Influence of Surface Structure on Single or Mixed Component Self-Assembled Monolayers via in Situ Spectroelectrochemical Fluorescence Imaging of the Complete Stereographic Triangle on a Single Crystal Au Bead Electrode

FRET Imaging of Nonuniformly Distributed DNA SAMs on Gold Reveals the Role Played by the Donor/Acceptor Ratio and the Local Environment in Measuring the Rate of Hybridization

Mixed DNA SAMs labeled with a fluorophore (either AlexaFluor488 or AlexaFluor647) were prepared on a single crystal gold bead electrode using potential-assisted thiol exchange and studied using Förster resonance energy transfer (FRET). A measure of the local environment of the DNA SAM (e.g., crowding) was possible using FRET imaging on these surfaces since electrodes prepared this way have a range of surface densities (Γ_DNA). The FRET signal was strongly dependent on Γ_DNA and on the ratio of AlexaFluor488 to AlexaFluor647 used to make the DNA SAM, which were consistent with a model of FRET in 2D systems. FRET was shown to provide a direct measure of the local DNA SAM arrangement on each crystallographic region of interest providing a direct assessment of the probe environment and its influence on the rate of hybridization. The kinetics of duplex formation for these DNA SAMs was also studied using FRET imaging over a range of coverages and DNA SAM compositions. Hybridization of the surface-bound DNA increased the average distance between the fluorophore label and the gold electrode surface and decreased the distance between the donor (D) and acceptor (A), both of which result in an increase in FRET intensity. This increase in FRET was modeled using a second order Langmuir adsorption rate equation, reflecting the fact that both D and A labeled DNA are required to become hybridized to observe a FRET signal. The self-consistent analysis of the hybridization rates on low and high coverage regions on the same electrode showed that the low coverage regions achieved full hybridization 5× faster than the higher coverage regions, approaching rates typically found in solution. The relative increase in FRET intensity from each region of interest was controlled by manipulating the donor to acceptor composition of the DNA SAM without changing the rate of hybridization. The FRET response can be optimized by controlling the coverage and the composition of the DNA SAM sensor surface and could be further improved with the use of a FRET pair with a larger (e.g., > 5 nm) Förster radius.

Redox-Controlled Energy Transfer Quenching of Fluorophore-Labeled DNA SAMs Enables In Situ Study of These Complex Electrochemical Interfaces

Interfaces modified by a molecular monolayer can be challenging to study, particularly in situ, requiring novel approaches. Coupling electrochemical and optical approaches can be useful when signals are correlated. Here we detail a methodology that uses redox electrochemistry to control surface-based fluorescence intensity for detecting DNA hybridization and studying the uniformity of the surface response. A mixed composition single-strand DNA SAM was prepared using potential-assisted thiol exchange with two alkylthiol-modified ssDNAs that were either labeled with a fluorophore (AlexaFluor488) or a methylene blue (MB) redox tag. A significant change in fluorescence was observed when reducing MB to colorless leuco-MB. In situ fluorescence microscopy on a single-crystal gold bead electrode showed that fluorescence intensity depended on (1) the potential controlling the oxidation state of MB, (2) the surface density of DNA, (3) the MB:AlexFluor488 ratio in the DNA SAM, and (4) the local environment around the DNA SAM. MB efficiently quenched AlexaFluor488 fluorescence. Reduction of MB showed a significant increase in fluorescence resulting from a decrease in quenching or energy transfer efficiency. Hybridization of DNA SAMs with its unlabeled complement showed a large increase in fluorescence due to MB reduction for surfaces with sufficient DNA coverage. Comparing electrochemical-fluorescence measurements to electrochemical (SWV) measurements showed an improvement in detection of a small fraction of hybridized DNA SAM for surfaces with optimal DNA SAM composition and coverage. Additionally, this coupled electrochemical redox-fluorescence microscopy method can measure the spatial heterogeneity of electron-transfer kinetics and the influence of the local interfacial environment.

Improved Thermal Stability and Homogeneity of Low Probe Density DNA SAMs Using Potential-Assisted Thiol-Exchange Assembly Methods

Methods for producing DNA SAM-based sensors with improved thermal stability and control over the homogeneity of low DNA probe density will enable advanced sensor development. The thermal stability of low-coverage DNA SAMs was studied for surfaces prepared using potential-assisted thiol exchange (E_dep) and compared to DNA SAMs prepared without control over the substrate potential (OCP_dep). Both surface preparation methods were studied using in situ fluorescence microscopy and electrochemistry with fluorophore or redox-modified DNA SAMs on a single-crystal gold bead electrode. Fluorescence microscopy showed that the influence of the underlying surface crystallography was important in both cases. The highest thermal stability was realized for square or rectangular surface atomic structure (e.g., surfaces from 110 to 100). The 111 and related surfaces were the least thermally stable. The low DNA coverage surfaces prepared by E_dep had better thermal stability and higher DNA probe mobility as compared to OCP_dep-prepared surfaces with the similar coverage. These results were correlated with methylene blue redox-tagged DNA probes, which directly measured the average DNA coverage. Both methods indicated that E_dep DNA SAMs were more uniformly distributed across the electrode surface, while the surfaces prepared via OCP_dep assembled into clusters with reduced mobility. The potential-assisted thiol-exchange approach to preparing low-coverage DNA SAMs was shown to quickly create modified surfaces that were consistent, had mobility characteristics which should yield superior DNA hybridization efficiencies, and having greater thermal stability which will translate into a longer shelf-life.

