Modification of the electrokinetic properties of reversible electrophoresis gels for the separation and preparation of DNA

The effect of adding linear polymers to a novel reversible electrophoretic was measured. Reversible gels are formed using the polyanionic carbohydrate polymer, gellan gum. Gellan gum forms strong stable gels in the presence of divalent cations or diamines. The gels are reversible (return to solution) by changing the ionic environment or pH. Gellan gum is an anionic polymer, and the electrophoresis gels have considerable electroosmotic flow (EOF) toward the negative electrode. We measured the EOF in gellan gum electrophoresis gels as a function of gel concentration, buffer composition, and linear polymer additive. The linear polymers used in this study were polyethylene oxide and hydroxyethyl cellulose. Both polymers reduced EOF in the gels, in a manner dependent on molecular weight. Polymers with high molecular weight were more effective at reducing EOF. The addition of polymers increased the resolution of low molecular weight DNA. Native gellan gum resolved DNA from approx 50,000 to 1000 bp. Addition of the polymers resolved DNA down to approx 50 bp, in some instances. The influence of the polymers on circular plasmid DNA was also investigated. Addition of high molecular weight polyethylene oxide reduced the electrophoretic mobility of the nicked circular form compared to the supercoiled form.     

First seco-C oleananes from nature

[structure: see text] The triterpenes 8,14-seco-oleana-8(26),13-dien-3beta-ol (1) and its acetyl derivative 2 were isolated from Stevia viscida and Stevia eupatoria, respectively. Their structures were elucidated by 2D NMR, including carbon-carbon connectivity experiments, and confirmed by X-ray diffraction analysis of ketone 3. The absolute configuration was determined by NMR analysis of the Mosher esters of 1. The biogenetic implications of the new substances are discussed.     

Bis(1,10‐phenanthroline)(thio­sulfato)­manganese(II) methanol solvate and catena‐poly­[[di­aqua(2,9‐di­methyl‐1,10‐phenanthroline)­manganese(II)]‐μ‐thio­sulfato]

The structure of bis(1,10‐phenanthroline‐κ²N,N′)(thio­sulfato‐κ²O:S)­manganese(II) methanol solvate, [Mn(S₂O₃)(C₁₂H₈N₂)₂]·CH₃OH, is made up of Mn²⁺ centers coordinated to two bidentate phenanthroline (phen) groups and an S,O‐chelating thio­sulfate anion, forming monomeric entities. The structure of catena‐poly­[[di­aqua(2,9‐di­methyl‐1,10‐phen­anthro­line‐κ²N,N′)­manganese(II)]‐μ‐thio­sulfato‐κ²O:S], [Mn(S₂O₃)(C₁₄H₁₂N₂)(H₂O)₂]_n, is polymeric, consisting of Mn(dmph)(H₂O)₂ units (dmph is 2,9‐di­methyl‐1,10‐phenanthroline) linked by thio­sulfate anions acting in an S,O‐chelating manner.     

New physically adsorbed polymer coating for reproducible separations of basic and acidic proteins by capillary electrophoresis

In this work, a new physically adsorbed coating for capillary electrophoresis (CE) is presented. The coating is based on a N,N-dimethylacrylamide-ethylpyrrolidine methacrylate (DMA-EPyM) copolymer synthesized in our laboratory. The capillary coating is simple and easy to obtain as only requires flushing the capillary with a polymer aqueous solution for 2 min. It is shown that by using these coated capillaries the electrostatic adsorption of a group of basic proteins onto the capillary wall is significantly reduced allowing their analysis by CE. Moreover, the DMA-EPyM coating provides reproducible separations of the basic proteins with RSD values for migration times lower than 0.75% for the same day (n = 5) and lower than 3.90% for three different days (n = 15). Interestingly, the electrical charge of the coated capillary wall can be modulated by varying the pH of the running buffer which makes possible the analysis of basic and acidic proteins in the same capillary. The usefulness of this coating is further demonstrated via the reproducible separation of whey (i.e. acidic) proteins from raw milk. The coating protocol should be compatible with both CE in microchips and CE-MS of different types of proteins.     

Two nickel complexes stabilized by nitrate counter‐ions

Two new nickel nitrates, di­aqua­bis(3,4,7,8‐tetra­methyl‐1,10‐phenanthroline‐κ²N,N′)­nickel(II) dinitrate methanol solvate, [Ni(C₁₆H₁₆N₂)₂(H₂O)₂](NO₃)₂·CH₄O, (I), and tri­aqua­[2,4,6‐tris(2‐pyridyl)‐1,3,5‐triazine‐κ³N¹,N²,N⁶]nickel(II) di­ni­trate trihydrate, [Ni(C₁₈H₁₂N₆)(H₂O)₃](NO₃)₂·3H₂O, (II), are reported. In both structures, the cation is octahedrally coordinated, to two bidentate 3,4,7,8‐tetra­methyl‐1,10‐phenanthroline (tmp) and two water mol­ecules in (I), and to one tridentate 2,4,6‐tris(2‐pyridyl)‐1,3,5‐triazine (tpt) and three water mol­ecules in (II). Both structures are stabilized by extensive hydrogen‐bonding interactions.     

