DNA hybridization mechanism in an interfacial environment: What hides beneath first order k (s(-1)) kinetic constant?

The scientific question addressed in this work is: what hides beneath first order kinetic constant k (s(-1)) measured for hybridization of a DNA target on a biosensor surface. Kinetics hybridization curves were established with a 27 MHz quartz microbalance (9 MHz, third harmonic) biosensor, constituted of a 20-base probe monolayer deposited on a gold covered quartz surface. Kinetics analysis, by a known two-step adsorption-hybridization mechanism, is well appropriate to fit properly hybridization kinetics curves, for complementary 20-base to 40-base targets over two concentration decades. It was found that the K-1 (M-1) adsorption constant, relevant to the first step, concerns an equilibrium between non hybridized targets and hybridized pre-complex and increases with DNA target length. It was established that k(2) (s(-1)), relevant to irreversible formation of a stable duplex, varies in an opposite way to K-1 with DNA target length. (C) 2012 Published by Elsevier B.V.

Kinetic studies on the reactions of Ru(II) tetraammines with CS2N- 3

The kinetics of the reactions of Ru(II) complexes with CS2N- 3 ions were studied spectrophotometrically. The formation rate constants data for trans-[Ru(NH3)4L(CS2N3)] are 2.2 × 102, 1.8 × 10 and 1.3 × 102 M-1 s-1 for L = SO2- 3, HSO- 3 and P(OEt)3), respectively [μ = 1.0 M (NaCF3COO), 25°C]. Under the same experimental conditions, the values of k-1 (specific rate for the aquation reaction) are 1.5 × 10-2, 5.0 × 10-2 and 4.5 × 10 s-1 for L = SO2- 3, HSO- 3 and P(OEt)3, respectively. The free-energy change (ΔG≠) for the systems where L = P(OEt)3 and SO2- 3 are in agreement within the experimental error. It was observed that the affinity of the CS2N- 3 ion decreases with the increasing π-acidity of the auxiliary ligand L. The order of affinity of the CS2N- 3 ion for the Ru(II) center studies is SO2- 3 > HSO- 3 > P(OEt)3 >SO2. © 1986.

Hydration-dependent conformational states of hemoglobin. Equilibrium and kinetic behavior

The equilibrium and kinetics of methemoglobin conversion to hemichrome induced by dehydration were investigated by visible absorption spectroscopy. Below about 0.20 g water per g hemoglobin only hemichrome was present in the sample; above this value, an increasing proportion of methemoglobin appeared with the increase in hydration. The transition between the two derivatives showed a time-dependent biphasic behavior and was observed to be reversible. The rates obtained for the transition of methemoglobin to hemichrome were 0.31 and 1.93 min-1 and for hemichrome to methemoglobin 0.05 and 0.47 min-1. We suggest that hemichrome is a reversible conformational state of hemoglobin and that the two rates observed for the transition between the two derivatives reflect the α- and β-chains of hemoglobin.

Kinetic properties of de-repressible alkaline phosphatase (EC 3.1.3.1) from Neurospora crassa

De-repressible alkaline phosphatase from N. crassa shows inhibition by PNP-P and a hyperbolic mixed-type inhibition by Pi. Both increasing concentrations of Pi and decreases in assay pH abolished inhibition by the substrate. Also, Pi promoted polymerization of the enzyme molecule, whose effect may account for the inhibitory behaviour shown by the enzyme in the presence of low Pi concentrations. © 1991 Rapid Communications of Oxford Ltd.

