The Use of Xenonucleic Acids Significantly Reduces the In Vivo Drift of Electrochemical Aptamer-Based Sensors

Electrochemical aptamer-based sensors support the high-frequency, real-time monitoring of molecules-of-interest in vivo. Achieving this requires methods for correcting the sensor drift seen during in vivo placements. While this correction ensures EAB sensor measurements remain accurate, as drift progresses it reduces the signal-to-noise ratio and precision. Here, we show that enzymatic cleavage of the sensor's target-recognizing DNA aptamer is a major source of this signal loss. To demonstrate this, we deployed a tobramycin-detecting EAB sensor analog fabricated with the DNase-resistant "xenonucleic acid" 2'O-methyl-RNA in a live rat. In contrast to the sensor employing the equivalent DNA aptamer, the 2'O-methyl-RNA aptamer sensor lost very little signal and had improved signal-to-noise. We further characterized the EAB sensor drift using unstructured DNA or 2'O-methyl-RNA oligonucleotides. While the two devices drift similarly in vitro in whole blood, the in vivo drift of the 2'O-methyl-RNA-employing device is less compared to the DNA-employing device. Studies of the electron transfer kinetics suggested that the greater drift of the latter sensor arises due to enzymatic DNA degradation. These findings, coupled with advances in the selection of aptamers employing XNA, suggest a means of improving EAB sensor stability when they are used to perform molecular monitoring in the living body.

Codeposition Enhances the Performance of Electrochemical Aptamer-Based Sensors

Electrochemical aptamer-based (EAB) sensors, a minimally invasive means of performing high-frequency, real-time measurement of drugs and biomarkers in situ in the body, have traditionally been fabricated by depositing their target-recognizing aptamer onto an interrogating gold electrode using a "sequential" two-step method involving deposition of the thiol-modified oligonucleotide (typically for 1 h) followed by incubation in mercaptohexanol solution (typically overnight) to complete the formation of a stable, self-assembled monolayer. Here we use EAB sensors targeting vancomycin, tryptophan, and phenylalanine to show that "codeposition", a less commonly employed EAB fabrication method in which the thiol-modified aptamer and the mercaptohexanol diluent are deposited on the electrode simultaneously and for as little as 1 h, improves the signal gain (relative change in signal upon the addition of high concentrations of the target) of the vancomycin and tryptophan sensors without significantly reducing their stability. In contrast, the gain of the phenylalanine sensor is effectively identical irrespective of the fabrication approach employed. This sensor, however, appears to employ binding-induced displacement of the redox reporter rather than binding-induced folding as its signal transduction mechanism, suggesting in turn a mechanism for the improvement observed for the other two sensors. Codeposition thus not only provides a more convenient means of fabricating EAB sensors but also can improve their performance.

High-Affinity Aptamers for In Vitro and In Vivo Cocaine Sensing

The ability to quantify cocaine in biological fluids is crucial for both the diagnosis of intoxication and overdose in the clinic as well as investigation of the drug's pharmacological and toxicological effects in the laboratory. To this end, we have performed high-stringency in vitro selection to generate DNA aptamers that bind cocaine with nanomolar affinity and clinically relevant specificity, thus representing a dramatic improvement over the current-generation, micromolar-affinity, low-specificity cocaine aptamers. Using these novel aptamers, we then developed two sensors for cocaine detection. The first, an in vitro fluorescent sensor, successfully detects cocaine at clinically relevant levels in 50% human serum without responding significantly to other drugs of abuse, endogenous substances, or a diverse range of therapeutic agents. The second, an electrochemical aptamer-based sensor, supports the real-time, seconds-resolved measurement of cocaine concentrations in vivo in the circulation of live animals. We believe the aptamers and sensors developed here could prove valuable for both point-of-care and on-site clinical cocaine detection as well as fundamental studies of cocaine neuropharmacology.

Implantable Hydrogel-Protective DNA Aptamer-Based Sensor Supports Accurate, Continuous Electrochemical Analysis of Drugs at Multiple Sites in Living Rats

The ability to track the levels of specific molecules, such as drugs, metabolites, and biomarkers, in the living body, in real time and for long durations, would improve our understanding of health and our ability to diagnose, treat, and monitor disease. To this end, we are developing electrochemical aptamer-based (EAB) biosensors, a general platform supporting high-frequency, real-time molecular measurements in the living body. Here we report that the use of an agarose hydrogel protective layer for EAB sensors significantly improves their signaling stability when deployed in the complex, highly time-varying environments found in vivo. The improved stability is sufficient that these hydrogel-protected sensors achieved good baseline stability and precision when deployed in situ in the veins, muscles, bladder, or tumors of living rats without the use of the drift correction approaches traditionally required in such placements. Finally, our implantable gel-protective EAB sensors achieved good biocompatibility when deployed in vivo in the living rats without causing any severe inflammation.

Using seconds-resolved pharmacokinetic datasets to assess pharmacokinetic models encompassing time-varying physiology

AIM

Pharmacokinetics have historically been assessed using drug concentration data obtained via blood draws and bench-top analysis. The cumbersome nature of these typically constrains studies to at most a dozen concentration measurements per dosing event. This, in turn, limits our statistical power in the detection of hours-scale, time-varying physiological processes. Given the recent advent of in vivo electrochemical aptamer-based (EAB) sensors, however, we can now obtain hundreds of concentration measurements per administration. Our aim in this paper was to assess the ability of these time-dense datasets to describe time-varying pharmacokinetic models with good statistical significance.

METHODS

We used seconds-resolved measurements of plasma tobramycin concentrations in rats to statistically compare traditional one- and two-compartmental pharmacokinetic models to new models in which the proportional relationship between a drug's plasma concentration and its elimination rate varies in response to changing kidney function.

