Electrochemistry using self-assembled DNA monolayers on highly oriented pyrolytic graphite

Duplex DNA functionalized with pyrene has been utilized to fabricate DNA-modified electrodes on highly oriented pyrolytic graphite (HOPG). Films have been characterized using AFM and radioactive labeling as well as electrochemically. The data obtained are consistent with a close-packed structure in the film with helices oriented in a nearly upright orientation, as seen earlier with the fabrication of thiol-tethered duplexes on gold. Also as on gold, we observe the reduction of DNA-bound intercalators in a DNA-mediated reaction. The reduction of the intercalator is attenuated in the presence of the single-base mismatches, CA and GT, independent of the sequence composition of the oligonucleotide. This sensitivity to single-base mismatches is enhanced when methylene blue reduction is coupled in an electrocatalytic cycle with ferricyanide. The extended potential range afforded by the HOPG surface has allowed us also to investigate the electrochemistry of previously inaccessible metallointercalators, Ru(bpy)2dppz2+ and Os(phen)2dppz2+, at the DNA-modified HOPG surface. These results support the application of DNA-modified HOPG as a convenient and reproducible surface for electrochemical DNA sensors using DNA-mediated charge transport.     

Monitoring the formation of self-assembled monolayers of alkanedithiols using a micromechanical cantilever sensor

Using a micromechanical cantilever device, the surface stress induced during the growth of alkanedithiol (HS(CH2)nSH) monolayers on gold in solution is continuously monitored and reported. Adsorption of alkanedithiols of varying chain lengths is observed and compared to each other, as well as to the adsorption of hydroxyalkanethiols (HS(CH2)nOH) and alkanethiols (HS(CH2)nCH3). The results have revealed a significant change in surface stress on the basis of the chain length of the alkanedithiol. The long-chain (n > 10) alkanedithiol adsorption imposes a tensile stress on the gold-coated surface of the cantilever rather than the compressive stress exhibited by both alkanethiols and short-chain dithiols. Our results suggest a phenomenon in which the two thiols of the alkanedithiol adsorb onto the gold surface forming a loop inducing a tensile stress on the cantilever for long chain lengths. This study shows that micromechanical cantilever sensors can be very valuable tools in the exploration and characterization of self-assembled monolayers.     

Soft-UV photolithography using self-assembled monolayers

We report thiol-on-gold self-assembled monolayers (SAMs) that can be photodeprotected using soft UV irradiation (lambda = 365 nm) to yield CO(2)H functionalized surfaces complementing those reported previously, which yielded NH(2) functionalized surfaces. The photolysis of these SAMs were monitored using a combination of surface sensitive techniques. In the SAM environment the photodeprotection yields are lower than those obtained for equivalent reactions in dilute solution. The protected carboxylic acids SAMs are shown to have a low yield approximately 50% due to competing photoreduction reactions of the nitro group. The results from infrared studies show that, as the photolysis progresses, the long chain protected residues reorganize and shield the functional COOH groups, thereby reducing the hydrophilic character of the surface.     

Engineering silicon oxide surfaces using self-assembled monolayers

Although a molecular monolayer is only a few nanometers thick it can completely change the properties of a surface. Molecular monolayers can be readily prepared using the Langmuir-Blodgett methodology or by chemisorption on metal and oxide surfaces. This Review focuses on the use of chemisorbed self-assembled monolayers (SAMs) as a platform for the functionalization of silicon oxide surfaces. The controlled organization of molecules and molecular assemblies on silicon oxide will have a prominent place in "bottom-up" nanofabrication, which could revolutionize fields such as nanoelectronics and biotechnology in the near future. In recent years, self-assembled monolayers on silicon oxide have reached a high level of sophistication and have been combined with various lithographic patterning methods to develop new nanofabrication protocols and biological arrays. Nanoscale control over surface properties is of paramount importance to advance from 2D patterning to 3D fabrication.     

Patterning multiple aligned self-assembled monolayers using light

This work describes a method for patterning a gold substrate with multiple, aligned self-assembled monolayers (SAMs) using light at different wavelengths. It describes the synthesis and characterization of an alkanethiolate SAM that is photosensitive to light at both 220 and 365 nm. A photomask acts as an area-selective filter for light at 220 and 365 nm, and a single set of exposures at these two wavelengths through one photomask, without steps of alignment between the exposures, can produce three aligned SAMs on one gold substrate. We demonstrate the versatility of this method of photopatterning by modifying individual aligned SAMs chemically to produce surfaces having different properties. We characterize the modified SAMs using immunolabeling, matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy, and surface plasmon resonance spectroscopy. We also describe the patterning of two aligned SAMs that resist the adsorption of proteins and a third region that does not resist the adsorption of proteins. The ability to produce multiple, aligned patterns of SAMs in a single step, without alignment of photomasks in separate steps, increases the versatility of SAMs for studying a range of physical phenomena.     

