A Simple, Universal Colorimetric Assay for Endonuclease/Methyltransferase Activity and Inhibition Based on an Enzyme-Responsive Nanoparticle System

An enzyme responsive nanoparticle system that uses a DNA-gold nanoparticle (AuNP) assembly as the substrate has been developed for the simple, sensitive, and universal monitoring of restriction endonucleases in real time. This new assay takes advantage of the palindromic recognition sequence of the restriction nucleases and the unique optical properties of AuNPs and is simpler than the procedure previously described by by Xu et al. (Angew. Chem. Int. Ed. Engl. 2007, 46, 3468-3470). Because it involves only one type of ssDNA modified AuNPs, this assay can be directed toward most of the endonucleases by simply changing the recognition sequence found within the linker DNA. In addition, the endonuclease activity could be quantitatively analyzed by the value of the reciprocal of hydrolysis half time (t(1/2)(-1). Furthermore, our new design could also be applied to the assay of methyltransferase activity since the methylation of DNA inhibits its cleavage by the corresponding restriction endonuclease, and thus, this new methodology can be easily adapted to high-throughput screening of methyltransferase inhibitors.

Characterization of procaine metabolism as probe for the butyrylcholinesterase enzyme investigation by simultaneous determination of procaine and its metabolite using capillary electrophoresis with electrochemiluminescence detection

Capillary electrophoresis with electrochemiluminescene detection was used to characterize procaine hydrolysis as a probe for butyrylcholinesterase by in vitro procaine metabolism in plasma with butyrylcholinesterase acting as bioscavenger. Procaine and its metabolite N,N-diethylethanolamine were separated at 16 kV and then detected at 1.25 V in the presence of 5.0 mM Ru(bpy)(3)(2+), with the detection limits of 2.4 x 10(-7) and 2.0 x 10(-8) mol/L (S/N=3), respectively. The Michaelis constant K-m value was 1.73 x 10(-4) mol/L and the maximum velocity V-max was 1.62 x 10(-6) mol/L/min. Acetylcholine bromide and choline chloride presented inhibition effects on the enzymatic cleavage of procaine, with the 50% inhibition concentration (IC50) of 6.24 x 10(-3) and 2.94 x 10(-4) mol/L.

Kinetic study of DNA/DNA hybridization with electrochemical impedance spectroscopy

The hybridization of immobilized oligonucleotides probe strands with solution phase targets is the underlying principle of microarraybased techniques for the analysis of DNA variation. To study the kinetics of DNA/DNA hybridization, target DNA is often prior labeled with markers. A label-free method of electrochemical impedance spectra (EIS) for study the hybridization in process was reported. The Langmuir model was used to determine the association rate constant (K-on), the dissociation rate constant (K-off) and the affinity rate constant (K-A), for perfect matched DNA hybridization. The results show that, EIS is a successful technique possessing high effectivity and sensitivity to study DNA/DNA hybridization kinetics. This work can provide another view on EIS for the studying of DNA/DNA hybridization.

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion.Including the configurational dependence will challenge the transition state theory of protein folding.

Primary and secondary crystallization kinetic analysis of nylon 1212

The isothermal and non-isothermal melt-crystallization kinetics of nylon 1212 were investigated by differential scanning calorimetry. Primary and secondary crystallization behaviors were analysed based on different approaches. The results obtained suggested that primary crystallization under isothermal conditions involves three-dimensional spherulite growth initiated by athermal nucleation, while under non-isothermal conditions, the mechanism of primary crystallization is more complex. Secondary crystallization displays a lower-dimensional crystal growth, both in the isothermal and non-isothermal processes. The crystallite morphology of nylon 1212, isothermally crystallized at various temperatures, was observed by polarized optical microscopy. The activation energies of crystallization under isothermal and non-isothermal conditions were also calculated based on different approaches.

Morphology and structure of poly(di-n-butylsilane) single crystals prepared by controlling kinetic process of solvent evaporation

The silicon backbone conformation in poly(di-n-butylsilane) (PDBS) has been shown to be a 7/3 helix at ambient conditions, which is in marked contrast to the near-planar conformation of its homologous polymers with side chain lengths of one to three or six to eight carbon atoms. In this work, both the 7/3 helical and near-planar chain conformations are achieved by controlling the solvent evaporation rate around room temperature. The chain conformation and crystal structure obtained in this method have been correlated to the crystal morphology by wide-angle X-ray diffraction, transmission electron microscopy, electron diffraction, optical microscopy, atomic force microscopy, and UV absorption spectrum. The lath-shaped single crystals obtained at 12 degreesC correspond to an orthorhombic form with near-planar chain conformation whereas the lozenge-shaped single crystals obtained at 30 degreesC (in coexistence with the lath-shaped crystals) are orthohexagonal with a 7/3 helix.

Polymeric pH indicators immobilized PVA membranes for optical sensors of high basicity based on a kinetic process

Two kinds of polymeric pH indicators PPF (phenolphthalein-formaldehyde product) and CPF (o-cresolphthalein-formaldehyde product) immobilized cross-linked poly(vinyl alcohol) membranes (PPF-PVA and CPF-PVA) for optical intermittent determination of high basicity ([OH-] = 1-8 M) based on a kinetic process were developed. In our previous work, we had demonstrated that PPF-PVA and CPF-PVA could perform the determination of high pH values from pH 10.0 to 14.0. Here the discoloring kinetic behaviors of PPF-PVA and CPF-PVA were compared with those of free phenolphthalein, o-cresolphthalein and thymolphthalein. Experimental results and theoretical analysis indicated that the response behaviors of the optodes' membranes in concentrated NaOH solutions were diffusion-independent and still complied with the pseudo-first-order kinetics. In addition, two data analysis methods for determination were presented. One was directly based on the reduced absorbance: the other was based on the discoloring kinetic constant. It was found that the latter could perform a rapid (60 s) and reliable (relative standard deviation: 2.6%) determination for high basicity.

Electrodepositing redox polymer on sandwich complex for the improvement of sensitivity in sandwich enzyme-linked immunoassay

Improvement of the sensitivity of electrochemical sandwich enzyme immunoassay has been achieved by electrodepositing redox polymer on screen-printed carbon electrode surface, on which the sandwich complex was formed.

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.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of 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. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. 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. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.