Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

Aptamer-based label-free method for hemin recognition and DNA assay by capillary electrophoresis with chemiluminescence detection

An aptamer-based label-free approach to hemin recognition and DNA assay using capillary electrophoresis with chemiluminescence detection is introduced here. Two guanine-rich DNA aptamers were used as the recognition element and target DNA, respectively. In the presence of potassium ions, the two aptamers folded into the G-quartet structures, binding hemin with high specificity and affinity. Based on the G-quartet-hemin interactions, the ligand molecule was specifically recognized with a K (d)approximate to 73 nM, and the target DNA could be detected at 0.1 mu M. In phosphate buffer of pH 11.0, hemin catalyzed the H2O2-mediated oxidation of luminol to generate strong chemiluminescence signal; thus the target molecule itself served as an indicator for the molecule-aptamer interaction, which made the labeling and/or modification of aptamers or target molecules unnecessary. This label-free method for molecular recognition and DNA detection is therefore simple, easy, and effective.

Study of controllable aggregation morphology of ABA amphiphilic triblock copolymer in dilute solution by changing the solvent property

We have studied, both experimentally and theoretically, the aggregation morphology of the ABA amphiphilic triblock copolymer in dilute solution by changing the solvent property. Experimental results showed that the micellar morphology changed from spheres to rods and then to vesicles by changing the common solvent from N-N-dimethylformamide (DMF) to dioxane and then to tetrahydrofuran (THF). These controllable aggregates were also obtained by Monte Carlo simulation. The simulative results showed that the solvent property is a key factor that determines the copolymer aggregation morphology. The morphology changed from spheres to rods and then to vesicles by increasing the solvent solubility, corresponding to the change of stretched of the copolymer chains in the micellar cores. This result is in good agreement with the experimental one. Moreover, the simulative results revealed that the end-to-end distant of the ABA triblock copolymer in the vesicle was larger than that in the spheres and rods, indicating that the copolymer chains were more stretched in vesicles than in the spheres and rods. Furthermore, we gave the distribution of the fraction of the chain number with the end-to-end distance. The results indicated that the amount of folded chains is almost the same as that of stretched chains in the vesicle. Although most chains were folded, stretched chains could be found in the rod and sphere micelles.

Crystallization kinetics and morphology of nylon 1212

The isothermal and non-isothermal crystallization processes of nylon 1212 were investigated by polarized optical microscopy. The crystal growth rates of nylon 1212 measured in isothermal conditions at temperatures ranged from 182 to 132 degreesC are well comparable with those measured by non-isothermal procedures (cooling rates ranged from 0.5 to 11 degreesC/min). The kinetic data were examined with the Hoffman-Lauritzen nucleation theory on the basis of the obtained values of the thermodynamic parameters of nylon 1212. The classical regime I --> II and regime II --> III transitions occur at the temperatures of 179 and 159 degreesC, respectively. The crystal growth parameters were calculated with (100) plane assumed to be the growth plane. The regime I --> II --> III transition is accompanied by a morphological transition from elliptical-shaped structure to banded spherulite and then non-banded spherulite. The development of morphology during isothermal and non-isothermal processes shows a good agreement.

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.

Melting behaviors, isothermal and non-isothermal crystallization kinetics of nylon 1212

Isothermal crystallization, subsequent melting behavior and non-isothermal crystallization of nylon 1212 samples have been investigated in the temperature range of 160-171 degreesC using a differential scanning calorimeter (DSC). Subsequent DSC scans of isothermally crystallized samples exhibited three melting endotherms. The commonly used Avrami equation and that modified by Jeziorny were used, respectively, to fit the primary stage of isothermal and non-isothermal crystallizations of nylon 1212. The Avrami exponent n was evaluated, and was found to be in the range of 1.56-2.03 for isothermal crystallization, and of 2.38-3.05 for non-isothermal crystallization. The activation energies (DeltaE) were determined to be 284.5 KJ/mol and 102.63 KJ/mol, respectively, for the isothermal and non-isothermal crystallization processes by the Arrhenius' and the Kissinger's methods.

First-passage time distribution and non-Markovian diffusion dynamics of protein folding

We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described in terms of an order parameter given by the fraction of native conformations. The non-Markovian diffusion dynamics is analyzed in detail and an expression for the mean first-passage time (MFPT) from non-native unfolded states to native folded state is obtained. It was found that the MFPT has a V-shaped dependence on the temperature. We also find that the MFPT is shortened as one increases the gap between the energy of the native and average non-native folded states relative to the fluctuations of the energy landscape. The second- and higher-order moments are studied to infer the first-passage time distribution. At high temperature, the distribution becomes close to a Poisson distribution, while at low temperatures the distribution becomes a Levy-type distribution with power-law tails, indicating a nonself-averaging intermittent behavior of folding dynamics. We note the likely relevance of this result to single-molecule dynamics experiments, where a power law (Levy) distribution of the relaxation time of the underlined protein energy landscape is observed.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

Local structure and valences of samariurn in SrB4O7 : Sm and SrB6O10 : Sm prepared in-air

The coordination numbers for the samarium atoms and the Sm-O bond distances in SrB4O7:Sm and SrB6O10:Sm prepared in air were determined by means of Sm-L-3 edge EXAFS. The coordination. was found to be nine-folded for both these hosts and the bond distance was 2.40-2.42 Angstrom in SrB4O7:Sm and 2.42-2.44 Angstrom in SrB6O10:Sm. For SrB4O7:Sm the coordination number is coincident with that of the strontium. atoms suggesting the substitution of the samarium atoms at the strontium sites. The coordination number of the strontium atoms in SrB6O10 was also suggested to be nine assuming the same type of substitution. The valences of samarium were determined from the luminescent spectra. Both divalent and trivalent ions were present in both SrB4O7:Sm and SrB6O10:Sm, while the fraction of Sm2+ was higher in the former than in the latter. This difference has been assigned to the difference in rigidity between the B-O networks in these structures.

