Activationless Electron Transfer of Redox-DNA in Electrochemical Nanogaps.

Our recent discovery of decreased reorganization energy in electrode-tethered redox-DNA systems prompts inquiries into the origin of this phenomenon and suggests its potential use to lower the activation energy of electrochemical reactions. Here, we show that the confinement of the DNA chain in a nanogap amplifies this effect to an extent to which it nearly abolishes the intrinsic activation energy of electron transfer. Employing electrochemical atomic force microscopy (AFM-SECM), we create sub-10 nm nanogaps between a planar electrode surface bearing end-anchored ferrocenylated DNA chains and an incoming microelectrode tip. The redox cycling of the DNA's ferrocenyl (Fc) moiety between the surface and the tip generates a measurable current at the scale of ∼10 molecules. Our experimental findings are rigorously interpreted through theoretical modeling and original molecular dynamics simulations (Q-Biol code). Several intriguing findings emerge from our investigation: (i) The electron transport resulting from DNA dynamics is many times faster than predicted by simple diffusion considerations. (ii) The current in the nanogap is solely governed by the electron transfer rate at the electrodes. (iii) This rate rapidly saturates as overpotentials applied to the nanogap electrodes increase, implying near-complete suppression of the reorganization energy for the oxidation/reduction of the Fc heads within confined DNA. Furthermore, evidence is presented that this may constitute a general, previously unforeseen, behavior of redox polymer chains in electrochemical nanogaps.

Ballistic Brownian Motion of Nanoconfined DNA.

Theoretical treatments of polymer dynamics in liquid generally start with the basic assumption that motion at the smallest scale is heavily overdamped; therefore, inertia can be neglected. We report on the Brownian motion of tethered DNA under nanoconfinement, which was analyzed by molecular dynamics simulation and nanoelectrochemistry-based single-electron shuttle experiments. Our results show a transition into the ballistic Brownian motion regime for short DNA in sub-5 nm gaps, with quality coefficients as high as 2 for double-stranded DNA, an effect mainly attributed to a drastic increase in stiffness. The possibility for DNA to enter the underdamped regime could have profound implications on our understanding of the energetics of biomolecular engines such as the replication machinery, which operates in nanocavities that are a few nanometers wide.

Electrochemical Shot Noise of a Redox Monolayer.

Redox monolayers are the base for a wide variety of devices including high-frequency molecular diodes or biomolecular sensors. We introduce a formalism to describe the electrochemical shot noise of such a monolayer, confirmed experimentally at room temperature in liquid. The proposed method, carried out at equilibrium, avoids parasitic capacitance, increases the sensitivity, and allows us to obtain quantitative information such as the electronic coupling (or standard electron transfer rates), its dispersion, and the number of molecules. Unlike in solid-state physics, the homogeneity in energy levels and transfer rates in the monolayer yields a Lorentzian spectrum. This first step for shot noise studies in molecular electrochemical systems opens perspectives for quantum transport studies in a liquid environment at room temperature as well as highly sensitive measurements for bioelectrochemical sensors.

Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics.

The mechanism responsible for electron transport within layers of redox DNA anchored to electrodes has been extensively studied over the last twenty years, but remains controversial. Herein, we thoroughly study the electrochemical behavior of a series of short, model, ferrocene (Fc) end-labeled dT oligonucleotides, terminally attached to gold electrodes, using high scan rate cyclic voltammetry complemented by molecular dynamics simulations. We evidence that the electrochemical response of both single-stranded and duplexed oligonucleotides is controlled by the electron transfer kinetics at the electrode, obeying Marcus theory, but with reorganization energies considerably lowered by the attachment of the ferrocene to the electrode via the DNA chain. This so far unreported effect, that we attribute to a slower relaxation of water around Fc, uniquely shapes the electrochemical response of Fc-DNA strands and, being markedly dissimilar for single-stranded and duplexed DNA, contributes to the signaling mechanism of E-DNA sensors.

Enzymatic activity of individual bioelectrocatalytic viral nanoparticles: dependence of catalysis on the viral scaffold and its length.

