Energetic basis of molecular recognition in a DNA aptamer

The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T-m = 50.2 +/- 0.2 degrees C and a folding enthalpy Delta H degrees(fold) = -49.0 +/- 2.1 kcal mol(-1). These values agree with values of T-m = 49.6 degrees C and Delta H degrees(fold) = -51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy Delta G degrees(bind) = -5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with Delta H degrees(bind) = -8.7 kcal mol(-1). Combination of enthalpy and free energy produce ail unfavorable entropy of -T Delta S degrees = +3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K-1 was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures.

Daunomycin binding to detergent micelles: A model system for evaluating the hydrophobic contribution to drug-DNA interactions

The interaction of daunomycin with sodium dodecyl sulfate and Triton X-100 micelles was investigated as a model for the hydrophobic contribution to the free energy of DNA intercalation reactions. Measurements of visible absorbance, fluorescence lifetime, steady-state fluorescence emission intensity, and fluorescence anisotropy indicate that the anthraquinone ring partitions into the hydrophobic micelle interior. Fluorescence quenching experiments using both steady-state and lifetime measurements demonstrate reduced accessibility of daunomycin in sodium dodecyl sulfate micelles to the anionic quencher iodide and to the neutral quencher acrylamide. Quenching of daunomycin fluorescence by iodide in Triton X-100 micelles was similar to that seen with free daunomycin. Studies of the energetics of the interaction of daunomycin with micelles by fluorescence and absorbance titration methods and by isothermal titration calorimetry in the presence of excess micelles revealed that association with sodium dodecyl sulfate and Triton X-100 micelles is driven by a large negative enthalpy. Association of the drug with both types of micelles also has a favorable entropic contribution, which is larger in magnitude for Triton X-100 micelles than for sodium dodecyl sulfate micelles.

Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.

Stability of ZrTiCuNiBe Bulk Metallic Glass Upon Isothermal Annealing Near the Glass Transition Temperature

The stability of Zr41Ti14Cu12.5Ni10Be22.5 bulk metallic glass (BMG) upon isothermal annealing near the glass transition temperature has been investigated by using x-ray diffraction, differential scanning calorimetry, and the pulse echo overlap method. The density, elastic constants, and thermodynamic parameters as well as their annealing time dependence have been determined. The microstructural and properties changes of the annealed BMG were checked by acoustic measurement. Obvious structural and property changes were observed with prolonged annealing of the BMG near the glass transition temperature.

Rapid detection of porcine circovirus type 2 by loop-mediated isothermal amplification

A method of loop-mediated isothermal amplification (LAMP) was employed to develop a rapid and simple detection system for porcine circovirus type 2 (PCV2). The amplification could be finished in 60 min under isothermal condition at 64 degrees C by employing a set of four primers targeting the cap gene of PCV2. The LAMP assay showed higher sensitivity than the conventional PCR, with a detection limit of five copies per tube of purified PCV2 genomic DNA. No cross-reactivity was observed from the samples of other related viruses including porcine circovirus type 1 (PCV1), porcine parvovirus (PPV), porcine pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The detection rate of PCV2 LAMP for 86 clinical samples was 96.5% and appeared greater than that of the PCR method. The LAMP assay reported can provide a rapid yet simple test of PCV2 suitable for laboratory diagnosis and pen-side detection due to ease of operation and the requirement of only a regular water bath or heat block for the reaction. (c) 2008 Elsevier B.V. All rights reserved.

Gas-phase isothermal chromatography with short-lived technetium isotopes

In order to study the gas-phase chemical behavior of transactinides, an on-line isothermal chromatography apparatus has been developed and applied to separate short-lived technetium isotopes in the form of TcO3 from fission products. The fission products from a Cf-252 source were continuously and rapidly transported through the capillary to the isothermal chromatography apparatus using the N-2/KBr gas-jet techniques. Volatile oxide molecules were formed at the reaction zone kept at 900 degrees C since a trace amount of oxygen existed in the N-2 carrier gas. With the new developed isothermal chromatography apparatus, a selective separation of Tc from fission products was achieved. After isothermal chromatographic separation, Tc-101,Tc-103,Tc-104,Tc-105,Tc-106,Tc-107,Tc-108 were dominantly observed together with their Ru daughters in the gamma-spectrum, The chemical yields of Tc-101, and Tc-104 and Tc-105 isotopes with longer half-lives are about 55-57%, and those of Tc-103, Tc-106 and Tc-108 isotopes with shorter half-lives dropped down to 25-28%. The adsorption enthalpy of the investigated compounds on quartz surfaces was determined to be -150 +/- 5 kJ/mol by fitting the measured retention curves with a Monte Carlo model. The observed species of technetium oxide is attributed to TcO3, which is in good agreement with previous experimental results. That means our system worked properly and it can be used to investigate the gas-phase chemical behavior of transactinides.