RESULTS

We found that a modified one-compartment model in which the proportionality between the plasma concentration of tobramycin and its elimination rate falls reciprocally with time either meets or is preferred over the standard two-compartment pharmacokinetic model for half of the datasets characterized. When we reduced the impact of the drug's rapid distribution phase on the model, this one-compartment, time-varying model was statistically preferred over the standard one-compartment model for 80% of our datasets.

CONCLUSIONS

Our results highlight both the impact that simple physiological changes (such as varying kidney function) can have on drug pharmacokinetics and the ability of high-time resolution EAB sensor measurements to identify such impacts.

Calibration-Free, Seconds-Resolved In Vivo Molecular Measurements using Fourier-Transform Impedance Spectroscopy Interrogation of Electrochemical Aptamer Sensors

Electrochemical aptamer-based (EAB) sensors are capable of measuring the concentrations of specific molecules in vivo, in real time, and with a few-second time resolution. For their signal transduction mechanism, these sensors utilize a binding-induced conformational change in their target-recognizing, redox-reporter-modified aptamer to alter the rate of electron transfer between the reporter and the supporting electrode. While a variety of voltammetric techniques have been used to monitor this change in kinetics, they suffer from various drawbacks, including time resolution limited to several seconds and sensor-to-sensor variation that requires calibration to remove. Here, however, we show that the use of fast Fourier transform electrochemical impedance spectroscopy (FFT-EIS) to interrogate EAB sensors leads to improved (here better than 2 s) time resolution and calibration-free operation, even when such sensors are deployed in vivo. To showcase these benefits, we demonstrate the approach's ability to perform real-time molecular measurements in the veins of living rats.

Survey of oligoethylene glycol-based self-assembled monolayers on electrochemical aptamer-based sensor in biological fluids

The ability to monitor levels of endogenous markers and clearance profiles of drugs and their metabolites can improve the quality of biomedical research and precision with which therapies are individualized. Towards this end, electrochemical aptamer-based (EAB) sensors have been developed that support the real-time monitoring of specific analytes in vivo with clinically relevant specificity and sensitivity. A challenge associated with the in vivo deployment of EAB sensors, however, is how to manage the signal drift which, although correctable, ultimately leads to unacceptably low signal-to-noise ratios, limiting the measurement duration. Motivated by the correction of signal drift, in this paper, we have explored the use of oligoethylene glycol (OEG), a widely employed antifouling coating, to reduce the signal drift in EAB sensors. Counter to expectations, however, when challenged in 37 °C whole blood in vitro, EAB sensors employing OEG-modified self-assembled monolayers exhibit both greater drift and reduced signal gain, compared with those employ a simple, hydroxyl-terminated monolayer. On the other hand, when EAB sensor was prepared with a mix monolayer using MCH and lipoamido OEG 2 alcohol, reduced signal noise was observed compared to the same sensor prepared with MCH presumably due to improved SAM construction. These results suggest broader exploration of antifouling materials will be required to improve the signal drift of EAB sensors.

Precise Electrochemical Sizing of Individual Electro-Inactive Particles

Nanoimpact electrochemistry enables the time-resolved in situ characterization (e.g., size, catalytic activity) of single nanomaterial units, providing a means of elucidating heterogeneities that would be masked in ensemble studies. To implement this technique with redox inactive particles, a solution-phase redox reaction is used to produce a steady-state background current on a disk ultramicroelectrode. When a particle adsorbs onto the electrode, it produces a stepwise reduction in the exposed electrode area, which produces, in turn, a stepwise decrease in the current commensurate with the size of the adsorbing species. Historically, however, nanoimpact electrochemistry has suffered from "edge effects," in which the radial diffusion layer formed at the circumference of the ultramicroelectrodes renders the step size dependent not only on the size of the particle but also on where it lands on the electrode. The introduction of electrocatalytic current generation, however, mitigates the heterogeneity caused by edge effects, thus improving the measurement precision. In this approach, termed "electrocatalytic interruption," a substrate that regenerates the redox probe at the diffusion layer is introduced. This shifts the rate-limiting step of the current generation from diffusion to the homogeneous reaction rate constant, thus reducing flux heterogeneity and increasing the precision of particle sizing by an order of magnitude. The protocol described here explains the set-up and data collection employed in nanoimpact experiments implementing this effect for improved precision in the sizing of redox in-active materials.

Continuous molecular monitoring of human dermal interstitial fluid with microneedle-enabled electrochemical aptamer sensors

The ability to continually collect diagnostic information from the body during daily activity has revolutionized the monitoring of health and disease. Much of this monitoring, however, has been of physical "vital signs", with the monitoring of molecular markers having been limited to glucose, primarily due to the lack of other medically relevant molecules for which continuous measurements are possible in bodily fluids. Electrochemical aptamer sensors, however, have a recent history of successful in vivo demonstrations in rat animal models. Herein, we present the first report of real-time human molecular data collected using such sensors, successfully demonstrating their ability to measure the concentration of phenylalanine in dermal interstitial fluid after an oral bolus. To achieve this, we used a device that employs three hollow microneedles to couple the interstitial fluid to an ex vivo, phenylalanine-detecting sensor. The resulting architecture achieves good precision over the physiological concentration range and clinically relevant, 20 min lag times. By also demonstrating 90 days dry room-temperature shelf storage, the reported work also reaches another important milestone in moving such sensors to the clinic. While the devices demonstrated are not without remaining challenges, the results at minimum provide a simple method by which aptamer sensors can be quickly moved into human subjects for testing.