Oxidative dissolution of covellite by Thiobacillus ferrooxidans

Oxidation of research-grade covellite was investigated in respirometric and growth experiments with Thiobacillus ferrooxidans. Covellite was directly oxidized by T. ferrooxidans in respirometric experiments, but the pH of mineral salts medium increased to prohibitively high values because of high sulfide concentrations. In glycine-H 2SO 4 buffered medium the pH remained steady and the oxygen uptake activity of T. ferrooxidans was not inhibited. In cultures growing with covellite as the sole source of energy, the pH increased to about 4. Redox potential increased to 500-600 mV during bacterial oxidation of covellite in the presence and absence of additional Fe 2+, whereas it remained mostly at about 350 mV in abiotic control. Jarosite was a major solid-phase product in T. ferrooxidans cultures. The solubilization of copper from covellite in inoculated flasks was higher than that obtained in control flasks and was not enhanced in the presence of additional Fe 2+.The sample also contained bornite (Cu 5FeS 4) which released iron in solution under all experimental conditions. Accumulation of S 0 was apparent only in inoculated covellite samples. © 1997 Elsevier B.V. All rights reserved.

Oxidative dissolution of chalcopyrite by Thiobacillus ferrooxidans

The oxidative dissolution of research-grade chalcopyrite was characterized in respirometric and growth experiments with Thiobacillus ferrooxidans. In respirometric experiments with chalcopyrite, the pH of mineral salts medium increased to values that inhibited the oxygen uptake activity of T. ferrooxidans. In glycine-H 2SO 4 buffered medium the pH remained stable and oxygen uptake was not inhibited. In cultures growing with chalcopyrite as the sole source of energy, pH changes were only minor during the incubation. The redox potential values increased to about 600 mV during the bacterial oxidation of chalcopyrite in the presence and absence of additional Fe 2+, while they remained at about 350 mV in abiotic control flasks. Iron in chalcopyrite was solubilized and oxidized to Fe 3+ by T. ferrooxidans. In the abiotic controls, by comparison, less iron was solubilized and it remained as Fe 2+. Jarosite was a major solid- phase product in T. ferrooxidans cultures. The solub'flization of copper from chalcopyrite in inoculated flasks was enhanced in the presence of additional Fe 2+.Accumulation of S 0, reflecting partial oxidation of the S-entity of chalcopyrite, was apparent from the x-ray diffraction analysis of solid residues from the inoculated flasks as well the abiotic controls. © 1997 Elsevier B.V. All rights reserved.

A kinetic model of phosphorus metabolism in growing goats

The effect of increasing phosphorus (P) intake on P utilization was investigated in balance experiments using 12 Saanen goats, 4 to 5 mo of age and weighing 20 to 30 kg. The goats were given similar diets with various concentrations of P, and 32P was injected to trace the movement of P in the body. A P metabolism model with four pools was developed to compute P exchanges in the system. The results showed that P absorption, bone resorption, and excretion of urinary P and endogenous and fecal P all play a part in the homeostatic control of P. Endogenous fecal output was positively correlated to P intake (P < .01). Bone resorption of P was not influenced by intake of P, and P recycling from tissues to the blood pool was lesser for low P intake. Endogenous P loss occurred even in animals fed an inadequate P diet, resulting in a negative P balance. The extrapolated minimum endogenous loss in feces was .067 g of P/d. The minimum P intake for maintenance in Saanen goats was calculated to be .61 g of P/ d or .055 g of P/(kg.75·d) at 25 kg BW. Model outputs indicate greater P flow from the blood pool to the gut and vice versa as P intake increased. Intake of P did not significantly affect P flow from bone and soft tissue to blood. The kinetic model and regressions could be used to estimate P requirement and the fate of P in goats and could also be extrapolated to both sheep and cattle.

A joint theoretical and kinetic investigation on the fragmentation of (N-halo)-2-amino cycloalkanecarboxylates