Molecularly-tunable nanoelectrode arrays created by harnessing intermolecular interactions

Intermolecular interactions play a critical role in the binding strength of molecular assemblies on surfaces. The ability to harness them enables molecularly-tunable interfacial structures and properties. Herein we report the tuning of the intermolecular interactions in monolayer assemblies derived from organothiols of different structures for the creation of nanoelectrode arrays or ensembles with effective mass transport by a molecular-level perforation strategy. The homo- and hetero-intermolecular interactions can be fully controlled, which is demonstrated not only by thermodynamic analysis of the fractional coverage but also by surface infrared reflection absorption and X-ray photoelectron spectroscopic characterizations. This understanding enables controllable electrochemical perforation for the creation of ensembles or arrays of channels across the monolayer thickness with molecular and nanoscale dimensions. Redox reactions on the nanoelectrode array display molecular tunability with a radial diffusion characteristic in good agreement with theoretical simulation results. These findings have implications for designing membrane-type ion-gating, electrochemical sensing, and electrochemical energy storage devices with molecular level tunability.

Intermolecular interactions in monolayer assembly are harnessed for creating molecularly-tunable nanoelectrode arrays or ensembles.

Thermal Stability of Thiolated DNA SAMs in Buffer: Revealing the Influence of Surface Crystallography and DNA Coverage via In Situ Combinatorial Surface Analysis

The thermal stability of thiol based DNA SAMs prepared on gold surfaces is an important parameter that is correlated to sensor lifetime. The thermal stability of DNA SAMs was evaluated in aqueous buffer through the use of fluorophore labeled DNA, a single crystal gold bead electrode, and microscopy. The stability of different crystallographic regions on the electrode was studied for thermal treatments up to 95 °C for 90 min. Using a in situ combinatorial surface analytical measurement showed that the crystallography of the underlying gold surface played a significant role, with the square or rectangular lattices (e.g., 110, 100, 210) having the highest stability. Surfaces with hexagonal lattices (e.g., 111, 311, 211) were less stable toward thermal treatments. These crystallographic trends were observed for both high and low coverage DNA SAMs. High coverage DNA SAMs were the most stable, with stability decreasing with decreasing coverage on average. Increasing DNA SAM coverage appears to slow the kinetics of thermal desorption, but the coordination to the underlying surface determined their relative stability. Preparing the DNA SAMs under nominally similar conditions were found to create surfaces that were similar at room temperature, but had significantly different thermal stability. Optimal DNA sensing with these surfaces most often requires low coverage DNA SAMs which results in poor thermal stability, which is predictive of a poor shelf life, making optimization of both parameters challenging. Furthermore, the crystallographically specific results should be taken into account when studying the typically used polycrystalline substrates since the underlying surface crystallography maybe different for different samples. It appears that preparing DNA SAMs with low coverage and significant thermal stability will be challenging using the current SAM preparation procedures.

Measuring and Controlling the Local Environment of Surface-Bound DNA in Self-Assembled Monolayers on Gold When Prepared Using Potential-Assisted Deposition

DNA self-assembled monolayers (SAMs) were prepared using potential-assisted deposition on clean gold single-crystal bead electrodes under a number of conditions (constant or square-wave potential perturbations in TRIS or phosphate immobilization buffers with and without Cl^-). The local environment around the fluorophore-labeled DNA tethered to the electrode surface was characterized using in situ fluorescence microscopy during electrochemical measurements as a function of the underlying surface crystallography. Potential-assisted deposition from a TRIS buffer containing Cl^- created DNA SAMs that were uniformly distributed on the surface with little preference to the underlying crystallography. A constant (+0.4 V/SCE) or a square-wave potential perturbation (+0.4 to -0.3 V/SCE, 50 Hz) resulted in similar DNA-modified surfaces in TRIS immobilization buffer. Deposition using a square-wave potential without Cl^- resulted in lower DNA surface coverage. Despite this, the local environment around the DNA in the SAM appears to be densely packed. This implies the formation of clusters of densely packed DNA in the SAM. This effect was also demonstrated when depositing from a phosphate buffer. DNA clusters were significantly reduced when Cl^- was present in the buffer. Clusters were most prevalent on the low-index plane surfaces (e.g., {111} and {100}) and less on the higher-index planes (e.g., {210} or {311}). A mechanism is proposed to rationalize the formation of DNA-clustered regions for deposition using a square-wave potential perturbation. The conditions for creating clusters of DNA in a SAM or for preventing these clusters from forming provide an approach for tailoring the surfaces used for biosensing.