High-precision monitoring of and feedback control over drug concentrations in the brains of freely moving rats

Knowledge of drug concentrations in the brains of behaving subjects remains constrained on a number of dimensions, including poor temporal resolution and lack of real-time data. Here, however, we demonstrate the ability of electrochemical aptamer-based sensors to support seconds-resolved, real-time measurements of drug concentrations in the brains of freely moving rats. Specifically, using such sensors, we achieve <4 μM limits of detection and 10-s resolution in the measurement of procaine in the brains of freely moving rats, permitting the determination of the pharmacokinetics and concentration-behavior relations of the drug with high precision for individual subjects. In parallel, we have used closed-loop feedback-controlled drug delivery to hold intracranial procaine levels constant (±10%) for >1.5 hours. These results demonstrate the utility of such sensors in (i) the determination of the site-specific, seconds-resolved neuropharmacokinetics, (ii) enabling the study of individual subject neuropharmacokinetics and concentration-response relations, and (iii) performing high-precision control over intracranial drug levels.

A tight squeeze: geometric effects on the performance of three-electrode electrochemical-aptamer based sensors in constrained, in vivo placements

Electrochemical, aptamer-based (EAB) sensors are the first molecular monitoring technology that is (1) based on receptor binding and not the reactivity of the target, rendering it fairly general, and (2) able to support high-frequency, real-time measurements in situ in the living body. To date, EAB-derived in vivo measurements have largely been performed using three electrodes (working, reference, counter) bundled together within a catheter for insertion into the rat jugular. Exploring this architecture, here we show that the placement of these electrodes inside or outside of the lumen of the catheter significantly impacts sensor performance. Specifically, we find that retaining the counter electrode within the catheter increases the resistance between it and the working electrode, increasing the capacitive background. In contrast, extending the counter electrode outside the lumen of the catheter reduces this effect, significantly enhancing the signal-to-noise of intravenous molecular measurements. Exploring counter electrode geometries further, we find that they need not be larger than the working electrode. Putting these observations together, we have developed a new intravenous EAB architecture that achieves improved performance while remaining short enough to safely emplace in the rat jugular. These findings, though explored here with EAB sensors may prove important for the design of many electrochemical biosensors.

Conformational-switch biosensors as novel tools to support continuous, real-time molecular monitoring in lab-on-a-chip devices

Recent years have seen continued expansion of the functionality of lab on a chip (LOC) devices. Indeed LOCs now provide scientists and developers with useful and versatile platforms across a myriad of chemical and biological applications. The field still fails, however, to integrate an often important element of bench-top analytics: real-time molecular measurements that can be used to "guide" a chemical response. Here we describe the analytical techniques that could provide LOCs with such real-time molecular monitoring capabilities. It appears to us that, among the approaches that are general (i.e., that are independent of the reactive or optical properties of their targets), sensing strategies relying on binding-induced conformational change of bioreceptors are most likely to succeed in such applications.

Efforts toward the continuous monitoring of molecular markers of performance

OBJECTIVES

Technologies supporting the continuous, real-time measurement of blood oxygen saturation and plasma glucose levels have improved our ability to monitor performance status. Our ability to monitor other molecular markers of performance, however, including the hormones known to indicate overtraining and general health, has lagged. That is, although a number of other molecular markers of performance status have been identified, we have struggled to develop viable technologies supporting their real-time monitoring in the body. Here we review biosensor approaches that may support such measurements, as well as the molecules potentially of greatest interest to monitor.

DESIGN

Narrative literature review.

METHOD

Literature review.

RESULTS

Significant effort has been made to harness the specificity, affinity, and generalizability of biomolecular recognition in a platform technology supporting continuous in vivo molecular measurements. Most biosensor approaches, however, are either not generalizable to most targets, or fail when challenged in the complex environments found in vivo. Electrochemical aptamer-based sensors, in contrast, are the first technology to simultaneously achieve both of these critical attributes. In an effort to illustrate the potential of this platform technology, we both critically review the literature describing it and briefly survey some of the molecular performance markers we believe will prove advantageous to monitor using it.

CONCLUSIONS

Electrochemical aptamer-based sensors may be the first truly generalizable technology for monitoring specific molecules in situ in the body and how adaptation of the platform to subcutaneous microneedles will enable the real-time monitoring of performance markers via a wearable, minimally invasive device.

On the Rational Design of Cooperative Receptors

Cooperativity (homotropic allostery) is the primary mechanism by which evolution steepens the binding curves of biomolecular receptors to produce more responsive input-output behavior in biomolecular systems. Motivated by the ubiquity with which nature employs this effect, over the past 15 years we, together with other groups, have engineered this mechanism into several otherwise noncooperative receptors. These efforts largely aimed to improve the utility of such receptors in artificial biotechnologies, such as synthetic biology and biosensors, but they have also provided the first quantitative, experimental tests of longstanding ideas about the mechanisms underlying cooperativity. In this article, we review the literature on the design of this effect, paying particular attention to the design strategies involved, the extent to which each can be rationally applied to (and optimized for) new receptors, and what each teaches us about the origins and optimization of this important phenomenon. Expected final online publication date for the Annual Review of Biophysics, Volume 52 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Real-Time, Seconds-Resolved Measurements of Plasma Methotrexate In Situ in the Living Body