The enzymatic activity of tobacco mosaic virus (TMV) nanorod particles decorated with an integrated electro-catalytic system, comprising the quinoprotein glucose-dehydrogenase (PQQ-GDH) enzyme and ferrocenylated PEG chains as redox mediators, is probed at the individual virion scale by atomic force microscopy-scanning electrochemical atomic force microscopy (AFM-SECM). A marked dependence of the catalytic activity on the particle length is observed. This finding can be explained by electron propagation along the viral backbone, resulting from electron exchange between ferrocene moieties, coupled with enzymatic catalysis. Thus, the use of a simple 1D diffusion/reaction model allows the determination of the kinetic parameters of the virus-supported enzyme. Comparative analysis of the catalytic behavior of the Fc-PEG/PQQ-GDH system assembled on two differing viral scaffolds, TMV (this work) and bacteriophage-fd (previous work), reveals two distinct kinetic effects of scaffolding: An enhancement of catalysis that does not depend on the virus type and a modulation of substrate inhibition that depends on the virus type. AFM-SECM detection of the enzymatic activity of a few tens of PQQ-GDH molecules, decorating a 40 nm-long viral domain, is also demonstrated, a record in terms of the lowest number of enzyme molecules interrogated by an electrochemical imaging technique.

Converting Any Faradaic Current Generated at an Electrode under Potentiostatic Control into a Remote Fluorescence Signal.

We describe the development of an original faradaic current-to-fluorescence conversion scheme. The proposed instrumental strategy consists of coupling the electrochemical reaction of any species at an electrode under potentiostatic control with the fluorescence emission of a species produced at the counter electrode. In order to experimentally validate this scheme, the fluorogenic species resazurin is chosen as a fluorescent reporter molecule, and its complex reduction mechanism is first studied in unprecedented detail. This kinetic study is carried out by recording simultaneous cyclic voltammograms and voltfluorograms at the same electrode. Numerical simulations are used to account for the experimental current and fluorescence signals, to analyze their degree of correlation, and to decipher their relation to resazurin reduction kinetics. It is then shown that, provided that the reduction of resazurin takes place at a micrometer-sized electrode, the fluorescence emission perfectly tracks the faradaic current. By implementing this ideal configuration at the counter electrode of a potentiostatic setup, it is finally demonstrated that the oxidation reaction of a nonfluorescent species at the working electrode can be quantitatively transduced into simultaneous emission of fluorescence.

Redox-Immunofunctionalized Potyvirus Nanoparticles for High-Resolution Imaging by AFM-SECM Correlative Microscopy.

We present in this chapter a new experimental approach allowing the high resolution imaging of immune complexes on virus particles. Combined atomic force-electrochemical microscopy (AFM-SECM) is used to image the presence of ferrocene functionalized specific antibodies on the surface of potyvirus particles. For this purpose, potyviruses, flexuous filamentous phytoviruses with a high aspect ratio, have been chosen. This technique allows analysis of the distribution of antibody labeling over the virus population. But, more importantly, it opens up the imaging of immune complexes decorating a single viral particle. Finally, its high resolution allows the characterization in situ of the ultrastructure of a single immune complex on the particle.

Electrochemical Imaging of Dense Molecular Nanoarrays.

The aim of the present work is to explore the combination of atomic force electrochemical microscopy, operated in molecule touching mode (Mt/AFM-SECM), and of dense nanodot arrays, for designing an electrochemically addressable molecular nanoarray platform. A high density nanoarray of single grained gold nanodots (∼15 nm-diameter nanoparticles, 100 nm pitch) is decorated by a model molecular system, consisting of ferrocene (Fc) labeled polyethylene glycol (PEG) disulfide chains. We show that the high resolution of Mt/AFM-SECM enables the electrochemical interrogation of several hundreds of individual nanodots in a single image acquisition. As a result, the statistical dispersion of the nanodot molecular occupancy by Fc-PEG chains can be reliably quantified, evidencing that as little as a few tens of copies of redox-labeled macromolecules immobilized on individual nanodots can be detected. The electrochemical reactivity of individual nanodots can also be reliably sampled over a large population of nanodots. We evidence that the heterogeneous rate constant characterizing the electron transfer between the nanodots and the Fc heads displays some quantifiable variability but that the electron transfer remains in any case in the quasi-reversible regime. Overall, we demonstrate that Mt/AFM-SECM enables high throughput reading of dense nanoarrays, with a sensitivity and a read-out speed considerably higher than previously reported for scanning electrochemical microscopy (SECM) imaging of molecular microarrays.