Patterning of conducting polymers using charged self-assembled monolayers

We introduce a new approach to pattern conducting polymers by combining oppositely charged conducting polymers on charged self-assembled monolayers (SAMs). The polymer resist pattern behaves as a physical barrier, preventing the formation of SAMs. The patterning processes were carried out using commercially available conducting polymers: a negatively charged PEDOT/PSS (poly(3,4-ethylene-dioxythiophene)/poly(4-stylenesulphonic acid)) and a positively charged polypyrrole (PPy). A bifunctional NH 2 (positively charged) or COOH (negatively charged) terminated alkane thiol or silane was directly self-assembled on a substrate (Au or SiO 2). A suspension of the conducting polymers (PEDOT/PSS and PPy) was then spin-coated on the top surface of the SAMs and allowed to adsorb on the oppositely charged SAMs via an electrostatic driving force. After lift-off of the polymer resist, i.e., poly(methyl methacrylate, PMMA), using acetone, the conducting polymers remained on the charged SAMs surface. Optical microscopy, Auger electron spectroscopy, and atomic force microscopy reveal that the prepared nanolines have low line edge roughness and high line width resolution. Thus, conducting polymer patterns with high resolution could be produced by simply employing charged bifunctional SAMs. It is anticipated that this versatile new method can be applied to device fabrication processes of various nano- and microelectronics.     

Nanomechanics of the formation of DNA self-assembled monolayers and hybridization on microcantilevers

Biomolecular interactions over the surface of a microcantilever can produce its bending motion via changes of the surface stress, which is referred to nanomechanical response. Here, we have studied the interaction forces responsible for the bending motion during the formation of a self-assembled monolayer of thiolated 27-mer single-stranded DNA on the gold-coated side of a microcantilever and during the subsequent hybridization with the complementary nucleic acid. The immobilization of the single-stranded DNA probe gives a mean surface stress of 25 mN/m and a mean bending of 23 nm for microcantilevers with a length and thickness of about 200 microm and 0.8 microm, respectively. The hybridization with the complementary sequence could not be inferred from the nanomechanical response. The nanomechanical response was compared with data from well-established techniques such as surface plasmon resonance and radiolabeling, to determine the surface coverage and study the intermolecular forces between neighboring DNA molecules anchored to the microcantilever surface. From both techniques, an immobilization surface density of 3 x 10(12) molecules/cm(2) and a hybridization efficiency of 40% were determined. More importantly, label-free hybridization was clearly detected in the same conditions with a conventional sensor based on surface plasmon resonance. The results imply that the nanomechanical signal during the immobilization process arises mainly from the covalent attachment to the gold surface, and the interchain interactions between neighboring DNA molecules are weak, producing an undetectable surface stress. We conclude that detection of nucleic acid hybridization with nanomechanical sensors requires reference cantilevers to remove nonspecific signals, more sensitive microcantilever geometries, and immobilization chemistries specially addressed to enhance the surface stress variations.     

Multipotential electrochemical detection of primer extension reactions on DNA self-assembled monolayers

Electroactive nucleoside triphosphates ("electrotides") have been incorporated into primers by DNA polymerase and detected on oligonucleotide surface-assembled monolayers. Four electrotides bearing three different electroactive moieties-ferrocene, vinylferrocene, and anthraquinone-are detected in four alternative formats.     

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.     

Characterization of transparent conducting oxide surfaces using self-assembled electroactive monolayers

The electronic properties of various transparent conducting oxide (TCO) surfaces are probed electrochemically via self-assembled monolayers (SAMs). A novel graftable probe molecule having a tethered trichlorosilyl group and a redox-active ferrocenyl functionality (Fc(CH2) 4SiCl3) is synthesized for this purpose. This molecule can be self-assembled via covalent bonds to form monolayers on various TCO surfaces. On as-received ITO, saturation coverage of 6.6 x 10(-10) mol/cm2 by a close-packed monolayer and an electron-transfer rate of 6.65 s(-1) is achieved after 9 h of chemisorption, as determined by cyclic voltammetry (CV) and synchrotron X-ray reflectivity. With this molecular probe, it is found that O2 plasma-treated ITO has a significantly greater electroactive coverage of 7.9 x 10 (-10) mol/cm2 than as-received ITO. CV studies of this redox SAM on five different TCO surfaces reveal that MOCVD-derived CdO exhibits the greatest electroactive coverage (8.1 x 10(-10) mol/cm2) and MOCVD-derived ZITO (ZnIn2.0Sn1.5O) exhibits the highest electron transfer rate (7.12 s(-1)).     