Dose-limiting toxicity and significant patient-to-patient pharmacokinetic variability often render it difficult to achieve the safe and effective dosing of drugs. This is further compounded by the slow, cumbersome nature of the analytical methods used to monitor patient-specific pharmacokinetics, which inevitably rely on blood draws followed by post-facto laboratory analysis. Motivated by the pressing need for improved "therapeutic drug monitoring", we are developing electrochemical aptamer-based (EAB) sensors, a minimally invasive biosensor architecture that can provide real-time, seconds-resolved measurements of drug levels in situ in the living body. A key advantage of EAB sensors is that they are generalizable to the detection of a wide range of therapeutic agents because they are independent of the chemical or enzymatic reactivity of their targets. Three of the four therapeutic drug classes that have, to date, been shown measurable using in vivo EAB sensors, however, bind to nucleic acids as part of their mode of action, leaving open questions regarding the extent to which the approach can be generalized to therapeutics that do not. Here, we demonstrate real-time, in vivo measurements of plasma methotrexate, an antimetabolite (a mode of action not reliant on DNA binding) chemotherapeutic, following human-relevant dosing in a live rat animal model. By providing hundreds of drug concentration values, the resulting seconds-resolved measurements succeed in defining key pharmacokinetic parameters, including the drug's elimination rate, peak plasma concentration, and exposure (area under the curve), with unprecedented 5 to 10% precision. With this level of precision, we easily identify significant (>2-fold) differences in drug exposure occurring between even healthy rats given the same mass-adjusted methotrexate dose. By providing a real-time, seconds-resolved window into methotrexate pharmacokinetics, such measurements can be used to precisely "individualize" the dosing of this significantly toxic yet vitally important chemotherapeutic.

Using Spectroscopy to Guide the Adaptation of Aptamers into Electrochemical Aptamer-Based Sensors

Electrochemical aptamer-based (EAB) sensors utilize the binding-induced conformational change of an electrode-attached, redox-reporter-modified aptamer to transduce target recognition into an easily measurable electrochemical output. Because this signal transduction mechanism is single-step and rapidly reversible, EAB sensors support high-frequency, real-time molecular measurements, and because it recapitulates the reagentless, conformation-linked signaling seen in vivo among naturally occurring receptors, EAB sensors are selective enough to work in the complex, time-varying environments found in the living body. The fabrication of EAB sensors, however, requires that their target-recognizing aptamer be modified such that (1) it undergoes the necessary binding-induced conformational change and (2) that the thermodynamics of this "conformational switch" are tuned to ensure that they reflect an acceptable trade-off between affinity and signal gain. That is, even if an "as-selected" aptamer achieves useful affinity and specificity, it may fail when adapted to the EAB platform because it lacks the binding-induced conformational change required to support EAB signaling. In this paper we reveal the spectroscopy-guided approaches we use to modify aptamers such that they support the necessary binding-induced conformational change. Specifically, using newly reported aptamers, we demonstrate the systematic design of EAB sensors achieving clinically and physiologically relevant specificity, limits of detection, and dynamic range against the targets methotrexate and tryptophan.

Pulsed transistor operation enables miniaturization of electrochemical aptamer-based sensors

By simultaneously transducing and amplifying, transistors offer advantages over simpler, electrode-based transducers in electrochemical biosensors. However, transistor-based biosensors typically use static (i.e., DC) operation modes that are poorly suited for sensor architectures relying on the modulation of charge transfer kinetics to signal analyte binding. Thus motivated, here, we translate the AC "pulsed potential" approach typically used with electrochemical aptamer-based (EAB) sensors to an organic electrochemical transistor (OECT). Specifically, by applying a linearly sweeping square-wave potential to an aptamer-functionalized gate electrode, we produce current modulation across the transistor channel two orders of magnitude larger than seen for the equivalent, electrode-based biosensor. Unlike traditional EAB sensors, our aptamer-based OECT (AB-OECT) sensors critically maintain output current even with miniaturization. The pulsed transistor operation demonstrated here could be applied generally to sensors relying on kinetics-based signaling, expanding opportunities for noninvasive and high spatial resolution biosensing.

Real-Time, In Vivo Molecular Monitoring Using Electrochemical Aptamer Based Sensors: Opportunities and Challenges

The continuous, real-time measurement of specific molecules in situ in the body would greatly improve our ability to understand, diagnose, and treat disease. The vast majority of continuous molecular sensing technologies, however, either (1) rely on the chemical or enzymatic reactivity of their targets, sharply limiting their scope, or (2) have never been shown (and likely will never be shown) to operate in the complex environments found in vivo. Against this background, here we review electrochemical aptamer-based (EAB) sensors, an electrochemical approach to real-time molecular monitoring that has now seen 15 years of academic development. The strengths of the EAB platform are significant: to date it is the only molecular measurement technology that (1) functions independently of the chemical reactivity of its targets, and is thus general, and (2) supports in vivo measurements. Specifically, using EAB sensors we, and others, have already reported the real-time, seconds-resolved measurements of multiple, unrelated drugs and metabolites in situ in the veins and tissues of live animals. Against these strengths, we detail the platform's remaining weaknesses, which include still limited measurement duration (hours, rather than the more desirable days) and the difficulty in obtaining sufficiently high performance aptamers against new targets, before then detailing promising approaches overcoming these hurdles. Finally, we close by exploring the opportunities we believe this potentially revolutionary technology (as well as a few, possibly competing, technologies) will create for both researchers and clinicians.

The sequestration mechanism as a generalizable approach to improve the sensitivity of biosensors and bioassays

Biosensors and bioassays, both of which employ proteins and nucleic acids to detect specific molecular targets, have seen significant applications in both biomedical research and clinical practice. This success is largely due to the extraordinary versatility, affinity, and specificity of biomolecular recognition. Nevertheless, these receptors suffer from an inherent limitation: single, saturable binding sites exhibit a hyperbolic relationship (the "Langmuir isotherm") between target concentration and receptor occupancy, which in turn limits the sensitivity of these technologies to small variations in target concentration. To overcome this and generate more responsive biosensors and bioassays, here we have used the sequestration mechanism to improve the steepness of the input/output curves of several bioanalytical methods. As our test bed for this we employed sensors and assays against neutrophil gelatinase-associated lipocalin (NGAL), a kidney biomarker for which enhanced sensitivity will improve the monitoring of kidney injury. Specifically, by introducing sequestration we have improved the responsiveness of an electrochemical aptamer based (EAB) biosensor, and two bioassays, a paper-based "dipstick" assay and an enzyme-linked immunosorbent assay (ELISA). Doing so we have narrowed the dynamic range of these sensors and assays several-fold, thus enhancing their ability to measure small changes in target concentration. Given that introducing sequestration requires only the addition of the appropriate concentration of a high-affinity "depletant," the mechanism appears simple and easily adaptable to tuning the binding properties of the receptors employed in a wide range of biosensors and bioassays.

