Base-dependent competitive adsorption of single-stranded DNA on gold

We characterize the room-temperature adsorption of single-stranded DNA homo-oligonucleotides from solution onto polycrystalline Au films, including competitive adsorption between all possible pairs of unmodified oligomers. Fourier transform infrared (FTIR) and X-ray photoelectron (XPS) spectroscopy analysis of the resulting films shows that oligonucleotides adsorb with a strongly base-dependent affinity, adenine (A) > cytosine (C) >/= guanine (G) > thymine (T). In competitive adsorption experiments on Au, oligo(dA) strongly dominates over the other oligonucleotides. The relative adsorption affinity of oligo(dA) is so great that it competes effectively against adsorption of thiolated oligomers and even causes hybridized oligo(dA).oligo(dT) duplexes to denature in the presence of Au.     

Molecular orientation ordering in surface layers of polymer films

The spontaneous ordering of fragments of chain molecules near the surface in polymer films is described in terms of the multichain model that allows for local intra-and interchain orientational interactions of chain segments and for transverse fluctuation of their orientation in the approximation of strong planar-orientation order in the layers. Chain packing in the plane-ordered state is impossible unless the interchain interaction parameter has a value of b = 2K ₂/k _B T > b _c. The value of b _c decreases with a growth in chain rigidity (parameter a = 2K ₁/k _B T). The calculated dependence of the limiting values of the quadrupole orientation order parameter S ₀ on the length of the Kuhn statistical segment A = 2a reasonably well describes the experimental data obtained in a study of polymer-homolog (polysaccharide) films by means of the tilted polarized-beam technique at an interchain interaction parameter of b = 1.75. The monolayer thickness (d ? 10 mn) is films of some polysaccharides was calculated from the fit of the theoretical to the experimental dependences of the orientational order parameter and the birefringence on the number of layers.     

Evidence of impurities in thiolated single-stranded DNA oligomers and their effect on DNA self-assembly on gold

The diversity of techniques used in the synthesis, treatment, and purification of the single-stranded DNA oligomers containing a thiol anchor group (SH-ssDNA) has led to a significant variation in the purity of commercially available SH-ssDNA. In this work, we use X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study how the impurities present in commercially synthesized SH-ssDNA oligomers affected the structure of the resulting DNA films on Au. XPS results indicate that two of the purchased SH-ssDNA oligomers contain excess carbon and sulfur. The molecular fragmentation patterns obtained with ToF-SIMS were used to determine the identity of several contaminants in the DNA films, including poly(dimethylsiloxane) (PDMS), lipid molecules, and sulfur-containing molecules. In particular, the ToF-SIMS results determined that the excess sulfur detected by XPS was due to the presence of dithiothreitol, a reductant often used to cleave disulfide precursors. Furthermore, we found that the SH-ssDNA self-assembly process is affected by the presence of these contaminants. When relatively pure SH-ssDNA is used to prepare the DNA films, the P, N, O, and C atomic percentages were observed by XPS to increase over a 24-h time period. In contrast, surfaces prepared using SH-ssDNA containing higher levels of contaminants did not follow this trend. XPS result indicates that, after the initial SH-ssDNA adsorption, the remaining material incorporated into these films was due to contamination.     

Kinetics and mechanism of single-stranded DNA adsorption onto citrate-stabilized gold nanoparticles in colloidal solution

A variety of rapid biomolecular assays under development rely on the selective adsorption of single-stranded DNA onto unfunctionalized, negatively charged, citrate-stabilized gold nanoparticles. We investigate the adsorption mechanism with a study of the binding kinetics and find strong evidence for the dominance of hydrophobic effects including linear compensation between the activation energy and the natural log of the Arrhenius prefactor and the correlation of the adsorption rate in the presence of various salts with the Hofmeister series. These results explain the selectivity for single-stranded over double-stranded DNA adsorption and contradict previous work citing an electrostatic DLVO-like mechanism. Our understanding should facilitate improvements to the selective-adsorption-based assays and, more generally, contribute to the understanding of interactions between like-charged species in aqueous solution.     

