Single-walled carbon nanotubes binding to human telomeric i-motif DNA: significant acceleration of S1 nuclease cleavage rate

Single-walled carbon nanotubes (SWNTs) binding to human telomeric i-motif DNA can significantly accelerate S1 nuclease cleavage rate by increasing the enzyme turnover number.

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.

Metabolic profiling of serum from gadolinium chloride-treated rats by H-1 NMR spectroscopy

Metabolic profiling of serum from gadolinium chloride (GdCl3, 10 and 50 mg/kg body weight, intraperitoneal [i.p.])-treated rats was investigated by the NMR spectroscopic-based metabonomic strategy. Serum samples were collected at 48, 96, and 168 h postdose (p.d.) after exposure to GdCl3. H-1 NMR spectra of serum were analyzed by pattern recognition using principal components analysis. The studies showed that there was a dose-related biochemical effect of GdCl3 treatment on the levels of a range of low-molecular weight compounds in serum. The liver damage induced by GdCl3 was characterized by the elevation of lactate, pyruvate, and creatine as well as the decrease of branched-chain amino acids (valine and isoleucine), alanine, glucose, and trimethylamine-N-oxide concentration in serum samples. The biochemical effects of GdCl3 in rats could be consulted when evaluating the biochemical profile of gadolinium-containing compounds that are being developed for nuclear magnetic resonance imaging.

Extraction and separation of yttrium from the rare earths with sec-octylphenoxy acetic acid in chloride media

Extraction and separation of yttrium from the rare earths in chloride medium using sec-octylphenoxy acetic acid (CA-12), tri-n-butyl phosphate (TBP) as modifier, in kerosene has been investigated. The separation coefficients, beta, were obtained and the extraction selectivity has been enhanced when compared with that of naphthenic acid. The experimental results indicated that CA-12-TBP system could be employed to separate yttrium, from rare earths. Fractional extraction (15 stages for extraction and 10 stages for scrubbing) was studied, the raffinate of the first stage was abundant in purity yttrium of 99.5%, with a yield of > 95%, percentage of yttrium in the mixture rare earths was less than 5% in the loaded organic phase of the 25th stage and loaded capability was about 0.2 mol/L.

Extraction kinetics of Sc(III), Y(III), La(III) and Gd(III) from chloride medium by Cyanex 302 in heptane using the constant interfacial cell with laminar flow

The extraction kinetics of Sc, Y, La and Gd(III) from the hydrochloric acid medium using Cyanex 302 (hereafter HL) in heptane solution have been measured by the constant interfacial cell with laminar flow. Reaction regions are explored at liquid-liquid interface. Extraction regimes are deduced to be diffusion-controlled for Sc(Ill) and mixed controlled for Y, La and Gd(Ill). Extraction mechanisms are discussed according to the dimeric model of Cyanex 302 in non-polar solution. From the temperature dependence of rate measurement, the values of E-a, Delta H-+/-, Delta S-+/- and Delta G(300)(+/-) are calculated and it is found that the absolute values of these parameters keep crescent trend for Sc, Y, La and Gd(III). At the same time, it is found that it can easily achieve the mutual separation among the Sc, Y and La(III) with kinetics extraction methods.

Morphology evolutions of organically modified montmorillonite/polyamide 12 nanocomposites

Organically modified montmorillonites (OMMTs) by octadecylammonium chloride with two adsorption levels were dispersed in polyamide 12 (PA12) matrices with two molecular weights for different melt mixing times in order to investigate morphology evolutions and factors influencing fabrication of PA12 nanocomposites. Different adsorption levels of the modifier in the OMMTs provide different environments for diffusion of polymer chains and different attractions between MMT layers. Wide-angle X-ray diffraction (WAXD), transmission electron microscope (TEM) and gas permeability were used to characterize morphologies of the nanocomposites. Both OMMTs can be exfoliated in the PA12 matrix with higher molecular weight, but only OMMT with lower adsorption level can be exfoliated in the PA12 matrix with lower molecular weight. It was attributed to the differences in the levels of shear stress and molecular diffusion in the nanocomposites. The exfoliation of OMMT platelets results from a combination of molecular diffusion and shear. After intercalation of PA12 into interlayer of OMMT in the initial period of mixing, further dispersion of OMMTs in PA12 matrices is controlled by a slippage process of MMT layers during fabricating PA12 nanocomposites with exfoliated structure.