A combined theoretical and experimental study to elucidate the molecular mechanism for the Grob fragmentation of different (N-halo)-2-amino cyclocarboxylates with the nitrogen atom in exocyclic position: (N-Cl)-2-amino cyclopropanecarboxylate (1), (N-Cl)-2-amino cyclobutanecarboxylate (2), (N-Cl)-2-amino cyclopentanecarboxylate (3) and (N-Cl)-2-amino cyclohexanecarboxylate (4), and the corresponding acyclic compounds, (N-Cl)-2-amino isobutyric acid (A), (N-Cl)-2-amino butyric acid (B), has been carried out. The kinetics of decomposition for these compounds and related bromine derivatives were experimentally determined by conventional and stopped-flow UV spectrophotometry. The reaction products have been analyzed by GC and spectrophotometry. Theoretical analysis is based in the localization of stationary points (reactants and transition structures) on the potential energy surface. Calculations were carried out at B3LYP/6-31+G* and MP2/6-31+G* computing methods in the gas phase, while solvent effects have been included by means the self-consistent reaction field theory, PCM continuum model, at MP2/6-31+G* and MP4/6-31+G*//MP2/6-31+G* calculation levels. Based on both experimental and theoretical results, the different Grob fragmentation processes show a global synchronicity index close to 0.9, corresponding to a nearly concerted process. At the TSs, the N-Cl bond breaking is more advanced than the C-C cleavage process. An antiperiplanar configuration of these bonds is reached at the TSs, and this geometrical arrangement is the key factor governing the decomposition. In the case of 1 and 2 the ring strain prevents this spatial disposition, leading to a larger value of the activation barrier. Natural population analysis shows that the polarization of the N-Cl and C-C bonds along the bond-breaking process can be considered the driving force for the decomposition and that a negative charge flows from the carboxylate group to the chlorine atom to assist the reaction pathway. A comparison of theoretical and experimental results shows the relevance of calculation level and the inclusion of solvent effects for determining accurate unimolecular rate coefficients for the decomposition process. © 2002 Published by Elsevier Science B.V.

Synthesis and characterization of poly-o-toluidine: Kinetic and structural aspects

Poly(o-methylaniline) (poly-o-toluidine, PTOL) was synthesized by chemical oxidation of o-toluidine with ammonium peroxydisulfate in an aqueous 1.0 mol L -1 HCl solution. The progress of polymerization was followed by measuring the open-circuit potential (OCP) of a Pt electrode immersed in the reaction medium with the polymerization time. The chemical synthesis of PTOL was carried out at different monomer:oxidant (M:O) molar ratios (4:1, 2:1, 1.5:1, 1:1, and 0.66:1), and the products obtained were characterized by infrared spectroscopy, gel permeation chromatography, and X-ray diffraction. The molecular weight and percentage of crystallinity of PTOL are higher for samples synthesized in an excess of the monomer, i.e. at higher M:O ratios. However, the yield of PTOL prepared at higher M:O ratios is considerably low, in particular at a 4:1 M:O ratio, which is the M:O ratio most commonly used in the literature to synthesize polyaniline and its derivatives.

Kinetic study of the plastoquinone pool availability correlated with H2O2 release in seawater and antioxidant responses in the red alga Kappaphycus alvarezii exposed to single or combined high light, chilling and chemical stresses

Under biotic/abiotic stresses, the red alga Kappaphycus alvarezii reportedly releases massive amounts of H2O2 into the surrounding seawater. As an essential redox signal, the role of chloroplast-originated H2O2 in the orchestration of overall antioxidant responses in algal species has thus been questioned. This work purported to study the kinetic decay profiles of the redox-sensitive plastoquinone pool correlated to H2O2 release in seawater, parameters of oxidative lesions and antioxidant enzyme activities in the red alga Kappaphycus alvarezii under the single or combined effects of high light, low temperature, and sub-lethal doses of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), which are inhibitors of the thylakoid electron transport system. Within 24 h, high light and chilling stresses distinctly affected the availability of the PQ pool for photosynthesis, following Gaussian and exponential kinetic profiles, respectively, whereas combined stimuli were mostly reflected in exponential decays. No significant correlation was found in a comparison of the PQ pool levels after 24 h with either catalase (CAT) or ascorbate peroxidase (APX) activities, although the H2O2 concentration in seawater (R = 0.673), total superoxide dismutase activity (R = 0.689), and particularly indexes of protein (R = 0.869) and lipid oxidation (R = 0.864), were moderately correlated. These data suggest that the release of H2O2 from plastids into seawater possibly impaired efficient and immediate responses of pivotal H2O2-scavenging activities of CAT and APX in the red alga K. alvarezii, culminating in short-term exacerbated levels of protein and lipid oxidation. These facts provided a molecular basis for the recognized limited resistance of the red alga K. alvarezii under unfavorable conditions, especially under chilling stress. © 2006 Elsevier B.V. All rights reserved.