Aptamer based voltammetric determination of ampicillin using a single-stranded DNA binding protein and DNA functionalized gold nanoparticles

An aptamer based method is described for the electrochemical determination of ampicillin. It is based on the use of DNA aptamer, DNA functionalized gold nanoparticles (DNA-AuNPs), and single-stranded DNA binding protein (ssDNA-BP). When the aptamer hybridizes with the target DNA on the AuNPs, the ssDNA-BP is captured on the electrode surface via its specific interaction with ss-DNA. This results in a decreased electrochemical signal of the redox probe Fe(CN)₆ ^3? which is measured best at a voltage of 0.188 mV (vs. reference electrode). In the presence of ampicillin, the formation of aptamer-ampicillin conjugate blocks the further immobilization of DNA-AuNPs and ssDNA-BP, and this leads to an increased response. The method has a linear reposne that convers the 1 pM to 5 nM ampicillin concentration range, with a 0.38 pM detection limit (at an S/N ratio of 3). The assay is selective, stable and reproducible. It was applied to the determination of ampicillin in spiked milk samples where it gave recoveries ranging from 95.5 to 105.5%.

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Graphical abstract Schematic of a simple and sensitive electrochemical apta-biosensor for ampicillin detection. It is based on the use of gold nanoparticles (AuNPs), DNA aptamer, DNA functionalized AuNPs (DNA-AuNPs), and single-strand DNA binding protein (SSBP).

     

Molecular orientation of evaporated pentacene films on gold: alignment effect of self-assembled monolayer

Pentacene films deposited on self-assembled monolayers (SAMs) bearing different terminal functional groups have been studied by reflection-absorption IR, grazing angle XRD, NEXAFS, AFM, and SEM analyses. A film with pentacene molecules nearly perpendicularly oriented was observed on Au surfaces covered with an SAM of alkanethiol derivative of X-(CH2)(n)-SH, with X = -CH(3), -COOH, -OH, -CN, -NH(2), C(60), or an aromatic thiol p-terphenylmethanethiol. On the other hand, a film with the pentacene molecular plane nearly parallel to the substrate surface was found on bare Au surface. A similar molecular orientation was found in thinner ( approximately 5 nm) and thicker (100 nm) deposited films. Films deposited on different surfaces exhibit distinct morphologies: with apparently smaller and rod-shaped grains on clean bare Au surface but larger and islandlike crystals on SAM-modified surfaces. X-ray photoemission electron microscopy (X-PEEM) was used to analyze the orientation of pentacene molecules deposited on a SAM-patterned Au surface. With the micro-NEXAFS spectra and PEEM image analysis, the microarea-selective orientation control on Au was characterized. The ability to control the packing orientation in organic molecular crystals is of great interest in fabricating organic field effect transistors because of the anisotropic nature of charge transport in organic semiconducting materials.     

Interactions of single-stranded DNA on microcantilevers

The microcantilever approach has attracted considerable attention in recent years as a means of label-free detection of a variety of biomolecular and chemical reactions. The underlying physics of the intermolecular interactions that result in mechanical motions is yet to be fully explored, but it seems both rich in science and of technological importance. This paper presents an overview of experiments and theories related to interactions of single-stranded DNA immobilized on microcantilevers. Experiments and theories show that, at high grafting density, hydration forces are the dominant factor determining cantilever deflections, not electrostatics or conformational entropy.     

Molecular ordering and 2D conductivity in ultrathin poly(3-hexylthiophene)/gold nanoparticle composite films

