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.

Exploring the binding mechanism of Guaijaverin to human serum albumin: Fluorescence spectroscopy and computational approach

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Contribution of an extrinsic mechanism for the electrical polarization in BiMn2O5 ceramics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Abamectin affects the bioenergetics of liver mitochondria: A potential mechanism of hepatotoxicity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Kinetics and mechanism of the forward and reverse reactions between N,N′-dimethyl-4,4′-bipyridinium and hexacyanoferrate(II)

The kinetics of the hexacyanoferrate(III)-N,N′-dimethyl-4,4′-bipyridinium radical (MV+) reaction was studied by a laser flash photolysis technique. The radical was generated, in the presence of Fe(CN)6 3-, by quenching the excited state *Ru(bpy)3 2+ with MV2+. The second-order rate constant for the Fe(CN)6 3--MV+ reaction is (7.6 ± 0.5) × 109 M-1 s-1 at 23°C and ionic strength 0.10 M. Comparison with the rate constants calculated for the diffusion-controlled reaction (4.7 × 109 M-1 s-1) and the activation-controlled reaction (5.2 × 1012 M-1 s-1, on the basis of self-exchange rate constants of 8.0 × 105 M-1 s-1 and 1.9 × 104 M-1 s-1 for the MV2+/+ and Fe(CN)6 3-/4- couples, respectively) leads to the conclusion that the Fe(CN)6 3--MV+ reaction is diffusion controlled. The rate constant for the Fe(CN)6-MV2+ reaction, calculated from the rate constant for the Fe(CN)6 3--MV+ reaction and the appropriate equilibrium constant, is 2.4 × 10-5 M-1 s-1 at 23°C and ionic strength 0.10 M. Microscopic reversibility considerations require that the Fe(CN)6 4--MV2+ reaction be controlled by the dissociation of the successor complex Fe(CN)6 3-|MV+. The thermal and optical electron transfers in the ion pair Fe(CN)6 4-|MV2+ and in related systems are analyzed and discussed. © 1982 American Chemical Society.

An AM1 semiempirical study of the mechanism of sintering for ZnO in the presence of water and carbon dioxide

AM1 calculations were performed for the absorption of H2O and CO2 molecules on the surface of model ZnO crystals. The absorption of isolated molecules of each species and the co-absorption of both compounds simultaneously were considered. It was found that the absorption of H2O near a site where CO; is already absorbed favors the process of sintering, in agreement with the experimental findings. This is explained by the formation of Zn(OH)CO3H bound to the surface, a more mobile species than the ZnO unit itself. The roundening of the grains observed in atmospheres containing dry CO2 but suppressed when H2O is present, is also explained by these calculations. After absorption of CO2, the rupture of one bond - so that diffusion of the ZnCO3 species on the surface is allowed - requires much less energy than the breaking of two bonds, necessary for ZnO migration. These facts explain why the speed of surface transport does not decrease in CO2 atmospheres while sintering is indeed slowed down. © 1994.

HMDSO plasma polymerization and thin film optical properties

Thin films were deposited from hexamethyldisiloxane (HMDSO) in a glow discharge supplied with radiofrequency (rf) power. Actino-metric optical emission spectroscopy was used to follow trends in the plasma concentrations of the species SiH (414.2 nm), CH (431.4 nm), CO (520.0 nm), and H (656.3 nm) as a function of the applied rf power (range 5 to 35 W). Transmission infrared spectroscopy (IRS) was employed to characterize the molecular structure of the polymer, showing the presence of Si-H, Si-O-Si, Si-O-C and C-H groups. The deposition rate, determined by optical interferometry, ranged from 60 to 130 nm/min. Optical properties were determined from transmission ultra violet-visible spectroscopy (UVS) data. The absorption coefficient α, the refractive index n, and the optical gap E04 of the polymer films were calculated as a function of the applied power. The refractive index at a photon energy of 1 eV varied from 1.45 to 1.55, depending on the rf power used for the deposition. The absorption coefficient showed an absorption edge similar to other non-crystalline materials, amorphous hydrogenated carbon, and semiconductors. For our samples, we define as an optical gap, the photon energy E04 corresponding to the energy at an absorption of 104 cm-1. The values of E04 decreased from 5.3 to 4.6 as the rf power was increased from 5 to 35 W. © 1995.

Influence of polymerization on the synthesis of SrTiO3: Part I. Characteristics of the polymeric precursors and their thermal decomposition

The influence of polymerization on the thermal decomposition of polymeric precursors and phase formation was investigated during synthesis of SrTiO3. The precipitation of polymeric precursor in acetone produced a more thermal stable precursor with lower weight loss during decomposition. This more stable precursor retarded the formation of the SrTiO3 phase. From thermal analysis, XRD and FT-IR the presence of an intermediate phase during decomposition of the precursors was observed. This is a mixed (Sr,Ti) carbonate phase with the proposed composition of Sr2Ti2O5.CO3. © 1995.

Influence of polymerization on the synthesis of SrTiO3: Part II. Particle and agglomerate morphologies

Morphologies of SrTiO3 particles and agglomerates synthesized by the traditional Pechini route and by the polymer precipitation route were characterized by the nitrogen adsorption/desorption technique and by transmission electron microscopy (TEM). A cluster structure of nanometric particles forming large agglomerates which are broken during pressing followed by cluster rearrangement was observed. The mean particle size is larger for SrTiO3 obtained by the Pechini route and is related to the precursor thermal decomposition and particle growth during calcination. The particle growth is controlled by neck growth among particles and further motion of the particle boundary. © 1995.

Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution

Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.

Mechanism of phase formation in Pb(ZrxTi1-x)O3 synthesized by a partial oxalate method

The phase formation mechanism, as well as the morphotropic phase boundary, of lead zirconate titanate (PZT) processed by a partial oxalate method was investigated by simultaneous thermal analysis (TG-DTA) and by qualitative and quantitative X-ray diffraction (XRD). The results show that the ZrxTi1-xO2 (ZT) phase reacts with PbO forming the PZT phase without intermediate phases. XRD analysis showed the coexistence of rhombohedral and tetragonal phases for 0.47 ≤ x ≤ 0.55 with the phase boundary composition for x = 0.51. For low calcination temperatures, preferential formation of the PZT rhombohedral phase was observed. A model for phase formation of PZT by the partial oxalate method is proposed based on the existence of two interfaces of reaction (PbO-PZT and PZT-ZT) and diffusion of cations.

A SequenceSpace analysis of Lys49 phospholipases A2: Clues towards identification of residues involved in a novel mechanism of membrane damage and in myotoxicity

'SequenceSpace' analysis is a novel approach which has been used to identify unique amino acids within a subfamily of phospholipases A2 (PLA2) in which the highly conserved active site residue Asp49 is substituted by Lys (Lys49-PLA2s). Although Lys49-PLA2s do not bind the catalytic co-factor Ca2+ and possess extremely low catalytic activity, they demonstrate a Ca2+-independent membrane damaging activity through a poorly understood mechanism, which does not involve lipid hydrolysis. Additionally, Lys49-PLA2s possess combined myotoxic, oedema forming and cardiotoxic pharmacological activities, however the structural basis of these varied functions is largely unknown. Using the 'SequenceSpace' analysis we have identified nine residues highly unique to the Lys49-PLA2 sub-family, which are grouped in three amino acid clusters in the active site, hydrophobic substrate binding channel and homodimer interface regions. These three highly specific residue clusters may have relevance for the Ca2+-independent membrane damaging activity. Of a further 15 less stringently conserved residues, nine are located in two additional clusters which are well isolated from the active site region. The less strictly conserved clusters have been used in predictive sequence searches to correlate amino acid patterns in other venom PLA2s with their pharmacological activities, and motifs for presynaptic and combined toxicities are proposed.

Advanced ceramics: Evaluation of the mechanism of stock removal and ground surface quality

The aim of this work is to evaluate the mechanism of stock removal and the ground surface quality of advanced ceramics grounded by a plane tangential grinding process with diamond grinding wheels. The analysis of the grinding performance was done regarding the cutting surface wear behavior of the grinding wheel for ceramic workpieces. The discussion about the results emphasized the wear mechanism of the grinding wheel cutting surface and the cutting phenomenology of the grinding process. The grounded surface was evaluated using Scanning Electron Microscopy (SEM). © 1999 Society of Automotive Engineers, Inc.

Crystallization mechanism and properties of a blast furnace slag glass

The complex crystallization process of a Brazilian blast-furnace slag glass was investigated using differential scanning calorimetry (DSC), X-ray diffraction, optical microscopy, transmission electron microscopy (TEM), selected area diffraction (SAD), energy dispersive spectroscopy (EDS) and micro-Raman spectroscopy. Three crystalline phases (merwinite, melilite and larnite) were identified after heat treatment between Tg (742°C) and the DSC crystallization peak (T = 1000°C). Merwinite was identified as a metastable phase. A small amount (0.004 wt%) of metallic platinum was found in the glass composition. Particles of Pt3Fe, detected by EDS and SAD-TEM, were the starting points of crystallization acting, therefore, as heterogeneous nucleating sites. Only melilite and larnite precipitated in a glass sample heat-treated at 1000°C for 1 h. The flexural strength of this crystallized sample was less than that of the glass, probably due the allotropic phase transformation of larnite. © 2000 Published by Elsevier Science B.V. All rights reserved.

Toxic mechanism of nickel exposure on cardiac tissue

The incidence of cardiovascular disease has increased in the general population, and cardiac damage is indicated as one important cause of mortality. In addition, pollution and metal exposure have increased in recent years. For this reason, toxic effects of metals, such as nickel, and their relation to cardiac damage should be urgently established. Although free radical-mediated cellular damage and reactive oxygen species have been theorized as contributing to the nickel mechanism of toxicity, recent investigations have established that free radicals may be important contributors to cardiac dysfunction. However, there is little information on the effect of nickel exposure on markers of oxidative stress in cardiac tissue. Nickel exposure (Ni2+ 100 mg L-1 from NiSO4) significantly increased lipoperoxide and total lipid concentrations in cardiac tissue. We also observed increased serum levels of cholesterol (59%), lactate dehydrogenase (LDH-64%), and alanine transaminase (ALT-30%) in study animals. The biochemical parameters recovered to the control values with tocopherol intake (0.2 mg 200 g-1). Vitamin E alone significantly decreased the lipoperoxide concentration and increased superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities in the heart. Since no alterations were observed in catalase and GSH-Px activities by nickel exposure while SOD activities were decreased, we conclude that superoxide radical (O2 -) generated by nickel exposure is of primary importance in the pathogenesis of cardiac damage. Tocopherol, by its antioxidant activity, decreased the toxic effects of nickel exposure on heart of rats.