A Method for Determining the Actual Rate of Orientation Switching of DNA Self-Assembled Monolayers Using Optical and Electrochemical Frequency Response Analysis

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.

Potential-Modulated Total Internal Reflection Fluorescence for Measurement of the Electron Transfer Kinetics of Submonolayers on Optically Transparent Electrodes

An electroreflectance method to determine the electron transfer rate constant of a film of redox-active chromophores immobilized on an optically transparent electrode when the surface coverage of the film is very low (<0.1 monolayer) is described herein. The method, potential-modulated total internal reflection fluorescence (PM-TIRF) spectroscopy, is a fluorescence version of potential-modulated attenuated total reflection (PM-ATR) spectroscopy that is applicable when the immobilized chromophores are luminescent. The method was tested using perylene diimide (PDI) molecules functionalized with p-phenylene phosphonic acid (PA) moieties that bind strongly to indium-tin oxide (ITO). Conditions to prepare PDI-phenyl-PA films that exhibit absorbance and fluorescence spectra characteristic of monomeric (i.e., nonaggregated) molecules were identified; the electrochemical surface coverage was approximately 0.03 monolayer. The tilt angle of the long axis of the PDI molecular plane is 58° relative to the ITO surface normal, 25° greater than the tilt angle of aggregated PDI-phenyl-PA films, which have a surface coverage of approximately one monolayer. The more in-plane orientation of monomeric films is likely due to the absence of cofacial π-π interactions present in aggregated films and possibly a difference in PA-ITO binding modes. The electron transfer rate constant (k_s,opt) of monomeric PDI-phenyl-PA films was determined using PM-TIRF and compared with PM-ATR results obtained for aggregated films. For PDI monomers, k_s,opt = 3.8 × 10³ s^-1, which is about 3.7-fold less than k_s,opt for aggregated films. The slower kinetics are attributed to the absence of electron self-exchange between monomeric PDI molecules. Differences in the electroactivity of the binding sites on the ITO electrode surface also may play a role. This is the first demonstration of PM-TIRF for determining electron transfer rate constants at an electrode/organic film interface.