This paper reports the first comparison of the structure and electrical conductivity properties of spin cast (SC) and Langmuir-Schaeffer (LS) films of regioregular poly(3-hexylthiophene) (P3HT). In addition, the effect of incorporating highly monodisperse Au nanoparticles (NPs), with a core diameter of approximately 5 nm, into SC and LS P3HT films is described. A detailed picture of molecular organization in the films has been obtained using ultraviolet-visible absorption spectroscopy, atomic force microscopy, field-emission scanning electron microscopy, X-ray diffraction, and X-ray reflectivity. Film morphology was correlated with pseudo-two-dimensional conductivity measured using scanning electrochemical microscopy, with P3HT in the semiconducting regime. It was found that SC films, which were slightly thicker than those formed with the LS technique, exhibited greater organization. This resulted in an order of magnitude higher lateral conductivity for the SC films. Inclusion of Au NPs (50 wt %) into both SC and LS films resulted in the formation of uniform and relatively flat (rms roughness approximately 1 nm) composite films. Surprisingly, the addition of NPs did not disrupt the characteristic crystal structure found for the native P3HT films. The effect of Au NPs on film lateral conductivity was found to be determined by the distribution of Au NPs within the polymer, which varied significantly between SC and LS films. Whereas Au NPs aggregated into hexagonally packed clusters in SC films, NPs in LS films were predominantly uniformly distributed between the lamella bilayer. It was found that, while the inclusion of Au NPs caused the lateral conductivity to decrease in SC films, in LS films, the lateral conductivity increased by a factor of 2.     

Immobilization of single-stranded deoxyribonucleic acid on gold electrode with self-assembled aminoethanethiol monolayer for DNA electrochemical sensor applications

A synthesized 24-mer single-stranded deoxyribonucleic acid (ssDNA) was covalently immobilized onto a self-assembled aminoethanethiol monolayer modified gold electrode, using water-soluble 1-ethyl-3(3-dimethylaminopropyl)-carbodiimide (EDC). The covalently immobilized ssDNAs were hybridized with complementary ssDNA (cDNA) or yAL(3) gene in solution, forming double-stranded DNAs (dsDNA). Meanwhile, daunomycin as an electrochemical active intercalator in the hybridization buffer solution was intercalated into the dsDNA to form a dsDNA/daunomycin system on the gold electrode surface, which was used for DNA electrochemical sensor. The cathodic waves of daunomycin bound to the double-stranded DNA (dsDNA) by linear sweep voltammetry were utilized to detect the cDNA. The cathodic peak current (i(pc)) of duanomycin was linearly related to the concentrations of cDNA between 0.1 mug ml(-1) and 0.1 ng ml(-1). The detection limit was about 30 pg ml(-1).     

Modification of Escherichia coli single-stranded DNA binding protein with gold nanoparticles for electrochemical detection of DNA hybridization

The unique binding event between Escherichia coli single-stranded DNA binding protein (SSB) and single-stranded oligonucleotides conjugated to gold (Au) nanoparticles is utilized for the electrochemical detection of DNA hybridization. SSB was attached onto a self-assembled monolayer (SAM) of single-stranded oligonucleotide modified Au nanoparticle, and the resulting Au-tagged SSB was used as the hybridization label. Changes in the Au oxidation signal was monitored upon binding of Au tagged SSB to probe and hybrid on the electrode surface. The amplified oxidation signal of Au nanoparticles provided a detection limit of 2.17 pM target DNA, which can be applied to genetic diagnosis applications. This work presented here has important implications with regard to combining a biological binding event between a protein and DNA with a solid transducer and metal nanoparticles.     

Electronic excitations and spectra in single-stranded DNA

Using density functional theory and molecular dynamics simulations, we show that delocalized states extending over three bases can be directly excited in single-stranded poly(A) DNA. The results are in semiquantitative agreement with recent experimental results for the delocalization length of these states in single- and double-stranded DNA. The structures used in these molecular dynamics calculations are validated by comparing calculated circular dichroic spectra for d(A)2 and d(A)4 with experiment. These spectra, which arise from highly stacked structures, are in good agreement with experiment, suggesting that the short delocalization in ssDNA arises in spite of strong stacking.     