Analysis of specific gene by integration of isothermal amplification and electrophoresis on poly(methyl methacrylate) microchips

We have successfully achieved the integration of isothermal amplification and the subsequent analysis of specific gene fragments on poly(methyl methacrylate) microchips. In our experiments, loop-mediated isothermal amplification, which can offer higher specificity and efficiency than PCR, has been performed at a constant temperature (65 degreesC). After amplification, products could be either examined by the integrated microchip-based electrophoresis or directly observed by naked eye with SYBR Green I added into the reaction solution. By such an integrated microsystem, the amplification and the subsequent analysis of prostate-specific antigen gene with template concentration at 23 fg/muL could be finished within 15 min, which demonstrates its advantages of high specificity, good reproducibility, and fast speed in gene detection.

Determination of Point of Zero Charge of Tunisian Kaolinites by Potentiometric and Mass Titration Methods

This paper deals with determining points of zero charge of natural and Na+-saturated mineral kaolinites using two methods: (1) acid-base potentiometric titration was employed to obtain the adsorption of H+ and OH- on amphoteric surfaces in solutions of varying ionic strengths in order to determinate graphically the point of zero net proton charge (PZNPC) defined equally as point of zero salt effect (PZSE); (2) mass titration curve at different electrolyte concentrations in order to estimate PZNPCs by interpolation and to compare with those determined by potentiometric titrations. The two methods involved points of zero charge approximately similar for the two kaolinites between 6.5-7.8, comparable to those reported previously and were in the range expected for these clay minerals. The comparison of potentiometric surface titration curves obtained at 25 °C and those published in the literature reveals significant discrepancies both in the shape and in the pH of PZNPCs values.

Comparison of salt titration and potentiometric titration methods for the determination of zero point of charge

the salt ritration metod was evaluated as a method to determine zpc in comparison with the potentiometric titration method for 26 soil with variable charge clays,i.e.,Oxisols and Ultisols from Thailand and Andisols from Japan. In addition to the determination of ST-pH0 as the zero point of charge, a calculation procedure was adopted here in order to acquire more information from the titration curve . fuithermore, for the purpose of cross-checking of zpc determined by the pt method, the st procedure was successively applied to the samples analyzed by the pt method.

Isothermal Crystallization Behavior of Poly(L-lactic acid)/Organo-Montmorillonite Nanocomposites

The isothermal crystallization behavior of poly(L-lactic acid)/organo-montmorillonite nanocomposites (PLLA/OMMT) with different content of OMMT, using a kind of twice-functionalized organoclay (TFC), prepared by melt intercalation process has been investigated by optical depolarizer. In isothermal crystallization from melt, the induction periods (t(i)) and half times for overall PLLA crystallization (100 degrees C <= T-c <= 120 degrees C) were affected by the temperature and the content of TFC in nanocomposites. The kinetic of isothermal crystallization of PLLA/TFC nanocomposites was studied by Avrami theory. Also, polarized optical photomicrographs supplied a direct way to know the role of TFC in PLLA isothermal crystallization process. Wide angle X-ray diffraction (WAXD) patterns showed the nanostructure of PLLA/TFC material, and the PLLA crystalline integrality was changed as the presence of TFC. Adding TFC led to the decrease of equilibrium melting point of nanocomposites, indicating that the layered structure of clay restricted the full formation of crystalline structure of polymer.

Precipitates formed in a Mg-7Y-4Gd-0.5Zn-0.4Zr alloy during isothermal ageing at 250 degrees C

The ageing behavior of an extruded Mg-7Y-4Gd-0.5Zn-0.4Zr alloy during ageing at 250 degrees C has been investigated. Two types of phases have been observed during the ageing process. One is a lamellar phase with a 14H long periodic stacking structure, the other is the beta' phase with an ellipsoidal morphology. The increased mechanical properties of the peak-aged alloy are mainly ascribed to the presence of both of these phases at peak hardness.