The Potyvirus Particle Recruits the Plant Translation Initiation Factor eIF4E by Means of the VPg covalently Linked to the Viral RNA.

The viral protein genome-linked (VPg) of potyviruses is a protein covalently linked to the 5' end of viral RNA. It interacts with eIF4E, a component of the cellular translation initiation complex. It has been suggested that the 5' RNA-linked VPg could mimic the cellular mRNA cap, promoting synthesis of viral proteins. Here, we report evidence for recruitment of the plant eIF4E by Lettuce mosaic virus (LMV, potyvirus) particles via the 5' RNA-linked VPg. Analysis of the viral population was performed by enzyme-linked immunosorbent assay-based tests, either with crude extracts of LMV-infected tissues or purified viral particles. In both cases, LMV-VPg and LMV-eIF4E subpopulations could be detected. After reaching a maximum within the first 2 weeks postinoculation, these populations decreased and very few labeled particles were found later than 3 weeks postinoculation. The central domain of VPg (CD-VPg) was found to be exposed at the surface of the particles. Using a purified recombinant lettuce eIF4E and CD-VPg-specific antibodies, we demonstrate that the plant factor binds to the VPg via its central domain. Moreover, the plant eIF4E factor could be imaged at one end of the particles purified from LMV plant extracts, by immunoredox atomic force microscopy coupled to scanning electrochemical microscopy. We discuss the biological significance of these results.

Scaffolding of Enzymes on Virus Nanoarrays: Effects of Confinement and Virus Organization on Biocatalysis.

Organizing active enzyme molecules on nanometer-sized scaffolds is a promising strategy for designing highly efficient supported catalytic systems for biosynthetic and sensing applications. This is achieved by designing model nanoscale enzymatic platforms followed by thorough analysis of the catalytic activity. Herein, the virus fd bacteriophage is considered as an enzyme nanocarrier to study the scaffolding effects on enzymatic activity. Nanoarrays of randomly oriented, or directionally patterned, fd bacteriophage virus are functionalized with the enzyme glucose oxidase (GOx), using an immunological assembly strategy, directly on a gold electrode support. The scaffolding process on the virus capsid is monitored in situ by AFM (atomic force microscopy) imaging, while cyclic voltammetry is used to interrogate the catalytic activity of the resulting functional GOx-fd nanoarrays. Kinetic analysis reveals the ability to modulate the activity of GOx via nanocarrier patterning. The results evidence, for the first time, enhancement of the enzymatic activity due to scaffolding on a filamentous viral particle.

Electrochemical atomic force microscopy imaging of redox-immunomarked proteins on native potyviruses: from subparticle to single-protein resolution.

We show herein that electrochemical atomic force microscopy (AFM-SECM), operated in molecule touching (Mt) mode and combined with redox immunomarking, enables the in situ mapping of the distribution of proteins on individual virus particles and makes localization of individual viral proteins possible. Acquisition of a topography image allows isolated virus particles to be identified and structurally characterized, while simultaneous acquisition of a current image allows the sought after protein, marked by redox antibodies, to be selectively located. We concomitantly show that Mt/AFM-SECM, due to its single-particle resolution, can also uniquely reveal the way redox functionalization endowed to viral particles is distributed both statistically among the viruses and spatially over individual virus particles. This possibility makes Mt/AFM-SECM a unique tool for viral nanotechnology.

Probing the conformation and 2D-distribution of pyrene-terminated redox-labeled poly(ethylene glycol) chains end-adsorbed on HOPG using cyclic voltammetry and atomic force electrochemical microscopy.