Improved calibration of electrochemical aptamer-based sensors

Electrochemical aptamer-based (EAB) sensors support the real-time, high frequency measurement of pharmaceuticals and metabolites in-situ in the living body, rendering them a potentially powerful technology for both research and clinical applications. Here we explore quantification using EAB sensors, examining the impact of media selection and temperature on measurement performance. Using freshly-collected, undiluted whole blood at body temperature as both our calibration and measurement conditions, we demonstrate accuracy of better than ± 10% for the measurement of our test bed drug, vancomycin. Comparing titrations collected at room and body temperature, we find that matching the temperature of calibration curve collection to the temperature used during measurements improves quantification by reducing differences in sensor gain and binding curve midpoint. We likewise find that, because blood age impacts the sensor response, calibrating in freshly collected blood can improve quantification. Finally, we demonstrate the use of non-blood proxy media to achieve calibration without the need to collect fresh whole blood.

On the Disinfection of Electrochemical Aptamer-Based Sensors

Electrochemical aptamer-based (EAB) sensors encompass the only biosensor approach yet reported that is simultaneously: (1) independent of the chemical or enzymatic reactivity of its target, rendering it general; (2) continuous and real-time; and (3) selective enough to deploy in situ in the living body. Consistent with this, in vivo EAB sensors supporting the seconds-resolved, real-time measurement of multiple drugs and metabolites have been reported, suggesting the approach may prove of value in biomedical research and the diagnosis, treatment, and monitoring of disease. However, to apply these devices in long-duration animal models, much less in human patients, requires that they be free of any significant pathogen load. Thus motivated, here we have characterized the compatibility of EAB sensors with standard sterilization and high-level disinfection techniques. Doing so, we find that, while many lead to significant sensor degradation, treatment with CIDEX OPA (0.55% ortho-phthalaldehyde) leads to effective disinfection without causing any detectable loss in sensor performance.

Continuous monitoring of molecular biomarkers in microfluidic devices

The ability to monitor molecular targets is crucial in fields ranging from healthcare to industrial processing to environmental protection. Devices employing biomolecules to achieve this goal are called biosensors. Over the last half century researchers have developed dozens of different biosensor approaches. In this chapter we analyze recent advances in the biosensing field aiming at adapting these to the problem of continuous molecular monitoring in complex sample streams, and how the merging of these sensors with lab-on-a-chip technologies would be beneficial to both. To do so we discuss (1) the components that comprise a biosensor, (2) the challenges associated with continuous molecular monitoring in complex sample streams, (3) how different sensing strategies deal with (or fail to deal with) these challenges, and (4) the implementation of these technologies into lab-on-a-chip architectures.

Electrochemical Aptamer-Based Sensors: A Platform Approach to High-Frequency Molecular Monitoring In Situ in the Living Body

The monitoring of specific molecules in the living body has historically required sample removal (e.g., blood draws, microdialysis) followed by analysis via cumbersome, laboratory-bound processes. Those few exceptions to this rule (e.g., glucose, pyruvate, the monoamines) are monitored using "one-off" technologies reliant on the specific enzymatic or redox reactivity of their targets, and thus not generalizable to the measurement of other targets. In response we have developed in vivo electrochemical aptamer-based (E-AB) sensors, a modular, receptor-based measurement technology that is independent of the chemical reactivity of its targets, and thus has the potential to be generalizable to a wide range of analytes. To further the adoption of this in vivo molecular measurement approach by other researchers and to accelerate its ultimate translation to the clinic, we present here our standard protocols for the fabrication and use of intravenous E-AB sensors.

Catalytic Interruption Mitigates Edge Effects in the Characterization of Heterogeneous, Insulating Nanoparticles

Blocking electrochemistry, a subfield of nanochemistry, enables nondestructive, in situ measurement of the concentration, size, and size heterogeneity of highly dilute, nanometer-scale materials. This approach, in which the adsorptive impact of individual particles on a microelectrode prevents charge exchange with a freely diffusing electroactive redox mediator, has expanded the scope of electrochemistry to the study of redox-inert materials. A limitation, however, remains: inhomogeneous current fluxes associated with enhanced mass transfer occurring at the edges of planar microelectrodes confound the relationship between the size of the impacting particle and the signal it generates. These "edge effects" lead to the overestimation of size heterogeneity and, thus, poor sample characterization. In response, we demonstrate here the ability of catalytic current amplification (EC') to reduce this problem, an effect we term "electrocatalytic interruption". Specifically, we show that the increase in mass transport produced by a coupled chemical reaction significantly mitigates edge effects, returning estimated particle size distributions much closer to those observed using ex situ electron microscopy. In parallel, electrocatalytic interruption enhances the signal observed from individual particles, enabling the detection of particles significantly smaller than is possible via conventional blocking electrochemistry. Finite element simulations indicate that the rapid chemical kinetics created by this approach contributes to the amplification of the electronic signal to restore analytical precision and reliably detect and characterize the heterogeneity of nanoscale electro-inactive materials.