Formation of gold-methanethiyl self-assembled monolayers

The energetics of formation of thiyl-gold self-assembled monolayers is investigated using density-functional theory simulations. It is found that the chemisorption of dimethyl disulfide on the reconstructed Au(111) (22 x radical3) surface is most favored at the fcc reconstruction stripe, with initial physisorption leading to disulfide dissociation, adatom/vacancy-pair formation, and then, at a coverage of 7.8% sulfur atoms per gold atom, surface reconstruction lifting. At higher coverages, monolayer formation proceeds similarly on the unreconstructed surface, leading to surface pitting. Formation of the analogous adatom/vacancy-pair bound dissociated adsorbate complex on exposure of the clean unreconstructed surface to methanethiol is shown to be endothermic, however.     

Electrochemistry of redox-active self-assembled monolayers

Redox-active self-assembled monolayers (SAMs) provide an excellent platform for investigating electron transfer kinetics. Using a well-defined bridge, a redox center can be positioned at a fixed distance from the electrode and electron transfer kinetics probed using a variety of electrochemical techniques. Cyclic voltammetry, AC voltammetry, electrochemical impedance spectroscopy, and chronoamperometry are most commonly used to determine the rate of electron transfer of redox-activated SAMs. A variety of redox species have been attached to SAMs, and include transition metal complexes (e.g., ferrocene, ruthenium pentaammine, osmium bisbipyridine, metal clusters) and organic molecules (e.g., galvinol, C₆₀). SAMs offer an ideal environment to study the outer-sphere interactions of redox species. The composition and integrity of the monolayer and the electrode material influence the electron transfer kinetics and can be investigated using electrochemical methods. Theoretical models have been developed for investigating SAM structure. This review discusses methods and monolayer compositions for electrochemical measurements of redox-active SAMs.     

Smectic liquid crystal alignment using mechanically rubbed n-octadecylsiloxane self-assembled monolayers

In recent years a variety of techniques has appeared for the fabrication and manipulation of self-assembled monolayers (SAMs). This development now offers new tools for the study and control at the molecular level of the interaction of liquid crystals (LCs) with solid surfaces, a research area of great importance for liquid crystal applications. In this paper we show that mechanically rubbed octadecylsiloxane SAMs generate a novel surface alignment of LCs in which the in-plane surface anisotropy usually accompanying rubbing is operative, but only for smectics in which the mean molecular long axis, [ncirc], is tilted from the layer normal. On our SAMs smectic phases align with the layers parallel to the SAM surface, and in tilted smectics the surface component of [ncirc] is along the rubbing direction. This anisotropy is absent in the nematic phases which align with [ncirc] strictly normal to the surface. This behaviour can be understood in terms of a rubbed SAM monolayer surface, which is low energy, molecularly smooth, and rendered anisotropic by the rubbing. UV irradiation of rubbed SAMs gave excellent planar alignment ([ncirc] parallel to the surface). This type of control over LC alignment has not been previously reported.     

Adsorption behavior of plasmid DNA on binary self-assembled monolayers modified gold substrates

Gold is known to have good biocompatibility because of its inert activity and the surface property can be easily tailored with self-assembled monolayers (SAMs). In previous works, gold surfaces were tailored with homogeneously mixed amine and carboxylic acid functional groups to generate surfaces with a series of isoelectronic points (IEPs). In other words, by tailoring the chemical composition in binary SAMs, different surface potentials can be obtained under controlled pH environments. To understand how the surface potentials affect the interaction at the interface, a binary-SAMs-modified Au electrode on a quartz crystal microbalance with dissipation detection (QCM-D) was used owing to the high weight sensitivity of QCM-D. In QCM-D, the frequency shift and the energy dissipation are monitored simultaneously to determine the adsorption behaviors of the plasmid DNA to surfaces of various potentials in Tris-buffered NaCl solutions of different pH. The results revealed that the plasmid DNA can be adsorbed on the SAM-modified surfaces electrostatically; thus, in general, the amount of adsorbed plasmid DNA decreased with increasing environmental pH and the decreasing ratio of the amine functional groups on the surfaces owing to weaker positive potentials on the surface. For the high amine-containing surfaces, due to the strong electrostatic attraction, denser films were observed, and thus, the apparent thickness decreased slightly. The negatively charged carboxylic acid surfaces can still adsorb the negatively charged plasmid DNA at some conditions. In other words, the electrostatic model cannot explain the adsorption behavior completely, and the induced dipole (Debye) interaction between the charged and polarizable molecules needs to be considered as well.     

Structural characterization of self-assembled monolayers of neoglycoconjugates using atomic force microscopy

Thiolated self-assembled monolayers of carbohydrates may serve as useful polyvalent tools to mimic the organized presentation of such molecules at the cell surface. SAMs presenting the disaccharide maltose as a neoglycoconjugate were produced, and the structure was studied by high resolution atomic force microscopy. The molecules form highly ordered structures on a gold (111) surface, with lattice parameters determined by the linker moiety rather than the headgroup.     