The present paper aims at illustrating how end-attachment of water-soluble flexible chains bearing a terminal functional group onto graphene-like surfaces has to be carefully tuned to ensure the proper positioning of the functional moiety with respect to the anchoring surface. The model experimental system considered here consists of a layer of poly(ethylene glycol) (PEG) chains, bearing an adsorbing pyrene foot and a ferrocene (Fc) redox functional head, self-assembled onto highly oriented pyrolytic graphite (HOPG). Cyclic voltammetry is used to accurately measure the chain coverage and gain insights into the microenvironment experienced by the Fc heads. Molecule-touching atomic force electrochemical microscopy (Mt/AFM-SECM) is used to simultaneously probe the chain conformation and the position of the Fc heads within the layer, and also to map the 2D-distribution of the chains over the surface. This multiscale electrochemical approach allows us to show that whereas Fc-PEG-pyrene readily self-assembles to form extremely homogeneous layers, the strongly hydrophobic nature of graphite planes results in a complex coverage-dependent structure of the PEG layer due to the interaction of the ferrocene label with the HOPG surface. It is shown that, even though pyrene is known to adsorb particularly strongly onto HOPG, the more weakly adsorbing terminal ferrocene can also act as the chain anchoring moiety especially at low coverage. However we show that beyond a critical coverage value the Fc-PEG-pyrene chains adopt an ideal "foot-on" end-attached conformation allowing the Fc head to explore a volume away from the surface solely limited by the PEG chain elasticity.

Optimizing electrode-attached redox-peptide systems for kinetic characterization of protease action on immobilized substrates. Observation of dissimilar behavior of trypsin and thrombin enzymes.

In this work, we experimentally address the issue of optimizing gold electrode attached ferrocene (Fc)-peptide systems for kinetic measurements of protease action. Considering human α-thrombin and bovine trypsin as proteases of interest, we show that the recurring problem of incomplete cleavage of the peptide layer by these enzymes can be solved by using ultraflat template-stripped gold, instead of polished polycrystalline gold, as the Fc-peptide bearing electrode material. We describe how these fragile surfaces can be mounted in a rotating disk configuration so that enzyme mass transfer no longer limits the overall measured cleavage kinetics. Finally, we demonstrate that, once the system has been optimized, in situ real-time cyclic voltammetry monitoring of the protease action can yield high-quality kinetic data, showing no sign of interfering effects. The cleavage progress curves then closely match the Langmuirian variation expected for a kinetically controlled surface process. Global fit of the progress curves yield accurate values of the peptide cleavage rate for both trypsin and thrombin. It is shown that, whereas trypsin action on the surface-attached peptide closely follows Michaelis-Menten kinetics, thrombin displays a specific and unexpected behavior characterized by a nearly enzyme-concentration-independent cleavage rate in the subnanomolar enzyme concentration range. The reason for this behavior has still to be clarified, but its occurrence may limit the sensitivity of thrombin sensors based on Fc-peptide layers.

High-resolution mapping of redox-immunomarked proteins using electrochemical-atomic force microscopy in molecule touching mode.

We explore the possibility of using molecule touching atomic force electrochemical microcopy (Mt/AFM-SECM) for high-resolution mapping of proteins on conducting surfaces. The proposed imaging strategy relies on making surface-immobilized proteins electrochemically "visible" via redox-immunomarking by specific antibodies conjugated to poly(ethylene glycol) (PEG) chains terminated by redox ferrocene (Fc) heads. The flexibility and length of the PEG chains are such that, upon approaching a combined AFM-SECM microelectrode tip toward the surface, the Fc moieties can efficiently shuttle electrons from the surface to the tip. The so-generated SECM positive feedback tip current allows the specific localized detection of the sought protein molecules on the surface. This new electrochemical imaging scheme is validated experimentally on the basis of a model system consisting of mouse IgGs adsorbed onto electrode surfaces and recognized by Fc-PEG-labeled antimouse antibodies. In order to estimate the resolution of Mt/AFM-SECM for protein imaging, regular arrays of submicrometer-sized spots of mouse IgGs are fabricated onto gold electrode surfaces using particle lithography. The Fc-PEG-immunomarked mouse IgG spots are imaged by Mt/AFM-SECM operated in tapping mode. Both an electrochemical image, reflecting the surface distribution of the redox-labeled IgGs, and a topography image are then simultaneously and independently acquired, with a demonstrated resolution in the ~100 nm range. The strength of Mt/AFM-SECM imaging is to combine the nanometric resolution of AFM with the selectivity of the electrochemical detection, potentially allowing individual target proteins to be identified amidst similarly sized "nano objects" present on a conducting surface.

Touching surface-attached molecules with a microelectrode: mapping the distribution of redox-labeled macromolecules by electrochemical-atomic force microscopy.