Downhill kinetics of biomolecular interface binding: Globally connected scenario

We study the kinetics of the biomolecular binding process at the interface using energy landscape theory. The global kinetic connectivity case is considered for a downhill funneled energy landscape. By solving the kinetic master equation, the kinetic time for binding is obtained and shown to have a U-shape curve-dependence on the temperature. The kinetic minimum of the binding time monotonically decreases when the ratio of the underlying energy gap between native state and average non-native states versus the roughness or the fluctuations of the landscape increases. At intermediate temperatures,fluctuations measured by the higher moments of the binding time lead to non-Poissonian, non-exponential kinetics. At both high and very low temperatures, the kinetics is nearly Poissonian and exponential.

Drug-human serum albumin binding studied by capillary electrophoresis with electrochemiluminescence detection

A new technique for investigating drug-protein binding was developed employing capillary electrophoresis (CE) coupled with tris(2,2'-bipyridyl) ruthenium(II) [Ru(bPY)(3)(2+)] electrochemiluminescence (ECL) (CE-ECL) detection after equilibrium dialysis. Three basic drugs, namely pridinol, procyclidine and its analogue trihexyphenidyl, were successfully separated by capillary zone electrophoresis with end-column Ru(bPY)(3)(2+) ECL detection. The relative drug binding to human serum albumin (HSA) for each single drug as well'as for the three drugs binding simultaneously was calculated. It was found that the three antiparkinsonian drugs compete for the same binding site on HSA. This work demonstrated that Ru(bPY)(3)(2+) CE-ECL can be a suitable technique for studying drug-protein binding.

Synthesis of gold nanoplates by aspartate reduction of gold chloride

Single crystal nanoplates with thickness less than 30 nm, characterized by hexagonal and truncated triangular shapes bounded mainly by {111} facets, were obtained in large quantities by aspartate reduction of gold chloride.

mer-(4-aminobenzenesulfonato-kappa N)triapua(1,10-phenanthroline-kappa N-2,N ')cobalt(II) chloride

Both coordination and hydrogen bonds contribute to networking in the supramolecular title compound, [Co(C6H6NO3S)(C12H8N2)(H2O)(3)]Cl, which contains a discrete [Co(C6H6NO3S)(C12H8N2)(H2O)(3)](+) complex cation, formed by one 4-aminobenzenesulfonate ligand, one 1,10-phenanthroline ligand and three coordinated water molecules, together with one uncoordinated chloride anion. These discrete cations and chloride anions are connected by hydrogen-bonding interactions into a two-dimensional supramolecular motif. Further hydrogen-bonding interactions consolidate the structural architecture and extend the two-dimensional supramolecular structure into a three-dimensional network.

The influence of core-shell structured modifiers on the toughness of poly (vinyl chloride)

The core-shell structured grafted copolymer particles of polybutadiene grafted polymethyl methacrylate (PB-g-PMMA, MB) were prepared by emulsion polymerization. The MB particles were used to modify poly (vinyl chloride) (PVC) by melt blending. The mechanical properties of the PVC blends were investigated. The micro-morphology of the PVC blends was observed by scanning electron microscopy (SEM). The results indicated that the samples with the best impact strength could be obtained when the core-shell weight ratio of PB to PMMA is lower than 93:7, the mechanical properties correlated well with SEM morphologies, the addition of modifier with the ratio core to shell of 93:7 could reduce the domain size of the dispersed phase. Furthermore, the compatibility and properties of the blends were greatly enhanced and improved. The modifier particles could be well dispersed in the PVC matrix.

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.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS

The 24-mer DNA aptamer of Harada and Frankel ( Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.