Small Surface, Big Effects, and Big Challenges: Toward Understanding Enzymatic Activity at the Inorganic Nanoparticle-Substrate Interface

Enzymes are important biomarkers for molecular diagnostics and targets for the action of drugs. In turn, inorganic nanoparticles (NPs) are of interest as materials for biological assays, biosensors, cellular and in vivo imaging probes, and vectors for drug delivery and theranostics. So how does an enzyme interact with a NP, and what are the outcomes of multivalent conjugation of its substrate to a NP? This invited feature article addresses the current state of the art in answering this question. Using gold nanoparticles (Au NPs) and semiconductor quantum dots (QDs) as illustrative materials, we discuss aspects of enzyme structure-function and the properties of NP interfaces and surface chemistry that determine enzyme-NP interactions. These aspects render the substrate-on-NP configurations far more complex and heterogeneous than the conventional turnover of discrete substrate molecules in bulk solution. Special attention is also given to the limitations of a standard kinetic analysis of the enzymatic turnover of these configurations, the need for a well-defined model of turnover, and whether a "hopping" model can account for behaviors such as the apparent acceleration of enzyme activity. A detailed and predictive understanding of how enzymes turn over multivalent NP-substrate conjugates will require a convergence of many concepts and tools from biochemistry, materials, and interface science. In turn, this understanding will help to enable rational, optimized, and value-added designs of NP bioconjugates for biomedical and clinical applications.

Electrodepositing DNA Self-Assembled Monolayers on Au: Detailing the Influence of Electrical Potential Perturbation and Surface Crystallography

The preparation of DNA self-assembled monolayers (SAMs) on single-crystal gold bead electrodes using an applied potential is evaluated with in situ electrochemical fluorescence microscopy. Applying a constant deposition potential or a square-wave potential perturbation during the formation of DNA SAMs is compared for two different modification methods: DNA SAM formation on a clean gold surface followed by alkythiol backfilling (as is typically done in the literature) or via thiol-exchange on an alkylthiol-modified gold surface. DNA SAMs prepared from a chloride-containing deposition buffer were not significantly different when using either square-wave potential perturbation or at a constant applied potential even when considering different surface crystallographies. Greater variations were observed when applying more positive potentials for both DNA thiol-exchange and DNA adsorption on clean Au. Our results suggest that using either a constant potential or a square-wave potential perturbation for 5 min both create defects by weakening the gold-thiol interaction. When the deposition is performed with the adsorption of chloride ions from the electrolyte, the electrodeposition results in a similar increase in DNA coverage when compared to depositions performed at open circuit potentials.

Application of FRET Microscopy to the Study of the Local Environment and Dynamics of DNA SAMs on Au Electrodes

Immobilized DNA probe strands self-assembled on an electrode surface are the bases of many electrochemically based biosensors. Control or measurement of the local environment around each DNA molecule tethered to the electrode surface is needed because the local environment can influence the binding or hybridization efficiency of the target in solution. Measurement of this local environment in buffer or under electrochemical control can be challenging. Here we demonstrate the use of fluorescence microscopy and a Förster resonance energy transfer (FRET) methodology to characterize multicomponent DNA SAMs. The DNA SAMs that were studied were composed of a series of mole fraction ratios of alkylthiol-modified DNA which was labeled with either AlexaFluor488 or AlexaFluor647, a FRET donor and acceptor, respectively. The DNA SAMs were hybridized before assembly onto the electrode surface. Wide-field filter-based FRET microscopy was used to study the assembly of DNA SAMs onto gold bead electrodes. These single-crystal gold bead electrodes contain many surface crystallographic regions which enable the comparison of the adsorbed DNA local environment. These surfaces show that most surface modifications are uniformly prepared, and the FRET efficiency can be explained through simple surface density considerations. The FRET efficiency for different compositions of the donor and acceptor for these regions is also explained through 2D FRET modeling. Not all surfaces were similar to the (111) and (110) regions showing deviations from the expected FRET behavior. Also demonstrated is FRET imaging using a confocal microscope. This approach proves useful in the analysis of a more dynamic system, such as the analysis of reductive desorption of the mixed-component DNA SAM. FRET microscopy is useful for surface analysis of the DNA local environment, enabling a measure of the surface modification, local density, and clustering and eventually a new detection modality.