We report on the development of a mediator-free electrochemical-atomic force microscopy (AFM-SECM) technique designed for high-resolution imaging of molecular layers of nanometer-sized redox-labeled (macro)molecules immobilized onto electrode surfaces. This new AFM-SECM imaging technique, we call molecule touching atomic force electrochemical microscopy (Mt/AFM-SECM), is based on the direct contact between surface-anchored molecules and an incoming microelectrode (tip). To validate the working-principle of this microscopy, we consider a model system consisting of a monolayer of nanometer long, flexible, polyethylene glycol (PEG) chains covalently attached by one extremity to a gold surface and bearing at their free end a ferrocene (Fc) redox tag. Using Mt/AFM-SECM in tapping mode, i.e., by oscillating the tip so that it comes in intermittent contact with the grafted chains, we show that the substrate topography and the distribution of the redox-tagged PEG chains immobilized on the gold surface can be simultaneously and independently imaged at the sub-100 nm scale. This novel type of SECM imaging may be found useful for characterizing the surface of advanced biosensors which use electrode-grafted, redox-tagged, linear biochains, such as peptides or DNA chains, as sensing elements. In principle, Mt/AFM-SECM should also permit in situ imaging of the distribution of any kind of macromolecules immobilized on electrode surfaces or simply conducting surfaces, provided they are labeled by a suitable redox tag.

Electrochemical atomic force microscopy using a tip-attached redox mediator for topographic and functional imaging of nanosystems.

We describe the development of a new type of high-resolution atomic force electrochemical microscopy (AFM-SECM), labeled Tarm (for tip-attached redox mediator)/AFM-SECM, where the redox mediator, a ferrocene (Fc), is tethered to the AFM-SECM probe via nanometer long, flexible polyethylene glycol (PEG) chains. It is demonstrated that the tip-attached ferrocene-labeled PEG chains effectively shuttle electrons between the tip and substrate, thus acting as molecular sensors probing the local electrochemical reactivity of a planar substrate. Moreover the Fc-PEGylated AFM-SECM probes can be used for tapping mode imaging, allowing simultaneous recording of electrochemical feedback current and of topography, with a vertical and a lateral resolution in the nanometer range. By imaging the naturally nanostructured surface of HOPG, we demonstrate that Tarm/AFM-SECM microscopy can be used to probe the reactivity of nanometer-sized active sites on surfaces. This new type of SECM microscopy, being, by design, free of the diffusional constraints of classical SECM, is expected to, in principle, enable functional imaging of redox nanosystems such as individual redox enzyme molecules.

Epifluorescence imaging of electrochemically switchable Langmuir-Blodgett films of Nafion.

A combination of electrochemistry and luminescence methods was exploited to obtain information on the electrochemical activity and homogeneity of Nafion Langmuir-Blodgett films. The redox behavior of the Ru(bpy)3(2+) probe incorporated in the Nafion film was monitored by epifluorescence microscopy. The photoluminescent images, recorded by a charge-coupled device (CCD) camera, reflect the distribution of the probe in the film, which resulted as very uniform, particularly in comparison with spin-coated films. Apparent diffusion coefficients (Dapp) determined by cyclic voltammetry for films of less than 10 layers are in the range of 1 x 10(-12) to 8 x 10(-12) cm(2) s(-1), that is, 2 orders of magnitude lower than values reported in the literature for spin-coated Nafion films. The application to the electrode of a potential able to oxidize the luminescent Ru(bpy)3(2+) to the nonluminescent Ru(bpy)3(3+) switched off the photoluminescence with a response time that for the LB films was much shorter than that for the spin-coated ones. Experimental evidence and calculations indicate that lowering of the film thickness down to the nanometric level is very effective in shortening the switching time, notwithstanding the lowering of the Dapp value in LB films.

Remote NADH imaging through an ordered array of electrochemiluminescent nanoapertures.

