spectrometry. We have established the formation of 2,6-dichlorobenzoquinone-S-alkyl sulphenylimines. In the case of the bromo-derivative, halogen exchange and substitution on the quinone ring took place simultaneously leading to the formation of mixed halogenated 2,6-dihalo- and, in addition, 2,3,6-trihalobenzoquinone-S-alkyl sulphenylimines. The final product of the detection reaction, i.e. 2,6-dichlorobenzoquinone-S-alkyl sulphenylimine was reacted with 2,6-dibromobenzoquinone-N-chloroimine where 2,6-dichloro-3-bromobenzoquinone-S-alkyl sulphenylimine formed as a consequence of the looser bromine-carbon linkage on the 2 and 6 positions of the quinone ring.     

On the diffusion field in the neighborhood of two identical spheres

Summary Under steady state conditions the reduction in the diffusive flux into a sphere due the presence of a neighboring, identical sphere is calculated. Taking the flux into a sphere as 1 when the particles are at infinite separation, the flux decreases to a minimum value of 0.693 when the spheres are touching.

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Zusammenfassung Unter stationären Bedingungen wird die Abnahme des Diffusionsflusses in eine Kugel, bedingt durch eine benachbarte identische Kugel, berechnet.Wird der Diffusionsfluß in eine Kugel gleich 1 gesetzt, wenn die Partikel unendlich weit voneinander entfernt sind, so nimmt der Diffusionsfluß auf einen Minimalwert von 0,693 ab, wenn sich die Kugeln berühren.

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With 2 figures     

Hybridization and enzymatic extension of au nanoparticle-bound oligonucleotides

We have investigated the impact of steric effects on the hybridization and enzymatic extension of oligonucleotides bound to 12-nm colloidal Au particles. In these experiments, a nanoparticle-bound 12-mer sequence is hybridized either to its solution phase 12-mer complement or to an 88-mer template sequence. The particle-bound oligonucleotide serves as a primer for enzymatic extension reactions, in which covalent incorporation of nucleotides to form the complement of the template is achieved by the action of DNA polymerase. Primers were attached via-C(6)H(12)SH, -C(12)H(24)SH, and -TTACAATC(6)H(12)SH linkers attached at the 5' end. Primer coverage on the nanoparticles was varied by dilution with (5')HSC(6)H(12)AAA AAA(3'). Hybridization efficiencies were determined as a function of linker length, primer coverage, complement length (12-mer vs 88-mer), and primer:complement concentration ratio. In all cases, hybridization for the 88-mer was less efficient than for the 12-mer. Low primer surface coverage, greater particle-primer separation, and higher primer:complement ratios led to optimal hybridization. Hybridization efficiencies as high as 98% and 75% were observed for the 12-mer and 88-mer, respectively. Enzymatic extension of particle-bound primers was observed under all conditions tested; however, the efficiency of the reaction was strongly affected by linker length and primer coverage. Extension of primers attached by the longest linker was as efficient as the solution-phase reaction.     

Photochemical and Photophysical Studies of 3-Amino-6-lodoacridine and the Inactivation of λ Phage

Abstract— The photochemistry and photophysics of 3-amino-6-io-doacridine (Acr-I) was studied. Photolysis (350 nm) of Acr-I (free base) generates products consistent with a free radical intermediate in methanol, benzene and carbon tetrachloride. The Acr-I hydrochloride is shown to bind to calf thymus DNA and to the self-complementary dinucleotide cytidylyl-(3′-5′)-guanosine (CpG) minidu-plex in a manner similar to that of proflavine (Acr-NH₂), a known DNA intercalator. The Acr-I is shown to more efficiently nick supercoiled plasmid DNA pBR322 upon 350 nm or 420 nm photolysis than Acr-NH₂. The efficiency of Acr-I-sensitized DNA nicking is not oxygen dependent. Photolysis of the Acr-I/(CpG)₂ complex leads to cleavage of the dinucleotide and to cytidine base release by selective damage to a specific ribose moiety. Dinucleotide cleavage occurs equally well in the presence or absence of oxygen, thereby eliminating a singlet oxygen- or peroxyl radical-mediated process. Photolysis of Acr-I in the presence of a mononucleotide (GMP) or a non-self-complementary dinucleotide (uridylyl-[3′-5′]-cytidine– UpC) does not lead to fragmentation and base release. Similarly, photolysis of the Acr-NH₂/(CpG)₂ complex does not lead to fragmentation and base release. The data indicate that photolysis of an iodinated intercalator bound to CpG or plasmid DNA generates an intercalated aryl radical and that the reactive intermediate initiates a sequence of reactions that efficiently nick nucleic acids. The inactivation of Λ phage sensitized by Acr-I with UV (350 nm) light is oxygen independent but with visible (420 nm) light is strongly oxygen dependent. The Acr-I fluoresces more intensely when excited at 446 than at 376 nm. Thus, UV photolysis may lead to C-I bond homolysis and free radical formation, a process that is not energetically feasible with visible light. The results demonstrate the difficulty of extrapolating model studies involving simple molecules and DNA to understanding the mechanism of viral inactivation with a particular sensitizer.     

Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture

[FeFe]-hydrogenases are known for their high rates of hydrogen turnover, and are intensively studied in the context of biotechnological applications. Evolution has generated a plethora of different subclasses with widely different characteristics. The M2e subclass is phylogenetically distinct from previously characterized members of this enzyme family and its biological role is unknown. It features significant differences in domain- and active site architecture, and is most closely related to the putative sensory [FeFe]-hydrogenases. Here we report the first comprehensive biochemical and spectroscopical characterization of an M2e enzyme, derived from Thermoanaerobacter mathranii. As compared to other [FeFe]-hydrogenases characterized to-date, this enzyme displays an increased H₂ affinity, higher activation enthalpies for H⁺/H₂ interconversion, and unusual reactivity towards known hydrogenase inhibitors. These properties are related to differences in active site architecture between the M2e [FeFe]-hydrogenase and “prototypical” [FeFe]-hydrogenases. Thus, this study provides new insight into the role of this subclass in hydrogen metabolism and the influence of the active site pocket on the chemistry of the H-cluster.

Characterization of a group D putative sensory [FeFe]-hydrogenase reveals how the active site can be tuned to decrease CO inhibition and increase stability of a reduced H-cluster while retaining the ability to catalyze H⁺/H₂ interconversion.     

Decoupling the effects of hydrophilic and hydrophobic moieties at the neuron–nanofibre interface

Peptide-based nanofibres are a versatile class of tunable materials with applications in optoelectronics, sensing and tissue engineering. However, the understanding of the nanofibre surface at the molecular level is limited. Here, a series of homologous dilysine–diphenylalnine tetrapeptides were synthesised and shown to self-assemble into water-soluble nanofibres. Despite the peptide nanofibres displaying similar morphologies, as evaluated through atomic force microscopy and neutron scattering, significant differences were observed in their ability to support sensitive primary neurons. Contact angle and labelling experiments revealed that differential presentation of lysine moieties at the fibre surface did not affect neuronal viability; however the mobility of phenylalanine residues at the nanofibre surface, elucidated through solid- and gel-state NMR studies and confirmed through tethered bilayer lipid membrane experiments, was found to be the determining factor in governing the suitability of a given peptide as a scaffold for primary neurons. This work offers new insights into characterising and controlling the nanofibre surface at the molecular level.

The mobility of hydrophobic moieties at a peptide nanofibre surface determines its suitability as a scaffold for sensitive primary cells.     

Capillary liquid chromatography with MS3 for the determination of enkephalins in microdialysis samples from the striatum of anesthetized and freely-moving rats

In vivo microdialysis sampling was coupled to capillary liquid chromatography (LC)/electrospray ionization quadrupole ion trap mass spectrometry (MS) to monitor [Met]enkephalin and [Leu]enkephalin in the striatum of anesthetized and freely-moving rats. The LC system utilized a high-pressure pump to load 2.5 microl samples and desalt the 25 microm i.d. by 2 cm long column in 12 min. Samples were eluted with a separate pump at approximately 100 nl min(-1). A rapid gradient effectively separated the endogenous neuropeptides in 4 min. A comparison was made for operating the mass spectrometer in the MS2 and MS3 modes for detection of the peptides. In standard solutions, the detection limits were similar at 1-2 pM (2-4 amol injected); however, the reproducibility was improved with MS3 as the relative standard deviation was <5% compared with 20% for MS2 for 60 pM samples. For dialysate solutions, reconstructed ion chromatograms and tandem mass spectra had much higher signal-to-noise ratios in the MS3 mode, resulting in more confident detection at in vivo concentrations. The method was successfully used to monitor the peptides under basal conditions and with stimulation of peptide secretion by infusion of elevated K+ concentration.     

Multi-dimensional pulsed field gradient magic angle spinning NMR experiments on membranes

The benefits of gradient techniques in the study of lipid membranes are demonstrated on a sample of 1-palmitoyl-2-oleoyl-sn-glycero-3 phosphocholine (POPC) liposomes embedded with ibuprofen. Most techniques from gradient NMR spectroscopy on solution samples are directly applicable to membrane samples subjected to magic angle spinning (MAS). Gradient-enhanced homo- and heteronuclear chemical shift correlation techniques were used to make resonance assignments. Gradient NOESY experiments provide insight into the location and dynamics of lipids, ibuprofen and water. Application of gradients not only reduces experiment time but also the t(1) noise in the multi-dimensional spectra. Diffusion measurements with pulsed field gradients characterize lateral movements of lipid and drug molecules in membranes. The theoretical framework for data analysis of MAS diffusion experiments on randomly oriented multilamellar liposomes is presented.     

Coupled reference interaction site model/simulation approach for thermochemistry of solvation: theory and prospects

We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from a single molecular dynamics or Monte Carlo simulation. Here we describe in detail the coupled RISM/simulation approach, and offer some error analysis. Finally we give the results of its application to a set of small test molecules in aqueous solution. The success shown in some of our results demonstrates that the coupled RISM/simulation approach is worth considering further as a potentially useful tool in studies of solvated systems, such as aqueous molecular biosystems.