The effect of chloride ions and A. ferrooxidans on the oxidative dissolution of the chalcopyrite evaluated by electrochemical noise analysis (ENA)

It is believed that the dissolution of chalcopyrite (CuFeS2) in acid medium can be accelerated by the addition of Cl- ions, which modify the electrochemical reactions in the leaching system. Electrochemical noise analysis (ENA) was utilized to evaluate the effect of the Cl- ions and Acidithiobacillus ferrooxidans on the oxidative dissolution of a CPE-chalcopyrite (carbon paste electrode modified with chalcopyrite) in acid medium. The emphasis was on the analysis of the admittance plots (Ac) calculated by ENA. In general, a stable passive behavior was observed, mainly during the initial stages of CPE-chalcopyrite immersion, characterized by a low passive current and a low dispersion of the Ac plots, mainly after bacteria addition. This can be explained by the adhesion of bacterial cells on the CPE-chalcopyrite surface acting as a physical barrier. The greater dispersions in the Ac plots occurred immediately after the Cl- ions addition, in the absence of bacteria characterizing an active-state. In the presence of bacteria the addition of Clions only produced some effect after some time due to the barrier effect caused by bacteria adhesion. © (2009) Trans Tech Publications.

Pulp tissue dissolution when the use of sodium hypochlorite and EDTA alone or associated

Purpose: The aim of the present study was to evaluate the tissue dissolving capacity of various concentrations of sodium hypochlorite either alone or in combination with 17% EDTA. Methods: Eighty bovine pulp fragments were prepared, and their weight was determined using a precision balance. Each pulp fragment was immersed for 2 hours in a solution/mixture that was based on the following groups: G1-saline solution; G2-0.5% NaOCl; G3-1.0% NaOCl; G4-2.5% NaOCl; G5-17% EDTA; G6-0.5% NaOCl+17% EDTA; G7-1.0% NaOCl+ 17% EDTA; and G8-2.5% NaOCl+17% EDTA. The final weight was measured, and the weight loss was calculated. A statistical analysis was performed using either the Student's t-test for paired samples or an ANOVA and Tukey tests (P<0.05 was considered to be significant). Results: We measured a significant difference between the sample weight before and after treatment for each of the tested groups (P<0.05). The 2.5% sodium hypochlorite solution (G4) completely dissolved the pulp tissue within the test period. NaOCl+EDTA was less effective than sodium hypochlorite alone at dissolving the pulp tissue (P<0.05), and EDTA alone (G5) did not markedly dissolve the pulp tissue. Conclusion: Using EDTA together with NaOCl reduced the tissue dissolving properties compared with NaOCl alone, regardless of the concentration of NaOCl that was used. © 2011 Só et al.; licensee EDIPUCRS.

Kinetic parameters for thermal decomposition of supramolecular polymers derived from diclofenac-meglumine supramolecular adducts

Meglumine is an aminocarbohydrate able to form supramolecular adducts with organic acids. The recognition is based on hydrogen bonds and the structures resulting from the complexation have high solubility in water. This property has been exploited by the pharmaceutical industry in the improvement of existing drugs, and the successful example of this approach involves the poorly soluble non-steroidal anti-inflammatory drugs (NSAIDs). Investigation of the thermal behavior of adduct obtained from meglumine and the NSAID diclofenac revealed that a polymer-like material is formed from the self-assembly of diclofenac-meglumine adducts in the melt. This polymer showed a high molecular weight around 2.0×105kDa. The kinetic parameters for the thermal decomposition step of the polymer were determined by the Capela-Ribeiro non-linear isoconversional method. From data for the TG curves in nitrogen atmosphere and heating rates of 5, 10, 15 and 20°Cmin-1, the Eα and Bα terms could be determined, and consequently the pre-exponential factor, Aα, as well as the kinetic model, g(α). © 2012 Elsevier B.V.