Optimization of Vancomycin Aptamer Sequence Length Increases the Sensitivity of Electrochemical, Aptamer-Based Sensors In Vivo

Truncations and in silico docking to enhance the analytical response of aptamer-based biosensors

Aptamers are short oligonucleotides capable of binding specifically to various targets (i.e., small molecules, proteins, and whole cells) which have been introduced in biosensors such as in the electrochemical aptamer-based (E-AB) sensing platform. E-AB sensors are comprised of a redox-reporter-modified aptamer attached to an electrode that undergoes, upon target addition, a binding-induced change in electron transfer rates. To date, E-AB sensors have faced a limitation in the translatability of aptamers into the sensing platform presumably because sequences obtained from Systematic Evolution of Ligands by Exponential Enrichment (SELEX) are typically long (>80 nucleotides) and that obtaining structural information remains time and resource consuming. In response, we explore the utility of aptamer base truncations and in silico docking to improve their translatability into E-AB sensors. Here, we first apply this to the glucose aptamer, which we characterize in solution using NMR methods to guide design and translate truncated variants in E-AB biosensors. We further investigated the applicability of the truncation and computational approaches to four other aptamer systems (vancomycin, cocaine, methotrexate and theophylline) from which we derived functional E-AB sensors. We foresee that our strategy will increase the success rate of translating aptamers into sensing platforms to afford low-cost measurements of molecules directly in undiluted complex matrices.

"Binding" or "Binding and Switching"? A Perspective on Resolving Conformational Changes of Surface-Attached Biomolecular Receptors

Understanding the structural reconfiguration of a biomolecular receptor remains a topic of particular interest to the biosensing community. This is because conformationally changing receptors are commonly employed in biosensors to harness their capability to bind specifically to their target. Often, such receptors are attached to surfaces so that binding can be transduced into a measurable response. Doing so, however, can impose constraints on the possible configurations they can adopt. Such constraints can ultimately influence, for example, their receptor-target binding models or their affinity, which is essential to provide the desired analytical performances in biosensors. Motivated by the idea of gaining further insights into the impact of surface attachment on conformationally switching receptors attached to surfaces, we explore here the various surface-based techniques capable of monitoring structural changes. We decided to narrow our survey to techniques that have been applied to the investigation of nucleic acids to provide an overview of their key features. We envision that this will bring a broader perspective of the field and the challenges ahead with the hopes of "finding the switch" in surface-attached biomolecular receptors.

3D-printed electrochemical cells for multi-point aptamer-based drug measurements

Electrochemical aptamer-based (E-AB) sensors achieve detection and quantitation of biomedically relevant targets such as small molecule drugs and protein biomarkers in biological samples. E-ABs are usually fabricated on commercially available macroelectrodes which, although functional for rapid sensor prototyping, can be costly and are not compatible with the microliter sample volumes typically available in biorepositories for clinical validation studies. Seeking to develop a multi-point sensing platform for sensor validation in sample volumes characteristic of clinical studies, we report a protocol for in-house assembly of 3D-printed E-ABs. We employed a commercially available 3D stereolithographic printer (FormLabs, $5k USD) for electrochemical cell fabrication and directly embedded electrodes within the 3D-printed cell structure. This approach offers a reproducible and reusable electrode fabrication process resulting in four independent and simultaneous measurements for statistically weighted results. We demonstrate compatibility with aptamer sequences binding antibiotics and antineoplastic agents. We also demonstrate a proof-of-concept validation of serum vancomycin measurements using clinical samples. Our results demonstrate that 3D-printing can be used in conjunction with E-ABs for accessible, rapid, and statistically meaningful validation of E-AB sensors in biological matrices.