Nanometer-Scale Force Profiles of Short Single- and Double-Stranded DNA Molecules on a Gold Surface Measured Using a Surface Forces Apparatus

Using a surface forces apparatus (SFA), we have studied the nanomechanical behavior of short single-stranded and partially and fully double-stranded DNA molecules attached via one end to a self-assembled monolayer on a gold surface. Our results confirm the previously proposed "mushroom-like" polymer structure for surface-attached, single-stranded DNA at low packing density and a "brush-like" structure for the same construct at higher density. At low density we observe a transition to "rigid rod" behavior upon addition of DNA complementary to the surface-attached single strand as the fraction of molecules that are double-stranded increases, with a concomitant increase in the SFA-observed thickness of the monolayer and the characteristic length of the observed repulsive forces. At higher densities, in contrast, this transition is effectively eliminated, presumably because the single-stranded state is already extended in its "brush" state. Taken together, these studies offer insights into the structure and physics of surface-attached short DNAs, providing new guidance for the rational design of DNA-modified functional surfaces.

Switching the aptamer attachment geometry can dramatically alter the signalling and performance of electrochemical aptamer-based sensors

Electrochemical aptamer-based (EAB) sensors, composed of an electrode-bound DNA aptamer with a redox reporter on the distal end, offer the promise of high-frequency, real-time molecular measurements in complex sample matrices and even in vivo. Here we assess the extent to which switching the aptamer terminus that is electrode-bound and the one that is redox-reporter-modified affects the performance of these sensors. Using sensors against doxorubicin, cocaine, and vancomycin as our test beds, we find that both signal gain (the relative signal change seen in the presence of a saturating target) and the frequency dependence of gain depend strongly on the attachment orientation, suggesting that this easily investigated variable is a worthwhile parameter to optimize in the design of new EAB sensors.

The effect of charged residue substitutions on the thermodynamics of protein-surface interactions

The interactions of proteins with surfaces are important in both biological processes and biotechnologies. In contrast to decades of study regarding the biophysics of proteins in bulk solution, however, our mechanistic understanding of the biophysics of proteins interacting with surfaces remains largely qualitative. In response, we have set to explore quantitatively the thermodynamics of protein-surface interactions. In this work, we explore systematically the role of electrostatics in modulating the interaction between proteins and charged surfaces. In particular, we use electrochemistry to explore the extent to which a macroscopic, hydroxyl-coated surface held at a slightly negative potential affects the folding thermodynamics of surface-attached protein variants with different composition of charged amino acids. Doing so, we find that attachment to the surface generally leads to a net stabilization, presumably due to excluded volume effects that reduce the entropy of the unfolded state. The magnitude of this stabilization, however, is strongly correlated with the charged-residue content of the protein. In particular, we find statistically significant correlations with both the net charge of the protein, with greater negative charge leading to less stabilization by the surface, and with the number of arginines, with more arginines leading to greater stabilization. Such findings refine our understanding of protein-surface interactions, providing in turn a guiding rationale to achieve the functional deposition of proteins on artificial surfaces for implementation in, for example, protein-based biotechnologies.

Elucidating the Mechanisms Underlying the Signal Drift of Electrochemical Aptamer-Based Sensors in Whole Blood

The ability to monitor drugs, metabolites, hormones, and other biomarkers in situ in the body would greatly advance both clinical practice and biomedical research. To this end, we are developing electrochemical aptamer-based (EAB) sensors, a platform technology able to perform real-time, in vivo monitoring of specific molecules irrespective of their chemical or enzymatic reactivity. An important obstacle to the deployment of EAB sensors in the challenging environments found in the living body is signal drift, whereby the sensor signal decreases over time. To date, we have demonstrated a number of approaches by which this drift can be corrected sufficiently well to achieve good measurement precision over multihour in vivo deployments. To achieve a much longer in vivo measurement duration, however, will likely require that we understand and address the sources of this effect. In response, here, we have systematically examined the mechanisms underlying the drift seen when EAB sensors and simpler, EAB-like devices are challenged in vitro at 37 °C in whole blood as a proxy for in vivo conditions. Our results demonstrate that electrochemically driven desorption of a self-assembled monolayer and fouling by blood components are the two primary sources of signal loss under these conditions, suggesting targeted approaches to remediating this degradation and thus improving the stability of EAB sensors and other, similar electrochemical biosensor technologies when deployed in the body.

Nanoporous Gold for the Miniaturization of In Vivo Electrochemical Aptamer-Based Sensors

Electrochemical aptamer-based sensors enable real-time molecular measurements in the living body. The spatial resolution of these measurements and ability to perform measurements in targeted locations, however, is limited by the length and width of the device's working electrode. Historically, achieving good signal to noise in the complex, noisy in vivo environment has required working electrode lengths of 3-6 mm. To enable sensor miniaturization, here we have enhanced the signaling current obtained for a sensor of given macroscopic dimensions by increasing its surface area. Specifically, we produced nanoporous gold via an electrochemical alloying/dealloying technique to increase the microscopic surface area of our working electrodes by up to 100-fold. Using this approach, we have miniaturized in vivo electrochemical aptamer-based (EAB) sensors (here using sensors against the antibiotic, vancomycin) by a factor of 6 while retaining sensor signal and response times. Conveniently, the fabrication of nanoporous gold is simple, parallelizable, and compatible with both two- and three-dimensional electrode architectures, suggesting that it may be of value to a range of electrochemical biosensor applications.