Morphosynthesis of strontianite nanowires using polyacrylate templates tethered onto self-assembled monolayers

Strontianite nanowires have been synthesized on self-assembled monolayers (SAM) in the presence of polyacrylate templates. The morphology of this product exhibits characteristic differences from that of products obtained in the absence of polyacrylate. It is demonstrated that the template-induced crystallization process involves the interaction between the SAM surface, polyacrylate (a dissolved polyelectrolyte), and the cations/anions in solution. By the combination of these components, hierarchically ordered mineral hybrid structures are formed.     

Direct patterning of self-assembled monolayers on gold using a laser beam

The development of a methodology to manipulate surface properties of a self-assembled monolayer (SAM) of alkanethiol on a gold film using direct laser patterning is the objective of this paper. The present study demonstrates proof of the concept for the feasibility of laser patterning monolayers and outlines theoretical modeling of the process to predict the resulting feature size. This approach is unique in that it eliminates the need for photolithography, is noncontact, and can be extended to other systems such as SAMs on silicon wafers or potentially polymeric substrates. A homogeneous SAM made of 1-hexadecanethiol is formed on a 300-A sputtered film of gold (supported by a soda lime glass substrate). Localized regions are then desorbed by scanning the focal spot of a 488-nm continuous-wave argon ion laser beam under a nitrogen atmosphere. The desorption occurs as a result of a high substrate temperature produced by the moving laser beam with a Gaussian spatial profile at a constant speed of 200 microm/s. After completing the scans, the sample is dipped into a dilute solution of 16-mercaptohexadecanoic acid and a hydrophilic monolayer self-assembles along the previously irradiated regions. The resultant lines are viewed, and line widths are measured using both wetting with tridecane under a light microscope and scanning electron microscopy. Using the direct laser patterning method, we have produced straight line patterns with widths of 28-170 microm. A thermal model was constructed to predict the line width of the desorbed monolayer. The effect of the laser power, beam waist, and temperature dependence of the substrate conductivity on the theoretical predictions is considered. It is shown that the theoretical predictions are in good agreement with the experimental results, and, thus, the model can effectively be used to predict experimental results.     

Electrochemical studies on the permeable characteristics of thiol-modified double-stranded DNA self-assembled monolayers on gold

In this article we studied the permeable characteristics of thiol-modified double-stranded DNA (ds-DNA) self-assembled monolayers (SAMs) on a gold substrate assembled under different NaCl concentrations by electrochemical methods. It was based on the inspection of five important parameters including interfacial capacitance (C), phase angle (Φ(1?Hz)), ions transfer resistance (R(it)*), current density difference (Δj) and electron transfer rate (k(et)) through cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Three sections were included: (1) Investigation of the relationships of C, Φ(1?Hz), R(it)*, Δj and k(et) with NaCl concentrations and comparison with the reports from literature. Experimental results showed that ds-DNA-SAMs were permeable films. (2) Construction of a simple model for exploring the permeable characteristics of ds-DNA-SAMs on gold. (3) Confirmation of the simple model by chronocoulometry (CC) and application of the model to explain the permeable mechanism. This study was significant for exploring the mechanism of electron transfer through the interior of ds-DNA duplex helix.     

Measurement of the kinetics of photo-oxidation of self-assembled monolayers using friction force microscopy

The advancement of molecular nanotechnology requires new tools for the characterization of surface chemical reactivity with nanometer spatial resolution. While spectroscopy on sub-100 nm length scales remains challenging, friction force microscopy (FFM) is a promising tool for the characterization of molecular materials, although to date it has been little used in studies of surface reactivity. Here we report the use of FFM to measure the kinetics of photo-oxidation of self-assembled monolayers (SAMs) of alkanethiols adsorbed on gold surfaces. Two alternative approaches (analysis of friction-load plots and the use of line sections through images of patterned materials) are compared and found to yield data in very good agreement, with rate constants being found to be in good agreement despite being carried out on different microscopes. The use of line-section analysis provides a convenient method for the quantification of the extent of reaction in nanometer-scale patterns created in SAMs by the novel approach of scanning near-field photolithography.     

Water penetration of damaged self-assembled monolayers

The interaction of water with self-assembled monolayers (SAMs) on amorphous silica is investigated using classical molecular dynamics simulation. Damage is induced through shear simulations with model atomic force microscopy (AFM) tips and separately with controlled extraction. We find that SAM coatings that have been slightly damaged (by normal loads close to 10 nN from a 10-nm-diameter AFM tip) are susceptible to water penetration and migration to the underlying hydrophilic substrate. The controlled damage studies indicate that the presence of water tends to heal damage below a threshold radius and exploits and magnifies damage above this threshold. For the systems studied here, Si(OH)3(CH2)10CH3 alkylsilane chains on amorphous silica, this threshold radius is between 0.5 and 1.0 nm.