Label-free, real-time monitoring of cytochrome C drug responses in microdissected tumor biopsies with a multi-well aptasensor platform

Functional assays on intact tumor biopsies can complement genomics-based approaches for precision oncology, drug testing, and organs-on-chips cancer disease models by capturing key therapeutic response determinants, such as tissue architecture, tumor heterogeneity, and the tumor microenvironment. Most of these assays rely on fluorescent labeling, a semiquantitative method best suited for single-time-point assays or labor-intensive immunostaining analysis. Here, we report integrated aptamer electrochemical sensors for on-chip, real-time monitoring of cytochrome C, a cell death indicator, from intact microdissected tissues with high affinity and specificity. The platform features a multi-well sensor layout and a multiplexed electronic setup. The aptasensors measure increases in cytochrome C in the supernatant of mouse or human microdissected tumors after exposure to various drug treatments. Because of the sensor's high affinity, it primarily tracks rising concentrations of cytochrome C, capturing dynamic changes during apoptosis. This approach could help develop more advanced cancer disease models and apply to other complex in vitro disease models, such as organs-on-chips and organoids.

Tuning N-heterocyclic carbene wingtips to form electrochemically stable adlayers on metals

Self-assembled monolayers (SAMs) are employed in electrochemical biosensors to passivate and functionalize electrode surfaces. These monolayers prevent the occurrence of undesired electrochemical reactions and act as scaffolds for coupling bioaffinity reagents. Thiols are the most common adlayer used for this application; however, the thiol-gold bond is susceptible to competitive displacement by naturally occurring solvated thiols in biological fluids, as well as to desorption under continuous voltage interrogation. To overcome these issues, N-heterocyclic carbene (NHC) monolayers have been proposed as an alternative for electrochemical biosensor applications due to the strong carbon-gold bond. To maximize the effectiveness of NHCs for SAMs, a thorough understanding of both the steric effects of wingtip substituents and NHC precursor type to the passivation of electrode surfaces is required. In this study, five different NHC wingtips as well as two kinds of NHC precursors were evaluated. The best performing NHC adlayers can be cycled continuously for four days (over 30 000 voltammetric cycles) without appreciably desorbing from the electrode surface. Benchmark thiol monolayers, in contrast, rapidly desorb after only twelve hours. Investigations also show NHC adlayer formation on other biosensor-relevant electrodes such as platinum and palladium.

Surface-Based Multimeric Aptamer Generation and Bio-Functionalization for Electrochemical Biosensing Applications

Multimeric aptamers have gained more attention than their monomeric counterparts due to providing more binding sites for target analytes, leading to increased affinity. This work attempted to engineer the surface-based generation of multimeric aptamers by employing the room temperature rolling circle amplification (RCA) technique and chemically modified primers for developing a highly sensitive and selective electrochemical aptasensor. The multimeric aptamers, generated through surface RCA, are hybridized to modified spacer primers, facilitating the positioning of the aptamers in the proximity of sensing surfaces. These multimeric aptamers can be used as bio-receptors for capturing specific targets. The surface amplification process was fully characterized, and the optimal amplification time for biosensing purposes was determined, using SARS-CoV-2 spike protein (SP). Interestingly, multimeric aptasensors produced considerably higher response signals and affinity (more than 10-fold), as well as higher sensitivity (almost 4-fold) compared to monomeric aptasensors. Furthermore, the impact of surface structures on the response signals was studied by utilizing both flat working electrodes (WEs) and nano-/microislands (NMIs) WEs. The NMIs multimeric aptasensors showed significantly higher sensitivity in buffer and saliva media with the limit of detection less than 2 fg/ml. Finally, the developed NMIs multimeric aptasensors were clinically challenged with several saliva patient samples.

Integrating microneedles and sensing strategies for diagnostic and monitoring applications: The state of the art

Microneedles (MNs) offer minimally-invasive access to interstitial fluid (ISF) - a potent alternative to blood in terms of monitoring physiological analytes. This property is particularly advantageous for the painless detection and monitoring of drugs and biomolecules. However, the complexity of the skin environment, coupled with the inherent nature of the analytes being detected and the inherent physical properties of MNs, pose challenges when conducting physiological monitoring using this fluid. In this review, we discuss different sensing mechanisms and highlight advancements in monitoring different targets, with a particular focus on drug monitoring. We further list the current challenges facing the field and conclude by discussing aspects of MN design which serve to enhance their performance when monitoring different classes of analytes.