Programmable, Multiplexed DNA Circuits Supporting Clinically Relevant, Electrochemical Antibody Detection

Current health emergencies have highlighted the need to have rapid, sensitive, and convenient platforms for the detection of specific antibodies. In response, we report here the design of an electrochemical DNA circuit that responds quantitatively to multiple specific antibodies. The approach employs synthetic antigen-conjugated nucleic acid strands that are rationally designed to induce a strand displacement reaction and release a redox reporter-modified strand upon the recognition of a specific target antibody. The approach is sensitive (low nanomolar detection limit), specific (no signal is observed in the presence of non-targeted antibodies), and selective (the platform can be employed in complex media, including 90% serum). The programmable nature of the strand displacement circuit makes it also versatile, and we demonstrate here the detection of five different antibodies, including three of which are clinically relevant. Using different redox reporters, we also show that the antibody-responsive circuit can be multiplexed and responds to different antibodies in the same solution without crosstalk.

A wrinkled structure of gold film greatly improves the signaling of electrochemical aptamer-based biosensors

Electrochemical aptamer-based (E-AB) sensors provide a great opportunity towards the goal of point-of-care and wearable sensing technologies due to their good sensitivity and selectivity. Nevertheless, the output signals from this sensor class remain low when sensors are interrogated via square-wave voltammetry. This low signaling limits the sensor's precision for its capability to detect small changes in target concentrations. To circumvent this, we proposed here the use of a readily shrink-induced, wrinkled Au-coating polyolefin film to immobilize a greater number of DNA probes and thus improve the signaling. Specifically, wrinkled gold film exhibits a 5.5-fold increase of surface area in comparison to the unwrinkled ones. Using these substrates we fabricated a set of E-AB sensors of three biological molecules, including kanamycin, doxorubicin and ATP. We achieved up to 10-fold increase in its current and also good accuracies within ±20% error in the target concentration range across 2 orders of magnitude.

A wrinkled gold substrate greatly improves the signaling of electrochemical aptamer-based biosensors, achieving up to 10-fold increase in signals.

Subsecond-Resolved Molecular Measurements Using Electrochemical Phase Interrogation of Aptamer-Based Sensors

Recent years have seen the development of a number of biosensor architectures that rely on target binding-induced changes in the rate of electron transfer from an electrode-bound receptor. Most often, the interrogation of these sensors has relied on voltammetric methods, such as square-wave voltammetry, which limit their time resolution to a few seconds. Here, we describe the use of an impedance-based approach, which we have termed electrochemical phase interrogation, as a means of collecting high time resolution measurements with sensors in this class. Specifically, using changes in the electrochemical phase to monitor target binding in an electrochemical-aptamer based (EAB) sensor, we achieve subsecond temporal resolution and multihour stability in measurements performed directly in undiluted whole blood. Electrochemical phase interrogation also offers improved insights into EAB sensors' signaling mechanism. By modeling the interfacial resistance and capacitance using equivalent circuits, we find that the only parameter that is altered by target binding is the charge-transfer resistance. This confirms previous claims that binding-induced changes in electron-transfer kinetics drive signaling in this class of sensors. Considering that a wide range of electrochemical biosensor architectures rely on this signaling mechanism, we believe that electrochemical phase interrogation may prove generalizable toward subsecond measurements of molecular targets.

Attachment of Proteins to a Hydroxyl-Terminated Surface Eliminates the Stabilizing Effects of Polyols

The physics of proteins interacting with surfaces can differ significantly from those seen when the same proteins are free in bulk solution. As an example, we describe here the extent to which site-specific attachment to a chemically well-defined macroscopic surface alters the ability of several stabilizing and destabilizing cosolutes to modulate protein folding thermodynamics. We determined this via guanidinium denaturations performed in the presence of varying concentrations of cosolutes when proteins were either site-specifically attached to self-assembled monolayers on gold or free in bulk solution. Doing this we found that the extent to which guanidinium (a destabilizing Hofmeister cation), sulfate (a stabilizing Hofmeister anion), and urea (a neutral denaturant) alter the folding free energy remains indistinguishable whether proteins are surface-attached or free in bulk solution. In sharp contrast, however, neutral osmolytes sucrose and glycerol, which significantly stabilize proteins in bulk solution, do not measurably affect their stability when they are attached to a hydroxyl-terminated surface. In contrast, we recovered bulk solution-like stabilization when the attachment surface was instead carboxyl-terminated. It thus appears that chemistry-specific surface interactions can dramatically alter the way in which biomolecules interact with other components of the system.

An Electrochemical Biosensor Architecture Based on Protein Folding Supports Direct Real-Time Measurements in Whole Blood

The ability to monitor drug and biomarker concentrations in the body with high frequency and in real time would revolutionize our understanding of biology and our capacity to personalize medicine. The few in vivo molecular sensors that currently exist, however, all rely on the specific chemical or enzymatic reactivity of their targets and thus are not generalizable. In response, we demonstrate here an electrochemical sensing architecture based on binding-induced protein folding that is 1) independent of the reactivity of its targets, 2) reagentless, real-time, and with a resolution of seconds, and 3) selective enough to deploy in undiluted bodily fluids. As a proof of principle, we use the SH3 domain from human Fyn kinase to build a sensor that discriminates between the protein's peptide targets and responds rapidly and quantitatively even when challenged in whole blood. The resulting sensor architecture could drastically expand the chemical space accessible to continuous, real-time biosensors.

Optimizing the Specificity Window of Biomolecular Receptors Using Structure-Switching and Allostery

To ensure maximum specificity (i.e., minimize cross-reactivity with structurally similar analogues of the desired target), most bioassays invoke "stringency", the careful tuning of the conditions employed (e.g., pH, ionic strength, or temperature). Willingness to control assay conditions will fall, however, as quantitative, single-step biosensors begin to replace multistep analytical processes. This is especially true for sensors deployed in vivo, where the tuning of such parameters is not just inconvenient but impossible. In response, we describe here the rational adaptation of two strategies employed by nature to tune the affinity of biomolecular receptors so as to optimize the placement of their specificity "windows" without the need to alter measurement conditions: structure-switching and allosteric control. We quantitatively validate these approaches using two distinct, DNA-based receptors: a simple, linear-chain DNA suitable for detecting a complementary DNA strand and a structurally complex DNA aptamer used for the detection of a small-molecule drug. Using these models, we show that, without altering assay conditions, structure-switching and allostery can tune the concentration range over which a receptor achieves optimal specificity over orders of magnitude, thus optimally matching the specificity window with the range of target concentrations expected to be seen in a given application.

