Whereas spectroscopic and chromatographic techniques for the detection of small organic molecules have achieved impressive results, these methods are generally slow and cumbersome, and thus the development of a general means for the real-time, electronic detection of such targets remains a compelling goal. Here we demonstrate a potentially general, label-free electronic method for the detection of small-molecule targets by building a rapid, reagentless biosensor for the detection of cocaine. The sensor, based on the electrochemical interrogation of a structure-switching aptamer, specifically detects micromolar cocaine in seconds. Because signal generation is based on binding-induced folding, the sensor is highly selective and works directly in blood serum and in the presence of commonly employed interferents and cutting agents, and because all of the sensor components are covalently attached to the electrode surface, the sensor is also reusable: we achieve >99% signal regeneration upon a brief, room temperature aqueous wash. Given recent advances in the generation of highly specific aptamers, this detection platform may be readily adapted for the detection of other small molecules of a wide range of clinically and environmentally relevant small molecules.

Recent years have seen the development of a number of reagentless, electrochemical sensors based on the target-induced folding or unfolding of electrode-bound oligonucleotides, with examples reported to date, including sensors for the detection of specific nucleic acids, proteins, small molecules and inorganic ions. These devices, which are often termed electrochemical DNA (E-DNA) and E-AB (electrochemical, aptamer-based) sensors, are comprised of an oligonucleotide probe modified with a redox reporter (in this protocol methylene blue) at one terminus and attached to a gold electrode via a thiol-gold bond at the other. Binding of an analyte to the oligonucleotide probe changes its structure and dynamics, which, in turn, influences the efficiency of electron transfer to the interrogating electrode. This class of sensors perform well even when challenged directly with blood serum, soil and other complex, multicomponent sample matrices. This protocol describes the fabrication of E-DNA and E-AB sensors. The protocol can be completed in 12 h.

E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stem-loop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stemloop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor. We find that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons.

The development of a biosensor system capable of continuous, real-time measurement of smallmolecule analytes directly in complex, unprocessed aqueous samples has been a significant challenge, and successful implementation has been achieved for only a limited number of targets. Towards a general solution to this problem, we report here the Microfluidic Electrochemical Aptamer-based Sensor (MECAS) chip wherein we integrate target-specific DNA aptamers that fold, and thus generate an electrochemical signal, in response to the analyte with a microfluidic detection system. As a model, we demonstrate the continuous, real-time (~1 minute time resolution) detection of the small molecule drug cocaine at near physiological, low micromolar concentrations directly in undiluted, otherwise unmodified blood serum. We believe our approach of integrating folding-based electrochemical sensors with miniaturized detection systems may lay the ground work for the realtime, point-of-care detection of a wide variety of molecular targets.The capability to perform in situ, continuous, real-time monitoring of specific small molecules in complex, unprocessed aqueous samples is important for a broad spectrum of applications ranging from medical diagnostics to environmental monitoring. 1 However, successful implementation of such strategies has proven elusive, and thus far has been achieved for only a few, specialized targets (e.g., neurotransmitters, such as 5-hydroxytryptamine, 2 hydrogen ions 3 and glucose 4 ). The challenge of real-time sensing arises from the fact that, to meet this demanding application, a sensor needs not only be sensitive, stable and selective enough to deploy directly in complex sample matrices, but it also needs to be reagentless, regenerable and able to respond rapidly relative to the timescale with which the target concentration fluctuates.Previously-developed strategies for the real-time detection of small-molecule analytes have typically made use of sensors that measure changes in mass, 5 index of refraction 6 or charge 7 that occur when the target molecules bind to the sensor surface. Such measurements, however, suffer from often severe false positives; for example, it has proven difficult to discriminate between changes in mass arising from the binding of authentic target molecules and those *To whom all correspondence should be addressed. arising due to the non-specific adsorption of contaminants, which has significantly hindered the application of these adsorption-based sensors in complex samples, such as unprocessed clinical or environmental materials. [5][6][7] In contrast, sensors based on binding-induced conformational changes in a bimolecular probe [8][9] have proven more effective in rejecting such false positives. An example is the electrochemical, aptamer-based (E-AB) sensor platform, which operates via the target binding-induced folding of DNA and RNA aptamers and has been shown to work directly in blood serum, 10-12 crude cellular extracts, 13 soil extracts 14 and foodstuffs. 15 The high ...

We report an electrochemical, aptamer-based (E-AB) sensor for the detection of platelet-derived growth factor (PDGF) directly in blood serum. The E-AB approach employs alternating current voltammetry to monitor target-induced folding in a methylene blue-modified, PDGF-binding aptamer. The sensor is sensitive, highly selective, and essentially reagentless: we readily detect the BB variant of PDGF at 1 nM directly in undiluted, unmodified blood serum and at 50 pM (1.25 ng/mL) in serum-diluted 2-fold with aqueous buffer. The sensitivity and selectivity achieved by this sensor match or significantly exceed those of the best analogous optical approaches. For example, the detection limit attained in 50% serum is achieved against a >25 million-fold excess of contaminating blood proteins and represents a 4 order of magnitude improvement over the most sensitive optical PDGF aptasensor reported to date. Moreover, the E-AB sensor combines these promising attributes in a platform that is reusable, label-free, and electronic. Given these advantages, E-AB sensors appear well suited for implementation in portable microdevices directed at the direct detection of proteins and small molecules in complex, largely unprocessed clinical samples.