In this report, we present an ordered array comprising thousands of nanoapertures for the electrochemiluminescent (ECL) detection of NADH. It was fabricated on the distal face of a coherent optical fiber bundle. Such a high-density array of nanoapertures combines optical, imaging and electrochemical properties. Indeed, each nanoaperture is surrounded by a gold nanoring, which acts as an electrode material. The behavior of the array was characterized by cyclic voltammetry and it shows excellent electrochemical performances. NADH is the analyte, which is measured in presence of Ru(bpy)3(2+). The ruthenium complex mediates the NADH oxidation and this coenzyme acts as a co-reactant in the ECL mechanism. ECL light is generated at the distal face of the array by each gold ring electrode. A fraction of this ECL light is collected by the corresponding nanoaperture, transmitted through the optical fiber bundle and finally imaged on the proximal face with a CCD camera. In this work, we show that NADH concentration is remotely detected by an oxidative-reductive ECL mechanism. We present also some preliminary results about the ECL process of NADH with Ru(bpy)3(2+). The ECL behavior of NADH on gold surface is reported. The influence of the applied potential on the collected light intensity was investigated. The variation of the ECL intensity measured through the nanoaperture array with NADH concentration is linear. Remote ECL detection of NADH is spatially resolved over a large area with a micrometer resolution through the array. Therefore, such array integrates several complementary functions: ECL light generation, collection, transmission and remote imaging in an array format.

Remote fluorescence imaging of dynamic concentration profiles with micrometer resolution using a coherent optical fiber bundle.

Dynamic concentration profiles within the diffusion layer of an electrode were imaged in situ using fluorescence detection through a multichannel imaging fiber. In this work, a coherent optical fiber bundle is positioned orthogonal to the surface of an electrode and is used to report spatial and temporal micrometric changes in the fluorescence intensity of an initial fluorescent species. The fluorescence signal is directly related to the local concentration of a redox fluorescent reagent, which is electrochemically modulated by the electrode. Fluorescence images are collected through the optical fiber bundle during the oxidation of tris(2,2'-bipyridine)ruthenium(II) to ruthenium(III) at a diffusion-limited rate and allow the concentration profiles of Ru(II) reagent to be monitored in situ as a function of time. Tris(2,2'-bipyridine)ruthenium(II) is excited at 485 nm and emits fluorescence at 605 nm, whereas the Ru(III) oxidation state is not fluorescent. Our experiments emphasize the influence of two parameters on the micrometer spatial resolution: the numerical aperture of optical fibers within the bundle and the Ru(II) bulk concentration. The extent of the volume probed by each individual fiber of the bundle is discussed qualitatively in terms of a primary inner-filter effect and refractive index gradient. Experimentally measured fluorescence intensity profiles were found to be in very good agreement with concentration profiles predicted upon considering planar diffusion and thus validate the concept of this new application of imaging fibers. The originality of this remote approach is to provide a global view of the entire diffusion layer at a given time through one single image and to allow the time expansion of the diffusion layer to be followed quantitatively in real time.

Electrochemical modulation of remote fluorescence imaging at an ordered opto-electrochemical nanoaperture array.

An array of nanometer-sized apertures capable of electrochemically modulating the fluorescence of a model analyte is presented. The device, which combines near-field optical methods and ultramicroelectrode properties in an array format, is based on an etched coherent optical fiber bundle. Indeed, the fabrication steps produced an ordered array where each optical nanoaperture is surrounded by a ring-shaped gold nanoelectrode. The chronoamperometric behavior of the array shows stable diffusion-limited quasi-steady-state response. The model analyte, tris(2,2'-bipyridine) ruthenium, emits fluorescence in the Ru(II) state, but not in the oxidized Ru(III) state. Fluorescence is excited by visible light exiting from each nanoaperture since light is confined to the tip apex by the gold coating. A fraction of the isotropically emitted luminescence is collected by the same nanoaperture, transmitted by the corresponding fiber core and eventually detected by a charge-coupled device (CCD) camera. The array format provides a fluorescence image resolved at the nanometric scale which covers a large micrometric area. Therefore the high-density array plays a bridging role between these two fundamental scales. We established that the opto-electrochemical nanoapertures are optically independent. Fluorescence of the sample collected by each nanoaperture is modulated by changing the potential of the nanoring electrodes. Reversible electrochemical switching of remote fluorescence imaging is performed through the opto-electrochemical nanoaperture array itself. Eventually this ordered structure of nanometer light sources which are electrochemically manipulated provides promising photonic or electro-optical devices for various future applications. For example, such an array has potential in the development of a combined SNOM-electrochemical nanoprobe array to image a real sample concomitantly at the nanometer and micrometer scale.