Morphology and structure of nylon-2,14 single crystals from dilute solution

A perfect single crystal of nylon-2,14 was prepared from 0.02% (w/v) 1,4-butanediol solution by a "self-seeding" technique and isothermal crystallization at 120 and 145 degreesC. The morphology and structure features were examined by transmission electron microscopy with both image and diffraction modes, atomic force microscopy, and wide-angle X-ray diffraction (WAXD). The nylon-2,14 single crystal grown from 1,4-butanediol at 145 degreesC inhabited a lathlike shape with a lamellar thickness of about 9 nm. Electron diffraction and WAXD data indicated that nylon-2,14 crystallized in a triclinic system with lattice dimensions a = 0.49 nm, b = 0.51 nm, c = 2.23 nm, alpha = 60.4degrees, beta = 77degrees, and gamma = 59degrees. The crystal structure is different from that of nylon-6,6 but similar to that of other members of nylon-2Y.

High-temperature X-ray diffraction studies on polyamide6/clay nanocomposites upon annealing

The influence of nanodispersed clay on the alpha crystalline structure of polyamide 6 (PA6) was examined in-situ with X-ray diffraction (XRD) between room temperature and melting. In pure PA6 upon annealing the alpha crystalline phase was substituted by an unstable pseudohexagonal phase at 150degreesC, then it transformed into a new stable crystalline structure - high temperature alpha' phase above the transition temperature. However, in PA6/clay nanocomposite (PA6CN), the alpha phase did not present crystalline phase transition on heating. The increase in the annealing temperature only led to continuous intensity variation. The different behaviors were caused by the confined spaces formed by silicate layers, which constrained the mobility of the polymer chains in-between.

Polydispersity of ethylene sequence length in metallocene ethylene/alpha-olefin copolymers. II. Influence on crystallization and melting behavior

In this work, crystallization and melting behavior of metallocene ethylene/alpha-olefin copolymers were investigated by differential scanning calorimetry (DSC) and atomic force microscopy (AFM). The results indicated that the crystallization and melting temperatures for all the samples were directly related to the long ethylene sequences instead of the average sequence length (ASL), whereas the crystallization enthalpy and crystallinity were directly related to ASL, that is, both parameters decreased with a decreasing ASL. Multiple melting peaks were analyzed by thermal analysis. Three phenomena contributed to the multiple melting behaviors after isothermal crystallization, that is, the melting of crystals formed during quenching, the melting-recrystallization process, and the coexistence of different crystal morphologies. Two types of crystal morphologies could coexist in samples having a high comonomer content after isothermal crystallization. They were the chain-folded lamellae formed by long ethylene sequences and the bundlelike crystals formed by short ethylene sequences. The coexistence phenomenon was further proved by the AFM morphological observation.

Oriented crystallization process of polypropylene fractions

Melting recrystallization processes of melt-sheared films of polypropylene (S28C) fractions have been investigated in situ by polarized optical microscope equipped with CCD camera and hot-stage. Actually, the morphological developments in the melting recrystallization are partially reappearance of oriented crystallization processes during melt-shearing the fractions, which is due to a memory effect of oriented structure of polymer. For low molecular weight fraction, only incomplete spherulites with some orientation along shear direction are observed in the melting recrystallization processes of the sheared films. For middle molecular weight fractions, extended chain fiber crystals(or bands) are formed first at higher temperatures, and the bands can act as self-nuclei (i. e., row nuclei), resulting in epitaxial growth of chain-folded lamellae(or fibril), i. e., the formation of cylindrites, with further decrease of the crystallization temperature. For high molecular weight fraction, however, it is not possible to shear the melt film because of its high melt viscosity. When the low molecular weight fraction in which no fiber crystals or cylindrites are observed, are mixed with small amount(about 1%-2%) of the high molecular weight fraction, quite large number of cylindrites are formed during the melting recrystallization process of its sheared film, which implies that the component of high molecular weight plays an important role in the formation of cylindrites during the shear process of polypropylene.

Effect of branch content on the transition of crystalline structure and morphology of metallocene-catalyzed branched polyethylene

Transition of crystalline structure and morphology of metallocene-catalyzed butyl branched polyethylene with branch content has been studied. It was found that the long periods of the branched polyethylene were controlled by crystallization conditions for the lower branch content samples and by branch contents for the higher branch content samples. When the branch content increased to a critical value the branched polyethylene had no long period because the crystalline morphology was changed from folded chain crystal to a bundled crystal. The TEM observations supported the results. The transition of the crystalline morphology resulted from the reduction of lamellar thickness with increasing of branch content since the branches were rejected from the lattice. The reduction of lamellar thickness with increasing of branch content also resulted in lattice expansion and decrease of melt temperature of the branched polyethylene. (C) 2001 Kluwer Academic Publishers.