Real-Time Monitoring of a Protein Biomarker

The ability to monitor protein biomarkers continuously and in real-time would significantly advance the precision of medicine. Current protein-detection techniques, however, including ELISA and lateral flow assays, provide only time-delayed, single-time-point measurements, limiting their ability to guide prompt responses to rapidly evolving, life-threatening conditions. In response, here we present an electrochemical aptamer-based sensor (EAB) that supports high-frequency, real-time biomarker measurements. Specifically, we have developed an electrochemical, aptamer-based (EAB) sensor against Neutrophil Gelatinase-Associated Lipocalin (NGAL), a protein that, if present in urine at levels above a threshold value, is indicative of acute renal/kidney injury (AKI). When deployed inside a urinary catheter, the resulting reagentless, wash-free sensor supports real-time, high-frequency monitoring of clinically relevant NGAL concentrations over the course of hours. By providing an "early warning system", the ability to measure levels of diagnostically relevant proteins such as NGAL in real-time could fundamentally change how we detect, monitor, and treat many important diseases.

An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets

The specific detection in clinical samples of analytes with dimensions in the tens to hundreds of nanometers, such as viruses and large proteins, would improve disease diagnosis. Detection of these "mesoscale" analytes (as opposed to their nanoscale components), however, is challenging as it requires the simultaneous binding of multiple recognition sites often spaced over tens of nanometers. In response, we have adapted DNA origami, with its unparalleled customizability to precisely display multiple target-binding sites over the relevant length scale, to an electrochemical biosensor platform. Our proof-of-concept employs triangular origami covalently attached to a gold electrode and functionalized with redox reporters. Electrochemical interrogation of this platform successfully monitors mesoscale, target-binding-induced changes in electron transfer in a manner consistent with coarse-grained molecular dynamics simulations. Our approach enables the specific detection of analytes displaying recognition sites that are separated by ∼40 nm, a spacing significantly greater than that achieved in similar sensor architectures employing either antibodies or aptamers.

Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different

The argument that the hydrophobic effect is the primary effect driving the folding of globular proteins is nearly universally accepted (including by the authors). But does this view also imply that water is a "poor" solvent for the unfolded states of these same proteins? Here we argue that the answer is "no," that is, folding to a well-packed, extensively hydrogen-bonded native structure differs fundamentally from the nonspecific chain collapse that defines a poor solvent. Thus, the observation that a protein folds in water does not necessitate that water is a poor solvent for its unfolded state. Indeed, chain-solvent interactions that are marginally more favorable than nonspecific intrachain interactions are beneficial to protein function because they destabilize deleterious misfolded conformations and inter-chain interactions.

E-DNA scaffold sensors and the reagentless, single-step, measurement of HIV-diagnostic antibodies in human serum

The multiplexed, point-of-care measurement of specific antibodies could improve the speed with which diseases are diagnosed and their treatment initiated. To this end, we are developing E-DNA scaffold sensors, which consist of a rigid, nucleic acid "scaffold" attached on one end to an electrode and presenting both a redox reporter and an epitope on the other. In the absence of antibody, the reporter efficiently transfers electrons when interrogated electrochemically. Binding-induced steric hindrance limits movement, reducing electron transfer in a manner that is both easily measured and quantitatively related to target concentration. Previously we have used monoclonal antibodies to explore the analytical performance of E-DNA sensors, showing that they support the rapid, single-step, quantitative detection of multiple antibodies in small volume samples. Here, in contrast, we employ authentic human samples to better explore the platform's clinical potential. Specifically, we developed E-DNA sensors targeting three HIV-specific antibodies and then compared the analytical and clinical performance of these against those of gold standard serological techniques. Doing so we find that, although the multistep amplification of an ELISA leads to a lower detection limits, the clinical sensitivity of ELISAs, E-DNA sensors and lateral-flow dipsticks are indistinguishable across our test set. It thus appears that, by merging the quantitation and multiplexing of ELISAs with the convenience and speed of dipsticks, E-DNA scaffold sensors could significantly improve on current serological practice.

Calibration-Free Measurement of Phenylalanine Levels in the Blood Using an Electrochemical Aptamer-Based Sensor Suitable for Point-of-Care Applications

By analogy to the revolution the "home glucose monitor" created in the treatment of diabetes, the availability of a modular, "platform" technology able to measure nearly any metabolite, biomarker, or drug "at-home" in unprocessed, finger-prick volumes of whole blood could revolutionize the monitoring and treatment of disease. Thus motivated, we have adapted here the electrochemical aptamer-based sensing platform to the problem of rapidly and conveniently measuring the level of phenylalanine in the blood, an ability that would aid the monitoring and management of phenylketonuria (PKU). To achieve this, we exploited a previously reported DNA aptamer that recognizes phenylalanine in complex with a rhodium-based "receptor" that improves affinity. We re-engineered this to undergo a large-scale, binding-induced conformational change before modifying it with a methylene blue redox reporter and attaching it to a gold electrode that supports the appropriate electrochemical interrogation. The resultant sensor achieves a useful dynamic range of 90 nM to 7 μM. When challenged with finger-prick-scale sample volumes of the whole blood (diluted 1000-fold to match the sensor's dynamic range), the device achieves the accurate (±20%), calibration-free measurement of blood phenylalanine levels in minutes.