Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine

DNA-protein cross-linking is one of the many DNA lesions mediated by hydroxyl radicals, the most damaging among the reactive oxygen species in biological systems. Density functional theory methods are employed to investigate the complex reaction mechanisms of the formation of cytosine-tyrosine cross-links as observed in gamma-irradiated aqueous solutions of cytosine and tyrosine, as well as in gamma-irradiated nucleohistone. The majority of the radical addition mechanisms considered are found to have significant barriers and therefore to be thermodynamically unfavorable for the formation of the initial cross-linked product. Our calculated reaction potential energy surfaces suggest that a feasible complete mechanism consists of radical combination forming the initial cross-linked product, a hydrogen shuffle within the initial cross-linked product, and an acid-catalyzed dehydration reaction. Water and hydrogen-bonding interactions are suggested to play a key role in catalyzing the hydrogen-transfer step of the reaction.     

Simultaneous spectrophotometric determination of nitrite and nitrate by flow injection analysis

The flow injection principle is used in the photometric determination of nitrite and nitrate with sulfanilamide and N-(1-naphthyl)ethylenediamine as reagents. An on-line copper-coated cadmium reductor reduces nitrate to nitrite. The detection limit is 0.05 μM for nitrite and 0.1 mM for nitrate at a total sample volume of 200 μM. Up to 30 samples can be analyzed per hour with a relative precision of ca. 1%.     

Rapid prototyping of polymer microsystems via excimer laser ablation of polymeric moulds

This study presents a novel method for rapid prototyping of polymer microsystems. The method is based on excimer laser ablation of a thermally and mechanically stable polymer, such as PEEK (poly-ether-ether-ketone). A negative of the desired microsystem is laser machined in PEEK, which can then be used directly for hot embossing or injection moulding of a series of prototypes. This approach is very rapid and considerably cheaper than more traditional approaches to toolmaking, while still performing well in terms of reproduction of tool dimensions. The reduction in time and cost for a master tool using this method opens up new possibilities for testing small series in the R&D phase of a microsystem. Finally, two particular applications of the technique are presented.     

Photoinduced electron transfer in Zn(II)porphyrin-bridge-Pt(II)acetylide complexes: variation in rate with anchoring group and position of the bridge

The synthesis and photophysical characterization of two sets of zinc porphyrin platinum acetylide complexes are reported. The two sets of molecules differ in the way the bridging phenyl-ethynyl unit is attached to the porphyrin ring. One set is attached via an ethynyl unit on the β position, while the other set is attached via a phenyl unit on the meso position of the porphyrin. These were compared with previously studied complexes where attachment was made via an ethynyl unit on the meso position. Femtosecond transient absorption measurements showed in all systems a rapid quenching of the porphyrin singlet state. Electron transfer is suggested as the quenching mechanism, followed by an even faster recombination to form both the porphyrin ground and triplet excited states. This is supported by the variation in quenching rate and porphyrin triplet yield with solvent polarity, and the observation of an intermediate state in the meso-phenyl linked systems. The different linking motifs between the dyads resulted in significant variations in electron transfer rates.     

Direct electrochemistry and bioelectrocatalysis of a class II non-symbiotic plant haemoglobin immobilised on screen-printed carbon electrodes

In this study, direct electron transfer (ET) has been achieved between an immobilised non-symbiotic plant haemoglobin class II from Beta vulgaris (nsBvHb2) and three different screen-printed carbon electrodes based on graphite (SPCE), multi-walled carbon nanotubes (MWCNT-SPCE), and single-walled carbon nanotubes (SWCNT-SPCE) without the aid of any electron mediator. The nsBvHb2 modified electrodes were studied with cyclic voltammetry (CV) and also when placed in a wall-jet flow through cell for their electrocatalytic properties for reduction of H₂O₂. The immobilised nsBvHb2 displayed a couple of stable and well-defined redox peaks with a formal potential (E°′) of ?33.5 mV (vs. Ag|AgCl|3 M KCl) at pH 7.4. The ET rate constant of nsBvHb2, k _s, was also determined at the surface of the three types of electrodes in phosphate buffer solution pH 7.4, and was found to be 0.50 s^?1 on SPCE, 2.78 s^?1 on MWCNT-SPCE and 4.06 s^?1 on SWCNT-SPCE, respectively. The average surface coverage of electrochemically active nsBvHb2 immobilised on the SPCEs, MWCNT-SPCEs and SWCNT-SPCEs obtained was 2.85?×?10^?10 mol cm^?2, 4.13?×?10^?10 mol cm^?2 and 5.20?×?10^?10 mol cm^?2. During the experiments the immobilised nsBvHb2 was stable and kept its electrochemical and catalytic activities. The nsBvHb2 modified electrodes also displayed an excellent response to the reduction of hydrogen peroxide (H₂O₂) with a linear detection range from 1 μM to 1000 μM on the surface of SPCEs, from 0.5 μM to 1000 μM on MWCNT-SPCEs, and from 0.1 μM to 1000 μM on SWCNT-SPCEs. The lower limit of detection was 0.8 μM, 0.4 μM and 0.1 μM at 3σ at the SPCEs, the MWCNT-SPCEs, and the SWCNT-SPCEs, respectively, and the apparent Michaelis–Menten constant, $ {\hbox{K}}_{\rm{M}}^{\rm{app}} $ , for the H₂O₂ sensors was estimated to be 0.32 mM , 0.29 mM and 0.27 mM, respectively.     

