A novel strategy to construct a flat-lying DNA monolayer on a mica surface

Flat-lying, densely packed DNA monolayers in which DNA chains are well organized have been successfully constructed on a mica surface by dropping a droplet of a DNA solution on a freshly cleaved mica surface and subsequently transferring the mica to ultrapure water for developing. The formation kinetics of such monolayers was studied by tapping mode atomic force microscopy (TMAFM) technique. A series of TMAFM images of DNA films obtained at various developing times show that before the sample was immersed into water for developing the DNA chains always seriously aggregated by contacting, crossing, or overlapping and formed large-scale networks on the mica surface. During developing, the fibers of DNA networks gradually dispersed into many smaller fibers up to single DNA chains. At the same time, the fibers or DNA chains also experienced rearrangement to decrease electrostatic repulsion and interfacial Gibbs free energy. Finally, a flat-lying, densely packed DNA monolayer was formed. A formation mechanism of the DNA monolayers was proposed that consists of aggregation, dispersion, and rearrangement. The effects of both DNA and Mg2+ concentration in the formation solution on DNA monolayer formation were also investigated in detail.

Effect of DNA flanking sequence on charge transport in short DNA duplexes

Several factors can influence charge transport (CT)-mediated DNA, such as sequence, distance, base stacking, base pair mismatch, conformation, tether length, etc. However, the DNA context effect or how flanking sequences influence redox active drugs in the DNA CT reaction and later in DNA enzymatic repair and synthesis is still not well understood. The set of seven DNA molecules in this study have been characterized well for the study of flanking sequence effects. These DNA duplexes are formed from self-complementary strands and contain the common central four-base sequence 5'-A-G-C-T-3', flanked on both sides by either (AT)(n) or (AA)(n) (n = 2, 3, or 4) or AA(AT)(2). UV-vis, fluorescence, UV melting, circular dichroism, and cyclic voltammetry experiments were used to study the flanking sequence effect on CT-mediated DNA by using daunomycin or adriamycin cross-linked with these seven DNA molecules. Our results showed that charge transport was related to the flanking sequence, DNA melting free energy, and ionic strength. For (AA)(n) or (AT)(n) species of the same length, (AA)(n) series were more stable and more efficient CT was observed through the (AA)(n) series. The same trend was observed for (AA)(n) and (AT)(n) series at different ionic strengths, further supporting the idea that flanking sequence can result in different base stacking and modulate charge transport through these seven DNA molecules.

A novel self-consistent-field lattice model for block copolymers

We develop a self-consistent-field lattice model for block copolymers and propose a novel and general method to solve the self-consistent-field equations. The approach involves describing the polymer chains in a lattice and employing a two-stage relaxation procedure to evolve a system as rapidly as possible to a free-energy minimum. In order to test the validity of this approach, we use the method to study the microphases of rod-coil diblock copolymers. In addition to the lamellar and cylindrical morphologies, micellar, perforated lamellar, gyroid, and zigzag structures have been identified without any prior assumption of the microphase symmetry. Furthermore, this approach can also give the possible orientation of the rods in different structures.

Miscibility and crystallization behavior of PBT/epoxy blends

The miscibility and the isothermal crystallization kinetics for PBT/Epoxy blends have been studied by using differential scanning calorimetry, and several kinetic analyses have been used to describe the crystallization process. The Avrami exponents n were obtained for PBT/Epoxy blends. An addition of small amount of epoxy resin (3%) leads to an increase in the number of effective nuclei, thus resulting in an increase in crystallization rate and a stronger trend of instantaneous three-dimensional growth. For isothermal crystallization, crystallization parameter analysis showed that epoxy particles could act as effective nucleating agents, accelerating the crystallization of PBT component in the PBT/Epoxy blends. The Lauritzen-Hoffman equation for DSC isothermal crystallization data revealed that PBT/Epoxy 97/3 had lower nucleation constant K, than 100/0, 93/7, and 90/10 PBT/Epoxy blends. Analysis of the crystallization data of PBT/Epoxy blends showed that crystallization occurs in regime II. The fold surface free energy, sigma(e) = 101.7-58.0 x 10(-3) J/m(2), and work of chain folding, q = 5.79-3.30 kcal/mol, were determined. The equilibrium melting point depressions of PBT/Epoxy blends were observed and the Flory-Huggins interaction parameters were obtained.

Crystallization behavior of carbon nanotubes-filled polyamide 1010

The nanocomposites of polyamide1010 (PA1010) filled with carbon nanotubes (CNTs) were prepared by melt mixing techniques. The isothermal melt-crystallization kinetics and nonisothermal crystallization behavior of CNTs/PA1010 nanocomposites were investigated by differential scanning calorimetry. The peak temperature, melting point, half-time of crystallization, enthalpy of crystallization, etc. were measured. Two stages of crystallization are observed, including primary crystallization and secondary crystallization. The isothermal crystallization was also described according to Avrami's approach. It has been shown that the addition of CNTs causes a remarkable increase in the overall crystallization rate of PA1010 and affects the mechanism of nucleation and growth of PA1010 crystals. The analysis of kinetic data according to nucleation theories shows that the increment in crystallization rate of CNTs/PA1010 composites results from the decrease in lateral surface free energy.

