Atomic force microscopy of parallel DNA branched junction arrays

BACKGROUND: The four arms of the Holliday junction are known to stack in pairs forming two helical domains whose orientations are antiparallel, but twisted positively by about 60 degrees, based on electrophoretic, FRET and AFM measurements. Recent gel retardation studies suggest that a bowtie junction (containing 5',5' and 3',3' linkages in its crossover strands) may adopt a parallel conformation. RESULTS: An AFM study of two-dimensional arrays produced by parallelograms of bowtie junctions shows that the angle between helical domains is in the range of -68+/-2 degrees. We demonstrate by AFM that the domains are parallel by constructing V-shaped structures whose arms are separated by approximately 68 degrees and approximately 112 degrees. CONCLUSIONS: The arms of the bowtie junction are parallel rather than antiparallel. The parallel or antiparallel nature of the junction apparently is determined by the local structure of the junction, but the sign of the angle appears to be a consequence of interarm electrostatic interactions.     

2,3,4,5‐Tetrakis­[(2‐hydroxy­ethyl)­thio]­tetra­thia­fulvalene tetra­fluoro­borate

The title complex, C₁₄H₂₀O₄S₈^+.BF₄^?, is a charge‐transfer complex with typical charges for the donor and anion of +1 and ?1, respectively. Two centrosymmetrically related donors form a face‐to‐face π‐dimer with a strong intermolecular S?S interaction. These π‐dimers stack along the a axis to form a donor column. The structure is extensively hydrogen bonded.     

Study on the electroreduction process of oxygen to superoxide ion by using acetylene black powder microelectrode

In this paper, the powder microelectrode technique was employed in studying the voltametric response of the O₂/₂⁻ couple, which demonstrated a nearly reversible redox process at an acetylene black powder microelectrode in N,N-dimethylformamide (DMF). A well-developed steady state current plateau for the electrochemical reduction of oxygen was obtained in this system. The electron transfer number (n) and heterogeneous electron transfer rate constant k _s were measured by steady-state voltametric response, and the results were 1.08, 3.4 × 10⁻³ cm s⁻¹, respectively. Additionally, the scavenging activity of O₂⁻ with biological antioxidant (ascorbic acid) was evaluated by cyclic voltammetry; IC₅₀ came to 5 × 10⁻⁴ mol/l. Published in Russian in Elektrokhimiya, 2008, Vol. 44, No. 8, pp. 1040–1044. The text was submitted by the authors in English.     

Voltammetric determination of malachite green in fish samples based on the enhancement effect of anionic surfactant

In this work, an electrochemical method for the determination of malachite green was developed on the basis of enhancement effect of an anionic surfactant: sodium dodecyl benzene sulfonate. It is found that the oxidation peak current of malachite green at carbon paste electrode significantly increases in the presence of low concentration of sodium dodecyl benzene sulfonate in pH 6.5 phosphate buffer, suggesting that sodium dodecyl benzene sulfonate shows obvious enhancement effect for the determination of malachite green. The experimental parameters, such as supporting electrolyte, kind of surfactant, concentration of sodium dodecyl benzene sulfonate and accumulation time, were optimized, and then a sensitive and convenient electrochemical method was proposed for the determination of malachite green. The oxidation peak current is proportional to the concentration of malachite green over the range from 8.0 × 10⁻⁹ to 5.0 × 10⁻⁷ mol l⁻¹, and the detection limit is 4.0 × 10⁻⁹ mol l⁻¹ after 5 min of accumulation. Finally, this new method was successfully employed to detect malachite green in fish samples. Published in Russian in Elektrokhimiya, 2008, Vol. 44, No. 8, pp. 1019–1024. The text was submitted by the authors in English.     

Thermal degradation of copolymers from vinyl acetate and vinyl alcohol

The thermal degradation of poly(vinyl acetate) (PVA), poly(vinyl alcohol) (PVAL), vinyl acetate-vinyl alcohol (VAVAL), vinyl acetate-vinyl-3,5-dinitrobenzoate (VAVDNB) and vinyl alcohol-3,5-dinitrobenzoate (VALVDNB) copolymers have been studied using differential thermal analysis (DTA) and thermogravimetry (TG) under isothermal and dynamic conditions in nitrogen. Thermal analysis indicates that PVA and PVAL are thermally more stable than VAVAL copolymers, being PVAL the most stable polymer. The presence of small amounts of vinyl-3,5-dinitrobenzoate (VDNB) in PVA or PVAL produces a marked decrease in the thermal stability of both homopolymers, being VALVDNB copolymers the less stable materials. The apparent activation energy of the degradative process was determined by the Kissinger and Flynn-Wall methods which agree well.     

