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.

Investigation of charge-carrier injection characteristics in NPB/Alq3 heterojunction devices

The effect of copper phthalocyanine (CuPc) and LiF interfacial layers on the charge-carrier injection in NN'-di(naphthalene-l-yl)N,N'-diphenyl-benzidine (NPB)/tris(8-hydroxyquinoline) aluminium (Alq(3)) organic heterojunction devices have been studied through the analysis of current-voltage characteristics. The investigation clearly demonstrated that the hole injection into NPB from anode is Fowler-Nordheim (FN) tunneling and the electron injection into Alq3 from cathode is Richardson-Schottky (RS) thermionic emission. The barrier heights obtained from the FN and RS models proved that the band alignments for charge-carrier injection are greatly improved by the CuPc and LiF interfacial layers, which should fully clarify the role of the interfacial layer on the improvement of device performance.

Synthesis, structural and electrical characterizations of Sr2Fe1-xMxNbO6 (M = Zn and Cu) with double perovskite structure

Sr2Fe1-xZnxNbO6-x/2 (0 <= x <= 0.5) and Sr2Fe1-xCuxNbO6-x/2 (0.01 <= x <= 0.05) with the double perovskite structure have been synthesized. The crystal structures at room temperature were determined from Rietveld refinements of X-ray powder diffraction data. The plots of the imaginary parts of the impedance spectrum, Z '', and the electric modulus, M '', versus log (frequency), possess maxima for both curves separated by less than a half decade in frequency with associated capacities of 2 nF. The enhancement of the overall conductivity Of Sr2Fe1-xMxNbO6-x/2 (M = Cu and Zn) is observed, as increases from 2.48 (3) x 10(-4) S/cm for Sr2FeNbO6 to 3.82 (5) x 10(-3) S/cm for Sr2Fe0.8Zn0.2NbO5.9 at 673 K. Sr2Fe0.8Zn0.2NbO5.9 is chemically stable under the oxygen partial pressure from 1 atm to 10(-22) atm at 873 K. The p and n-type electronic conductions are dominant under oxidizing and reducing conditions, respectively, suggesting a small-polaron hopping mechanism of electronic conduction.

Direct electrochemistry and surface plasmon resonance characterization of alternate layer-by-layer self-assembled DNA-myoglobin thin films on chemically modified gold surfaces

Alternate layer-by-layer (L-by-L) polyion adsorption onto gold electrodes coated with chemisorbed cysteamine gave stable, electroactive multilayer films containing calf thymus double stranded DNA (CT ds-DNA) and myoglobin (Mb). Direct, quasi-reversible electron exchange between gold electrodes and proteins involved the Mb heme Fe2+/Fe3+ redox couple. The formation of L-by-L (DNA/Mb), films was characterized by both in situ surface plasmon resonance (SPR) monitoring and cyclic voltammetry (CV). The effective thickness of DNA and Mb monolayers in the (DNA/Mb)l bilayer were 1.0 +/- 0.1 and 2.5 +/- 0.1 mn, corresponding to the surface coverage of similar to65% and similar to89% of its full packed monolayer, respectively. A linear increase of film thickness with increasing number of layers was confirmed by SPR characterizations. At pH 5.5, the electroactive Mb in films are those closest to the electrode surface; additional protein layers did not communicate with the electrode. CV studies showed that electrical communication might occur through hopping conduction via the electrode/base pair/Mb channel, thanks to the DNA-Mb interaction. After the uptake of Zn2+, a special electrochemical behavior, where MbFe(2+) acts as a DNA-binding reduction catalyst in the Zn2+-DNA/Mb assembly, takes place.

Characteristics of the conductive polyimide film surfaces induced by ultraviolet laser beam

A conducting layer with the conductivity of 1.2 Omega(-1)cm(-1) stripped in a solvent from KrF-laser-irradiated polyimide thin film is taken as a sample to determine the microstructure of the conducting layer. Fourier-transform infrared and X-ray photoelectron spectroscopies show the formation of the carbon-rich clusters after irradiation. The element analysis gives the atomic ratio of C:H:N:O for the carbon-rich cluster as 60:20:3:1. Wide-angle X-ray diffraction indicates that the conducting layer is mainly amorphous carbon with a small amount of the short-range ordered carbon-rich clusters. This study suggests a structural model with three-layer carbon sheets linked together in a random fashion for the short-range ordered carbon-rich clusters. The interplanar spacing is 3.87 Angstrom and the layer diameter 25 Angstrom. The transport model of variable-range hopping in three dimensions is used to explain the conducting behavior of the conducting layer. In our case, the short-range ordered carbon-rich clusters are assumed to be conducting islands dispersed in the amorphous carbon-rich cluster matrix.