Synergistic extraction of rare earths(III) from chloride medium with mixtures of 1-phenyl-3-methyl-4-benzoyl-pyrazalone-5 and di-(2-ethylhexyl)-2-ethylhexylphosphonate

The synergistic effect of 1-phenyl-3-methyl-4-benzoyl-pyrazalone-5 (HPMBP, HA) and di-(2ethylhexyl)-2-ethylhexylphosphonate (DEHEHP, B) in the extraction of rare earths (RE) from chloride solutions has been investigated. Under the experimental conditions used, there was no detectable extraction when DEHEHP was used as a single extractant while the amount of RE(III) extracted by HPMBP alone was also low. But mixtures of the two extractants at a certain ratio had very high extractability for all the RE (III). For example, the synergistic enhancement coefficient was calculated to be 9.35 for Y3+, and taking Yb3+ and Y3+ as examples, RE3+ is extracted as RE(OH)A(2).B. The stoichiometry, extraction constants and thermodynamic functions such as Gibbs free energy change Delta G (-17.06kJmol(-1)), enthalpy change Delta H (-35.08kjmol(-1)) and entropy change Delta S (-60.47JK(-1)mol(-1)) for Y3+ at 298 K were determined. The separation factors (SF) for adjacent pairs of rare earths were calculated. Studies show that the binary extraction system not only enhances the extraction efficiency of RE(III) but also improves the selectivity, especially between La(III) and the other rare earth elements.

Investigation on isothermal and non-isothermal crystallization kinetics of poly (epsilon-caprolactone)

The crystallization kinetics and the development of lamellar structure during the isothermal crystallization of poly (epsilon-caprolactone) (PCL) were investigated by means of differential scanning calorimetry (DSC) and real-time synchrotron small angle X-ray scattering (SR-SAXS) techniques, respectively. The Avrami analysis was performed to obtain the kinetics parameters. The value of Avrami index, n, is about 3, demonstrating a three-dimensional spherulitic growth on heterogeneous nuclei in the process of isothermal crystallization. The activation energy and the surface free energy of chain folding for isothermal crystallization were determined according to the Arrhenius equation and Hoffman-Lauritzen theory, respectively. In the process of nonisothermal crystallization of PCL, the value of Avrami index, n, is about 4, which demonstrates a three-dimensional spherulitic growth on homogeneous nuclei. In addition, lamellar parameters were obtained from the analysis of SR-SAXS data.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Study on the origin of inverted phase in drying solution-cast block copolymer films

In a previous study, we reported observation of the novel inverted phase (the minority blocks comprising the continuum phase) in kinetically controlled phase separating solution-cast poly(styrene-b-butadiene-b-styrene) (SBS) triblock copolymer films [Zhang et al. Macromolecules 2000, 33, 9561-7]. In this study, we adopt the same approach to investigate the formation of inverted phase in a series of solution-cast poly(styrene-b-butadiene) (SB) asymmetric diblock copolymers having nearly equal polystyrene (PS) weight fraction (about 30 wt %) but different molecular weights. The microstructure of the solution-cast block copolymer films resulting from different solvent evaporation rates, R, was inspected, from which the kinetically frozen-in phase structures at qualitatively different block copolymer concentrations and correspondingly different effective interaction parameter, chieff, can be deduced. Our result shows that there is a threshold molecular weight or range of molecular weight below which the unusual inverted phase is accessible by controlling the solvent evaporation rate. In comparing the present result with that of our previous study on the SBS triblock copolymer, we find that the formation of the inverted phase has little bearing on the chain architecture. We performed numerical calculations for the free energy of block copolymer cylinders and found that the normal phase is always preferred irrespective of the interaction parameter and molecular weight, which suggests the formation of the inverted phase to have a kinetic origin.

Isothermal crystallization of poly(3-hydroxybutyrate-co-3-hydroxyvalerate)

Isothermal crystallization behavior of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) was investigated by means of differential scanning calorimetry and polarized optical microscopy (POM). The Avrami analysis can be used successfully to describe the isothermal crystallization kinetics of PHBV, which indicates that the Avrami exponent n = 3 is good for all the temperatures investigated. The spherulitic growth rate, G, was determined by POM. The result shows that the G has a maximum value at about 353 K. Using the equilibrium melting temperature (448 K) determined by the Flory equation for melting point depression together with U-* = 1500 cal mol(-1), T-infinity = 30 K and T-g = 278 K, the nucleation parameter K-g was determined, which was found to be 3.14+/-0.07 x 10(5) (K-2), lower than that for pure PHB. The surface-free energy sigma = 2.55 x 10(-2) J m(-2) and sigma(e) = 2.70+/-0.06 x 10-2 J m(-2) were estimated and the work of chain-folding (q = 12.5+/-0.2 kJ mol(-1)) was derived from sigma(e), and found to be lower than that for PHB. This implies that the chains of PHBV are more flexible than that of PHB.