Amperometric detection of DNA hybridization on a gold surface depends on the orientation of oligonucleotide chains

We tested the possibility of amperometric detection of DNA hybridization on a gold surface influenced by the immobilization of oligonucleotide giving different orientations of single stranded DNA relative to the gold surface. The DNA sensor was fabricated by chemisorption of 18-mer oligonucleotide modified by a phosphorothioate group either at its 3' or both 3' and 5' terminal. After immobilization of oligonucleotide to the gold support, the sensor was immersed in 11-mercaptoundecanoic acid (MUA) solution. Further chemisorption of MUA resulted in approximately 10-fold increase of resistance of the organic layer. Addition of complementary oligonucleotide resulted in an increase of conductivity for DNA sensor oriented perpendicular to the gold support (DNA with one thiol group), while the conductance decreased for DNA sensor with single stranded DNA oriented parallel to the gold support (with DNA modified by thiol groups at both 3' and 5' terminals). Addition of non-complementary chain resulted a slight decrease or no change of sensor conductivity. The hybridization process at both types of DNA orientations is not cooperative and can be described by Langmuir isotherms. The hybridization event on gold support has been confirmed by mass detection using the quartz crystal microbalance technique.     

Hybridization of oligonucleotide-modified silver and gold nanoparticles in aqueous dispersions and on gold films

Functionalization of silver and gold nanoparticles by 12mer-thiolated homo-oligonucleotides, SA and ST (containing only adenine or thymine, respectively), and their hybridization and dehybridization in aqueous dispersions have been described. In addition, ST and SA were self-assembled onto gold films and hybridized with their complementary pairs, unlabeled or labeled by gold and silver nanoparticles. The base pairing between DNA strands and the types of oligonucleotides (adenine or thymine) attached to the nanoparticles was detected by Polarization Modulated Fourier Transform Infrared Reflection Absorption Spectroscopy (PM-FTIRRAS).     

Electrochemical detection of DNA hybridization using methylene blue and electro-deposited zirconia thin films on gold electrodes

A novel electrochemical DNA biosensor based on methylene blue (MB) and zirconia (ZrO₂) thin films modified gold electrode for DNA hybridization detection is presented. Zirconia thin films were electrodynamically deposited onto the bare gold electrode in an aqueous electrolyte of ZrOCl₂ and KCl by cycling the potential between −1.1 and +0.7 V (versus Ag/AgCl) at a scan rate of 20 mV s⁻¹. Oligonucleotide probes with phosphate group at the 5′ end were attached onto the zirconia thin films because zirconia is affinity for phosphoric group. The surface density of the immobilized DNA molecules at the zirconia interface was investigated by fluorescence spectroscopy method. Hybridization was induced by exposure of the ssDNA-containing Au electrode to complementary ssDNA in solution. The decreases in the peak currents of MB, an electroactive label, were observed upon hybridization of probe with the target. The cathodic peak current (i_p) of MB after hybridization with the target DNA was linearly related to the logarithmic value of the target DNA concentration ranging from 2.25×10⁻¹⁰ to 2.25×10⁻⁸ mol l⁻¹. A detection limit of 1.0×10⁻¹⁰ mol l⁻¹ of oligonucleotides can be estimated.     

Hybridization with nanostructures of single-stranded DNA

Nanostructures of single-stranded DNA (ssDNA) were produced within alkanethiol self-assembled monolayers using nanografting, an atomic force microscopy (AFM) based lithography technique. Next, variations of the fabrication parameters, such as the concentration of ssDNA or lines per frame, allowed for the regulation of the density of ssDNA molecules within the nanostructures. The label-free hybridization of nanostructures, monitored using high-resolution AFM imaging, has proven to be highly selective and sensitive; as few as 50 molecules can be detected. The efficiency of the hybridization reaction at the nanometer scale highly depends on the ssDNA packing density within the nanostructures. This investigation provides a fundamental step toward sensitive DNA detection and construction of complex DNA architectures on surfaces.     

Application of FTIR-spectroscopy on orientation processes in polyethylene films

Summary The experimental possibilities of the FTIR spectrometers for the studies of crystallization, orientation, and relaxation phenomena in polymers are outlined. The experimental results on polyethylene films are discussed and related to changes in the state of order in the polymer films occurring during the stretching and relaxation process.With 5 figures     

Effect of monovalent cations (Li+, Na+, K+, Cs+) on self-assembly of thiol-modified double-stranded and single-stranded DNA on gold electrode