Mossbauer spectra of Fe-57 in a thick film of YBa2(Cu0.97Fe0.03)(3)O7-x irradiated by a large dose of gamma-rays

Mossbauer spectra of Fe-57 in a thick film YBa2(Cu0.97Fe0.03)(3)O7-x irradiated by a large dose of gamma-rays from Co-60 have been measured. The variation of the relative intensities of some subspectra of Fe-57 in the. Mossbauer spectra of the thick film YBa2(Cu0.97Fe0.03)(3)O7-x after irradiation can be observed. This variation indicates that the change of the coordination environment around some Fe atoms in the lattice occurs due to irradiation. The relative intensity of subspectrum D1(Fe) at the Cu(1) site decreases and that of subspectrum D4(Fe) at the Cu(1) site increases. This may be because of the possible oxygen atom hopping between the coordination environments of D1(Fe) and D4(Fe) in the lattice caused by irradiation. The effect of irradiation on the coordination environment around the Fe atom at the Cu(2) site is not appreciable. (C) 1997 Elsevier Science B.V.

A study of the electrochemical characteristics of the Co(salen)-Nafion modified electrode

A Co(salen)-Nafion modified electrode was prepared by immersing a glassy carbon electrode coated with the Nafion film into the aqueous solution with saturated Co(salen), The modified electrode showed a stable electrochemical reaction of Co(salen) at about 0 V(vs, SCE), The result of XPS indicated the valence of cobalt in Co(salen) changes from +2 before to +3 after Co(salen) enters the Nafion film, It is due to forming axis coordination of cobalt with sulfonic group in Nafion film, It was found that the mode of electron transfer in Co(salen)-Nafion modified electrode was controlled by physical diffusion and electron hopping, It was also found that the modified electrode could catalyze the reduction of O-2 to H2O2. The real catalyst may be the adduct of Co-I(salen) and O-2.

IONIC-CONDUCTIVITY AND DYNAMIC MECHANICAL RELAXATION OF A 2-COMPONENT EPOXY NETWORK-LICLO4 ELECTROLYTE SYSTEM

The correlation between mechanical relaxation and ionic conductivity was investigated in a two-component epoxy network-LiClO4 electrolyte system. The network was composed of diglycidyl ether of polyethylene glycol (DGEPEG) and triglycidyl ether of glycerol (TGEG). The effects of salt concentration, molecular weight of PEG in DGEPEG and the proportion of DGEPEG (1000) in DGEPEG/TGEG ratio on the ionic conductivity and the mechanical relaxation of the system were studied. It was found that, among the three influential factors, the former reinforces the network chains, reduces the free volume fraction and thus increases the relaxation time of the segmental motion, which in turn lowers the ionic conductivity of the specimen. Conversely, the latter two increase the free volume and thus the chain flexibility, showing an opposite effect. From the iso-free-volume plot of the shift factor log at and reduced ionic conductivity, it is noted that the plot can be used to examine the temperature dependence of segmental mobility and seems to be useful to judge whether the incorporated salt has been dissociated completely. Besides, the ionic conductivity and relaxation time at constant reference temperature are linearly correlated with each other in all the three cases. This result gives an additional experimental confirmation of the coordinated motion model of the ionic hopping with the moving polymer chain segment, which is generally used to explain the ionic conduction in non-glassy amorphous polymer electrolytes.

DOPING EFFECTS ON THE POLYMER-CHAIN STRUCTURE OF POLY(3-METHYLTHIOPHENE)

The C=C stretching Raman shifts and photoluminescence (PL) for poly(3-methylthiophene) (P3MT) are measured at various doping levels by in situ electrochemical Raman and PL spectroscopic techniques. It is found that the doping for P3MT induces the nonlinear excitations (soliton, Polaron, bipolaron), but also affects the polymer-chain structure, including the conjugated length and the interchain distance.