“Clickable” affinity ligands for effective separation of glycoproteins

In this paper, we present a new modular approach to immobilize boronic acid ligands that can offer effective separation of glycoproteins. A new “clickable” boronic acid ligand was synthesized by introducing a terminal acetylene group into commercially available 3-aminophenyl boronic acid. The clickable ligand, 3-(prop-2-ynyloxycarbonylamino)phenylboronic acid (2) could be easily coupled to azide-functionalized hydrophilic Sepharose using Cu(I)-catalyzed 1,3-dipolar cycloaddition reaction under mild condition. Compared to other boronic acid affinity gels, the new affinity gel displayed superior effectiveness in separating model glycoproteins (ovalbumin and RNase B) from closely related bovine serum albumin and RNase A in the presence of crude Escherichia coli proteins. Because of the simplicity of the immobilization through “click chemistry”, the new ligand 2 is expected to not only offer improved glycoprotein separation in other formats, but also act as a useful building block to develop new chemical sensors for analysis of other glycan compounds.     

Transverse, tilting and cross-coupling stiffness of cylindrical rubber isolators in the audible frequency range—The wave-guide solution

Audio-frequency wave-guide models for antisymmetric dynamic stiffness of arbitrary long elastomer cylinders are presented. The locally non-mixed boundary conditions at the lateral and radial surfaces are simultaneously satisfied by using the modes corresponding to the dispersion relation for axial waves in cylinders satisfying the stress free boundary conditions at the curved radial boundaries, while the displacement conditions on the flat cylinder ends are satisfied by mode matching. The elastomer is modelled as nearly incompressible with deviatoric visco-elasticity based on a fractional derivative, standard linear solid embodying a Mittag-Leffler relaxation kernel, the main advantage being the minimum parameter number required to successfully model the material properties over a broad frequency band. The stiffness is found to depend strongly on frequency; displaying resonances and anti-resonances. The method is compared with and verified against finite element models. In addition, comparison to thin beam theories, i.e. Euler and Timoschenko theory and a simple shear model, is presented, illustrating the limitations of these models.     

Random laser action in bovine semen

Experiments using bovine semen reveal that the addition of a high-gain water soluble dye results in random laser action when excited by a Q-switched, frequency doubled, Nd:Yag laser. The data shows that the linewidth collapse of the emission is correlated to the sperm count of the individual samples, potentially making this a rapid, low sample volume approach to count determination.     

Sub-nanometer distances and cluster shapes in dense hydrogen and in higher levels of hydrogen Rydberg matter by phase-delay spectroscopy

The inter-atomic distances in potassium clusters of Rydberg matter (RM) at excitation levels n _B = 4–8 were recently measured by phase-delay spectroscopy (Holmlid, J Nanopart Res 12: 273, 2010). Excitation levels n _B < 4 with shorter inter-atomic distances exist for hydrogen clusters, and distances down to 140 pm are now measured with this light-scattering method. The clusters studied have maximum dimensions from 0.3 nm up to several tens of nm, often being planar. A weak carbon dioxide laser beam interacts with the clusters in a tunable RM cavity. A strong fringe structure is observed as a function of the end-grating angular position. Delay lengths in the clusters are derived from the fringe structure, corresponding to twice the distance between rows or planes in the clusters. Good agreement with predicted and a few previously measured distances in excitation levels n _B = 1, 2, and 3 is found. Close-packing is the main structure both in planar and 3D clusters. Planar clusters are only observed for n _B = 1 and 3, while 3D clusters are found in excitation levels n _B = 1, 2 and 3. The cluster–cluster distance in stacks of planar clusters for n _B = 2 and 3 is now observed for the first time.