Direct Mapping of Heterogeneous Surface Coverage in DNA-Functionalized Gold Surfaces with Correlated Electron and Fluorescence Microscopy

The characterization of biofunctionalized surfaces such as alkanethiol self-assembled monolayers (SAMs) on gold modified with DNA or other biomolecules is a challenging analytical problem, and access to a routine method is desirable. Despite substantial investigation from structural and mechanistic perspectives, robust and high-throughput metrology tools for SAMs remain elusive but essential for the continued development of these devices. We demonstrate that scanning electron microscopy (SEM) can provide image contrast of the molecular interface during SAM functionalization. The high-speed, large magnification range, and ease of use make this widely available technique a powerful platform for measuring the structure and composition of SAM surfaces. This increased throughput allows for a better understanding of the nonideal spatial heterogeneity characteristic of SAMs utilized in real-world conditions. SEM image contrast is characterized through the use of fluorescently labeled DNA, which enables correlative SEM and fluorescence microscopy. This allows identification of the DNA-modified regions at resolutions that approach the size of the biomolecule. The effect of electron beam irradiation dose is explored, which leads to straightforward lithographic patterning of DNA SAMs with nanometer resolution and with control over the surface coverage of specifically adsorbed DNA.

Recent advances in spectroelectrochemistry

The integration of two quite different techniques, conventional electrochemistry and spectroscopy, into spectroelectrochemistry (SEC) provides a complete description of chemically driven electron transfer processes and redox events for different kinds of molecules and nanoparticles. SEC possesses interdisciplinary advantages and can further expand the scopes in the fields of analysis and other applications, emphasizing the hot issues of analytical chemistry, materials science, biophysics, chemical biology, and so on. Considering the past and future development of SEC, a review on the recent progress of SEC is presented and selected examples involving surface-enhanced Raman scattering (SERS), ultraviolet-visible (UV-Vis), near-infrared (NIR), Fourier transform infrared (FTIR), fluorescence, as well as other SEC are summarized to fully demonstrate these techniques. In addition, the optically transparent electrodes and SEC cell design, and the typical applications of SEC in mechanism study, electrochromic device fabrication, sensing and protein study are fully introduced. Finally, the key issues, future perspectives and trends in the development of SEC are also discussed.

Quantifying the Selective Modification of Au(111) Facets via Electrochemical and Electroless Treatments for Manipulating Gold Nanorod Surface Composition

Manipulating the composition of a mixed alkylthiol self-assembled monolayer (SAM) modified gold surface using both electrochemical and electroless methods is demonstrated. Through the use of fluorophore labeled thiolated DNA and in situ fluorescence microscopy with a gold single crystal bead electrode, a procedure was developed to study and quantify the selective desorption of an alkylthiolate SAM. This method enabled a self-consistent measurement of the removal of the SAM from the 111 surface compared to the 100 surface region at various potentials. A 20-fold increase in the electrochemical removal and replacement of the SAM from the 111 surface over the 100 surface was realized at -0.8 V/AgAgCl. A related procedure was developed for the solution-based electroless removal of the SAM using NaBH₄ achieving a similar selectivity at the same potential. Unfortunately, in the electroless process fine control over the reducing potential was difficult to achieve. In addition, working in the presence of O₂ complicates the solution potential measurement due to depolarization by the reduction of O₂, resulting in a less clear relationship between selectivity and measured solution potential. Interestingly, the electrochemical method was not disturbed by the presence of O₂. In preparation for work with Au nanorods, electrochemical measurements were performed in electrolyte that included 1 mM CTAB and was found to not interfere with this method. Preliminary results are promising for using this methodology for treatment of acid-terminated alkylthiol modified Au nanorods.

Nanoscale Chemical Imaging of Interfacial Monolayers by Tip-Enhanced Raman Spectroscopy

We report an investigation of interfacial fluorinated hydrocarbon (carboxylic-fantrip) monolayers by nanoscale imaging using tip-enhanced Raman spectroscopy (TERS) and density functional theory (DFT) calculations. By comparing TERS images of a sub-monolayer prepared by spin-coating and a π-π-stacked monolayer on Au(111) in which the molecular orientation is confined, specific Raman peaks shift and line widths narrow in the transferred LB monolayer. Based on DFT calculations that take into account dispersion corrections and surface selection rules, these specific effects are proposed to originate from π-π stacking and molecular orientation restriction. TERS shows the possibility to distinguish between a random and locked orientation with a spatial resolution of less than 10 nm. This work combines experimental TERS imaging with theoretical DFT calculations and opens up the possibility of studying molecular orientations and intermolecular interaction at the nanoscale and molecular level.

Surface-enhanced Raman scattering on a silver film-modified Au nanoparticle-decorated SiO2 mask array

SERS of R6G absorbed on this developed array exhibits a higher intensity by ca. 30-fold, as compared with that of R6G absorbed on the Au NP-based array without the modification of Ag films.