Carboxyl groups in pre-treated regenerated cellulose fibres

The influence of peroxide bleaching and slack-mercerization on the amount of acidic groups in regenerated fibres (viscose, modal and lyocell) were studied. Conductometric titration was used to determine the total content of acidic carboxylic groups. Polyelectrolyte titration was used for surface and total charge determination, and to obtain information about the charge distribution and accessibilities of charged groups. Changes in fibre crystallinity to pre-treatment processes were characterized using iodine sorption (Schwertassek method) and correlated to treatments and the amount of carboxylic groups. For all three types of fibres the amount of accessible carboxyl groups was lowered by an increase in the degree of crystallinity. Bleaching with hydrogen peroxide causes some oxidative cellulose damage and, therefore, a larger amount of carboxyl groups (presumably formed at the end of cellulose chains). Slack-mercerization did not significantly change the total amount of acidic groups in the fibres, but their accessibility to cationic polyelectrolytes, in particular to polymers with high molecular weight was substantially lowered. Lidija Fras Zemljič, Zdenka Peršin, and Karin Stana Kleinschek are the members of the European Polysaccharide Network of Excellence (EPNOE).     

Synthesis and spectroscopic properties of furyl-phenyl-acrylates and naphthofurans and their interaction with ct-<Emphasis Type="Italic">DNA</Emphasis>

A series of novel substituted derivatives related to furyl-phenyl-acrylates and naphthofurans, was synthesized and characterized by UV/Vis and fluorescence spectroscopy. Acyclic compounds can undergo photochemical dehydrocyclization by visible light irradiation in order to obtain their cyclic derivatives. The interactions of the prepared compounds with calf thymus DNA was investigated by means of electronic absorption and fluorescence spectra. It is intriguing that addition of ct-DNA induced a fluorescence increase of acyclic derivatives, exactly the opposite of the strong fluorescence quenching observed for cyclic derivatives 10 and 12. Compound 11 showed decreasing fluorescence intensity for lower concentrations of ct-DNA, while increasing of fluorescence is observed for high excess of added ct-DNA. Correspondence: Grace Karminski-Zamola, Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia.     

Monitoring enzyme reaction and screening of inhibitors of acetylcholinesterase by quantitative matrix-assisted laser desorption/ionization fourier transform mass spectrometry

A matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS)-based assay was developed for kinetic measurements and inhibitor screening of acetylcholinesterase. Here, FTMS coupled to MALDI was applied to quantitative analysis of choline using the ratio of choline/acetylcholine without the use of additional internal standard, which simplified the experiment. The Michaelis constant (K _m) of acetylcholinesterase (AChE) was determined to be 73.9 μmol L⁻¹ by this approach. For Huperzine A, the linear mixed inhibition of AChE reflected the presence of competitive and noncompetitive components. The half maximal inhibitory concentration (IC₅₀) value of galantamine obtained for AChE was 2.39 μmol L⁻¹. Inhibitory potentials of Rhizoma Coptidis extracts were identified with the present method. In light of the results the referred extracts as a whole showed inhibitory action against AChE. The use of high-resolution FTMS largely eliminated the interference with the determination of ACh and Ch, produced by the low-mass compounds of chemical libraries for inhibitor screening. The excellent correlation with the reported kinetic parameters confirms that the MS-based assay is both accurate and precise for determining kinetic constants and for identifying enzyme inhibitors. The obvious advantages were demonstrated for quantitative analysis and also high-throughput characterization. This study offers a perspective into the utility of MALDI-FTMS as an alternate quantitative tool for inhibitor screening of AChE.     

Brugnanin,a new syn-2,3-dihydrobenzofuran neolignan dioate from the mangrove <Emphasis Type="Italic">Bruguiera gymnorrhiza</Emphasis>

Brugnanin (1), a neolignan dioate, was isolated from a mangrove plant Bruguiera gymnorrhiza. Based on spectroscopic interpretation of MS, IR, and NMR data, 1 was elucidated as (7R*,8S*,E)-3-hydroxy-5,5′-dimethoxy-7-O-4′,8-3′-neolignan-7′-ene-9,9′-dioic acid dioctadecyl ester. MTT assay showed that 1 had weak inhibitory activity against growth of CNE-1 nasopharyngeal carcinoma cell line. Published in Khimiya Prirodnykh Soedinenii, No. 2, pp. 147–149, March–April, 2008.     

Synthesis of alpha-keto-imides via oxidation of ynamides

A de novo preparation of alpha-keto-imides via ynamide oxidation is described. With a number of alkyne oxidation conditions screened, a highly efficient RuO2-NaIO4 mediated oxidation and a DMDO oxidation have been identified to tolerate a wide range of ynamide types. In addition to accessing a wide variety of alpha-keto-imides, the RuO2-NaIO4 protocol provides a novel entry to the vicinal tricarbonyl motif via oxidation of push-pull ynamides, and imido acylsilanes from silyl-substituted ynamides. Chemoselective oxidation of ynamides containing olefins can be achieved by using DMDO, while the RuO2-NaIO4 protocol is not effective. These studies provide further support for the synthetic utility of ynamides.