In this article we investigate the effect of monovalent cations (Li(+), Na(+), K(+), Cs(+)) on self-assembly of thiol-modified double-stranded DNA (ds-DNA) and single-stranded DNA (ss-DNA) on gold electrodes. Electrochemical characteristics (surface coverage, ion penetration and charge transfer) of ds-DNA and ss-DNA self-assembled monolayers (SAMs) formed with different monovalent cations are inspected based on six important interfacial parameters including surface coverage (Γ(m)), interfacial capacitance (C), phase angle (Φ(1 Hz)), ion transfer resistance (R(it)*), current density difference (Δj) and charge transfer resistance (R(ct)) from chronocoulometry (CC), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Three sections are included: (1) Investigation of the relationships of parameters (Γ(m), C, Φ(1 Hz), R(it)*, Δj and R(ct)) for ds-DNA-SAMs and ss-DNA-SAMs with cation types and concentrations; (2) confirmation and explanation of our experimental results combined with our recently proposed simple DNA model and literature reports; (3) exploration of the mechanism for the orders of monovalent cations (Li(+), Na(+), K(+), Cs(+)) on availing the adsorption of ds-DNA and ss-DNA molecules on gold based on their physicochemical parameters (ion size, solvation free energy and enthalpy, ion-water bond length and water exchange rate) and possible binding modes with DNA molecules. This work might provide a useful reference for understanding interactional mechanism of cations with DNA molecules.     

Molecular orientation in electrodeposited polypyrrole films

The molecular arrangement in electrodeposited polypyrrole films was studied by means of linear dichroism in the near-edge X-ray absorption fine structure (NEXAFS) spectra measured at the K absorption edges of carbon and nitrogen. It has been found that the change of the exciting radiation incidence from normal to grazing leads to an increase in the intensity of π*-related resonances with simultaneous decrease in the intensity of σ*-related resonances in the spectra. Similar changes in the spectra measured for both absorption edges indicate a pronounced conjugation of π-bonds in the polypyrrole chains in the grown films. Preferential in-plane orientation of pyrrole rings relative to the substrate surface is observed for all the deposited films. The linear dichroism is more pronounced at the initial stages of deposition (2D growth) than at later stages characterized by “cauliflower”-like morphology of the grown film.     

Electrochemical self-assembly of melanin films on gold

An electrochemical method for self-assembling melanin films on the Au(111) surface from melanin aggregates in alkaline media is reported. Electrochemical data combined with scanning tunneling microscopy (STM), atomic force microscopy, and Auger electron spectoscopy show that the amount and structure of the deposited melanin film depend on the potential (E) applied to the electrochemical interface and deposition time. Film formation takes place at a noticeable rate at E = -1.0 V (vs SCE). High-resolution STM images at the early stages of growth show small particles, 5-8 nm in size and 0.3-0.4 nm in height, forming ordered arrays that follow closely the Au(111) topography. The size of the melanin particles increases as the film thickness increases, reaching 150 nm for deposits grown for 16 h. The deposited films are electrochemically active, showing well-defined redox couples preceding the hydrogen evolution reaction.     

Shear ordering in thin films of spherical block copolymer

We have investigated shear-induced alignment of a bilayer of spherical diblock copolymer micelles within thin films using molecular dynamics simulations at two different levels of coarse-graining. At the microscopic level, the copolymers are modeled as bead and spring chains with specific interaction potentials which produce strongly segregated spherical micelles. The simulations qualitatively reveal that long-range shear-induced ordering of hexagonally arranged micelles arises because of the tendency of micelles to pursue trajectories of minimum frictional resistance against micelles in the opposing layer. This influences their alignment in the direction of shear without them breaking apart and reforming within the time scale of the simulations. As observed in experiments, the ordering is shown to be very sensitive to the film thickness and shearing rates. To access larger lengths and longer time scales, we further coarse-grain our system to a mesoscopic level where an individual micelle is represented by a spherical particle, which interacts with other micelles through an effective potential obtained from the microscopic simulations. This approach enables us to follow the time evolution of global order from locally ordered domains. An exponentially fast growth of the orientational correlation length of the hexagonal pattern at early times, followed by a crossover to linear growth, is found in the presence of shear, in contrast to the much slower power-law scalings observed in experiments without shear.