Three-state 2',7'-difluorofluorescein excited-state proton transfer reactions in moderately acidic and very acidic media

2',7'-Difluorofluorescein (Oregon Green 488, OG488) is a novel fluorescein dye derivative which presents important advantages for improving the fluorimetric applications in the biomedical and biochemical sciences. In aqueous solution it displays four prototropic forms, namely cation (C), neutral (N), monoanion (M), and dianion (D). In previous works, we found (J. Phys. Chem. A 2005, 109, 734-747, 2840-2846) that OG488 undergoes excited-state proton transfer reactions, which may affect the results from applications using this dye. We established that the excited-state proton transfer (ESPT) reactions between neutral, monoanionic, and dianionic forms of OG488 are promoted by acetate buffer, and we characterized the ground and excited species involved. We also solved the kinetics of the prototropic reactions using global compartmental analysis. In the present paper, we extend our study on the ESPT reactions of OG488 to acidic media, in which only the three prototropic species cation, neutral, and monoanion coexist. We have solved the kinetics of the three-state ESPT reaction by means of global three-compartmental analysis of a fluorescence decay surface in moderately acidic media (pH between 1.1 and 3.0), recovering the kinetic and spectral parameters of this three-state system. This system is one of the most complex solved to date, due to the strong overlap of the absorption and emission spectra of the neutral and monoanionic forms of OG488. We also found that the cation behaves as "super" photoacid, showing a very high deprotonation rate constant (1.04 x 10(11) s(-1)) and an enhanced acidity. Therefore, we also carried out experiments at very high perchloric acid concentrations, dealing with some other effects which become noteworthy at these [H(+)]. The presence of xanthylium cation quenching due to "free" water molecules, and the reduction in the amount of water clusters acting as proton acceptors, are processes which alter notably the time course of the excited-species in this high [H(+)] range.     

Polymer-silica nanocomposites prepared by sol-gel technique: Nanoindentation and tapping mode AFM studies

Polymer-silica nanocomposites based on poly(2-hydroxyethyl acrylate) (PHEA) have been prepared by the simultaneous polymerization of the organic and the silica phases in a sol-gel process with the silica precursor tetraethyl orthosilicate (TEOS). The structure of this system is investigated using atomic force microscopy (AFM) in the tapping mode and in nanoindentation experiments. The structure of the PHEA/silica hybrids strongly depends on the ratio of both components in the system. For silica weight fractions lower than 0.15, the system consists of aggregated silica particles dispersed in the organic matrix; above that concentration of silica the structure is co-continuous with that of the organic matrix, similarly to two interpenetrated networks.     

Evaluation of a synergetic effect between Rh as permanent chemical modifier and acetylacetone as complexing agent in Sc determination in sediment slurry samples by ETAAS

In the present work, scandium was determined in sediment slurry samples (from three different rivers) by electrothermal atomic absorption spectrometry (ETAAS). Slurries were prepared by weighting 100 mg of dry sediment samples (≤53 μm particle sizes) and adding 6 ml of HCl:HNO₃:HF (3:1:2, v/v). Accurate results were only possible due to the synergetic effect between Rh as permanent chemical modifier and acetylacetone (Acac) as complexing agent. The same platform was used for 400 heating cycles. The performance of the chemical modification was evaluated by using scanning electron microscopy (SEM), synchrotron radiation X-ray fluorescence (SRXRF) and some figures of merit (precision and detectability). The best analytical conditions were attained using 1500 and 2550 °C as pyrolysis and atomization temperatures. The scandium content in the liquid phase of the slurries ranged from 61 to 73%, thus indicating, in this study, that both liquid and solid phases play an important role in slurry analyses. An amount of 5.0–20.0 μg l⁻¹ Sc linear range as well as LOD and LOQ of 0.19 and 0.62 μg l⁻¹, respectively, were obtained under these conditions. The accuracy was checked by using microwave-assisted decomposition, and the results compared to those obtained with the proposed methodology (slurry analysis). By checking both sets of the results, there is no statistical difference at the 95% confidence levels.     

Dynamic behavior of DNA base pairs containing 8-oxoguanine

The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.     

Regioselective homogeneous hydrogenation of heteroaromatic nitrogen compounds by use of [RuH(CO)(NCMe)2(PPh3)2]BF4 as the precatalyst

Summary The complex [RuH(CO)(NCMe)₂(PPh₃)₂]BF₄ (1) is an efficient and regioselective catalyst precursor for the hydrogenation of polyaromatic nitrogen compounds such as quinoline (Q), isoquinoline (iQ), indole (ln), 5,6- and 7,8-benzoquinoline (BQ) and acridine (A) under relatively mild reaction conditions (125 °C, 4 atm H₂). The order of individual initial rates was: A > Q > 5,6-BQ > 7,8-BQ > ln > iQ, reflecting both steric and electronic effects. For the regioselective homogeneous hydrogenation of A to 9,10-dihydroacridine (DHA) catalysed by complex (1), a kinetic study was carried out; the experimentally determined rate law was r = k ₁ [Ru] [H₂]. These findings are consistent with a mechanism involving the hydrogenation of [RuH(CO)(A)(NCMe)(PPh₃)₂]BF₄ to yield DHA and the unsaturated species [RuH(CO)(NCMe)(PPh₃)₂]BF₄ in the rate-determining step.