Formation of regular hole pattern in polymer films

Ordered macroporous materials recently have attracted much attention. A method that utilizes the condensation of monodisperse water droplets on a polymer solution is proposed for the preparation of honeycomb microporous films. Our results show that it is a general method that can be used for patterning a wide range of polymers. The presence of water vapor and polymer is necessary for the formation of regular holes in films. The formation of hexagonal packing instead of other kinds of packing takes place because the hexagonal packing has the lowest free energy. The formation mechanisms of regular hole pattern and imperfections in the hexagonal packing are proposed.

Triplex selective 2-(2-naphthyl)quinoline compounds: Origins of affinity and new design principles

A novel competition dialysis assay was used to investigate the structural selectivity of a series of substituted 2-(2-naphthyl)quinoline compounds designed to target triplex DNA. The interaction of 14 compounds with 13 different nucleic acid sequences and structures was studied. A striking selectivity for the triplex structure poly dA:[poly dT](2) was found for the majority of compounds studied. Quantitative analysis of the competition dialysis binding data using newly developed metrics revealed that these compounds are among the most selective triplex-binding agents synthesized to date. A quantitative structure-affinity relationship (QSAR) was derived using triplex binding data for all 14 compounds used in these studies. The QSAR revealed that the primary favorable determinant of triplex binding free energy is the solvent accessible surface area. Triplex binding affinity is negatively correlated with compound electron affinity and the number of hydrogen bond donors. The QSAR provides guidelines for the design of improved triplex-binding agents.

Functionalization of an ethylene-propylene copolymer with allyl (3-isocyanate-4-tolyl) carbamate

An ethylene-propylene copolymer (EPM) was functionalized with an iso cyanate-bearing unsaturated monomer, allyl(3-isocyanate-4-tolyl) carbamate (TAI), with dicumyl peroxide as an initiator in a xylene solution. Fourier transform infrared (FTIR) was used to confirm the formation of EPM-g-TAI. The peak at 2273 cm(-1), characteristic of -NCO groups in EPM-g-TAI, revealed evidence of grafting. The grafting degree was determined with both chemical titration and FTIR. The grafting degree could be adjusted, and the maximum was over 6 wt % without any gelation. The molar mass distribution of EPM-g-TAI was narrower than that of EPM. The rheological behavior of both EPM-g-TAI and EPM was investigated with a rotational rheometer. The apparent viscosity of EPM-g-TAI was higher than that of EPM and increased with an increasing grafting degree of TAI. Surface analysis by contact-angle measurements showed that contact angles of EPM-g-TAI samples to a given polar liquid decreased with an increasing grafting degree of TAI. We also obtained the dispersion component of the surface free energy (gamma(S)(d)), the polar component of the surface free energy (gamma(S)(d)), and the total surface free energy (gamma(S) = gamma(S)(d) + gamma(S)(p)) of the grafted EPM. These parameters increased with the enhancement of the grafting degree, which gave us a quantitative estimation of the polar contribution of the grafted TAI to the total surface free energy of EPM-g-TAI.

Isothermal and nonisothermal crystallization kinetics of nylon-46

Isothermal and nonisothermal crystallization kinetics of nylon-46 were investigated with differential scanning calorimetry. The equilibrium melting enthalpy and the equilibrium melting temperature of nylon-46 were determined to be 155.58 J/g and 307.10 degreesC, respectively. The isothermal crystallization process was described by the Avrami equation. The lateral surface free energy and the end surface free energy of nylon-46 were calculated to be 8.28 and 138.54 erg/cm(2), respectively. The work of chain folding was determined to be 7.12 kcal/mol. The activation energies were determined to be 568.25 and 337.80 kJ/mol for isothermal and nonisothermal crystallization, respectively. A convenient method was applied to describe the nonisothermal crystallization kinetics of nylon-46 by a combination of the Avrami and Ozawa equations.

Isothermal and nonisothermal melt-crystallization kinetics of syndiotactic polystyrene

Analyses of the isothermal and nonisothermal melt kinetics for syndiotactic polystyrene have been performed with differential scanning calorimetry, and several kinetic analyses have been used to describe the crystallization process. The regime II-->III transition, at a crystallization temperature of 239degrees, is found. The values of the nucleation parameter K-g for regimes II and III are estimated. The lateral-surface free energy, sigma = 3.24 erg cm(-2), the fold-surface free energy, sigma(e) = 52.3 +/- 4.2 erg cm(-2), and the average work of chain folding, q = 4.49 +/- 0.38 kcal/mol, are determined with the (040) plane assumed to be the growth plane. The observed crystallization characteristics of syndiotactic polystyrene are compared with those of isotactic polystyrene. The activation energies of isothermal and nonisothermal melt crystallization are determined to be DeltaE = -830.7 kJ/mol and DeltaE = -315.9 kJ/mol, respectively.