Dedicated global optimization search for ground state silica nanoclusters: (SiO2)(N) (N=6-12)

Flikkema, E., & Bromley, S. T. (2004). Dedicated global optimization search for ground state silica nanoclusters: (SiO2)(N) (N=6-12). Journal of Physical Chemistry B, 108 (28), 9638-9645. RAE2008

Molecular dynamics-based approach to study the anisotropic self-diffusion of molecules in porous materials with multiple cage types: Application to H-2 in losod

Van den Berg, A. W. C., Flikkema, E., Lems, S., Bromley, S. T., Jansen, J. C. (2006). Molecular dynamics-based approach to study the anisotropic self-diffusion of molecules in porous materials with multiple cage types: Application to H-2 in losod. Journal of physical chemistry b, 110 (1), 501-506. RAE2008

Neutron quasi-elastic scattering in disordered solids: a Monte Carlo study of metal-hydrogen systems

The dynamic structure factor of neutron quasi-elastic scattering has been calculated by Monte Carlo methods for atoms diffusing on a disordered lattice. The disorder includes not only variation in the distances between neighbouring atomic sites but also variation in the hopping rate associated with each site. The presence of the disorder, particularly the hopping rate disorder, causes changes in the time-dependent intermediate scattering function which translate into a significant increase in the intensity in the wings of the quasi-elastic spectrum as compared with the Lorentzian form. The effect is particularly marked at high values of the momentum transfer and at site occupancies of the order of unity. The MC calculations demonstrate how the degree of disorder may be derived from experimental measurements of the quasi-elastic scattering. The model structure factors are compared with the experimental quasi-elastic spectrum of an amorphous metal-hydrogen alloy.

Rotating-frame nuclear magnetic relaxation of spins diffusing on a disordered lattice: a Monte Carlo model

The rotating-frame nuclear magnetic relaxation rate of spins diffusing on a disordered lattice has been calculated by Monte Carlo methods. The disorder includes not only variation in the distances between neighbouring spin sites but also variation in the hopping rate associated with each site. The presence of the disorder, particularly the hopping rate disorder, causes changes in the time-dependent spin correlation functions which translate into asymmetry in the characteristic peak in the temperature dependence of the dipolar relaxation rate. The results may be used to deduce the average hopping rate from the relaxation but the effect is not sufficiently marked to enable the distribution of the hopping rates to be evaluated. The distribution, which is a measure of the degree of disorder, is the more interesting feature and it has been possible to show from the calculation that measurements of the relaxation rate as a function of the strength of the radiofrequency spin-locking magnetic field can lead to an evaluation of its width. Some experimental data on an amorphous metal - hydrogen alloy are reported which demonstrate the feasibility of this novel approach to rotating-frame relaxation in disordered materials.

Nonlinear transport and localization in single-walled carbon nanotubes

We have measured the electrical transport properties of mats of single-walled carbon nanotubes (SWNT) as a function of applied electric and magnetic fields. We find that at low temperatures the resistance as a function of temperature R(T) follows the Mott variable range hopping (VRH) formula for hopping in three dimensions. Measurement of the electric field dependence of the resistance R(E) allows for the determination of the Bohr radius of a localized state a = 700nm. The magnetoresistance (MR) of SWNT mat samples is large and negative at all temperatures and fields studied. The low field negative MR is proportional to H2, in agreement with variable range hopping in two or three dimensions. 3D VRH indicates good intertube contacts, implying that the localization is due to the disorder experienced by the individual tubes. The 3D localization radius gives a measure of the ID localization length on the individual tubes, which we estimate to be >700 nm. Implications for the electron-phonon mean free path are discussed.

A simple model of atomic interactions in noble metals based explicitly on electronic structure

A total energy tight-binding model with a basis of just one s state per atom is introduced. It is argued that this simplest of all tight-binding models provides a surprisingly good description of the structural stability and elastic constants of noble metals. By assuming inverse power scaling laws for the hopping integrals and the repulsive pair potential, it is shown that the density matrix in a perfect primitive crystal is independent of volume, and structural energy differences and equations of state are then derived analytically. The model is most likely to be of use when one wishes to consider explicitly and self-consistently the electronic and atomic structures of a generic metallic system, with the minium of computation expense. The relationship to the free-electron jellium model is described. The applicability of the model to other metals is also considered briefly.