Dual-Frequency, Ratiometric Approaches to EAB Sensor Interrogation Support the Calibration-Free Measurement of Specific Molecules In Vivo

Electrochemical aptamer-based (EAB) sensors represent the first molecular measurement technology that is both (1) independent of the chemical reactivity of the target, and thus generalizable to many targets and (2) able to function in an accurate, drift-corrected manner in situ in the living body. Signaling in EAB sensors is generated when an electrode-bound aptamer binds to its target ligand, altering the rate of electron transfer from an attached redox reporter and producing an easily detectable change in peak current when the sensor is interrogated using square wave voltammetry. Due to differences in the microscopic surface area of the interrogating electrodes, the baseline peak currents obtained from EAB sensors, however, can be highly variable. To overcome this, we have historically performed single-point calibration using measurements performed in a single sample of known target concentration. Here, however, we explore approaches to EAB sensor operation that negate the need to perform even single-point calibration of individual sensors. These are a ratiometric approach employing the ratio of the peak currents observed at two distinct square wave frequencies, and a kinetic differential measurement approach that employs the difference between peak currents seen at the two frequencies. Using in vivo measurements of vancomycin and phenylalanine as our test bed, we compared the output of these methods with that of the same sensor when single-point calibration was employed. Doing so we find that both methods support accurately drift-corrected measurements in vivo in live rats, even when employing rather crudely handmade devices. By removing the need to calibrate each individual sensor in a sample of known target concentration, these interrogation methods should significantly simplify the use of EAB sensors for in vivo applications.

Whole blood multiplex measurements using electrochemical aptamer-based biosensors

Simultaneous measurements of various molecules ("multiplex") using electrochemical biosensors typically require multiple electrode implementations, which for neonates, hemophiliacs, etc. is problematic. Here, we introduce the oxazine ATTO 700 into electrochemical aptamer-based biosensors to achieve "true" multiplex, continuous and real-time measurements of two different molecules in undiluted whole blood using a single electrode.

Utilization of Spontaneous Alkyne-Gold Self-Assembly Chemistry as an Alternative Method for Fabricating Electrochemical Aptamer-Based Sensors

Electrochemical aptamer-based (E-AB) sensors are a promising class of biosensors which use structure-switching redox-labeled oligonucleotides (aptamers) codeposited with passivating alkanethiol monolayers on electrode surfaces to specifically bind and detect target analytes. Signaling in E-AB sensors is an outcome of aptamer conformational changes upon target binding, with the sequence of the aptamer imparting specificity toward the analyte of interest. The change in conformation translates to a change in electron transfer between the redox label attached to the aptamer and the underlying electrode and is related to analyte concentration, allowing specific electrochemical detection of nonelectroactive analytes. E-AB sensor measurements are reagentless with time resolutions of seconds or less and may be miniaturized into the submicron range. Traditionally these sensors are fabricated using thiol-on-gold chemistry. Here we present an alternate immobilization chemistry, gold-alkyne binding, which results in an increase in sensor lifetimes under ideal conditions by up to ∼100%. We find that gold-alkyne binding is spontaneous and supports efficient E-AB sensor signaling with analytical performance characteristics similar to those of thiol generated monolayers. The surface modification differs from gold-thiol binding only in the time and aptamer concentration required to achieve similar aptamer surface coverages. In addition, alkynated aptamers differ from their thiolated analogues only by their chemical handle for surface attachment, so any existing aptamers can be easily adapted to utilize this attachment strategy.

Analytical Validation of Aptamer-Based Serum Vancomycin Monitoring Relative to Automated Immunoassays

The practice of monitoring therapeutic drug concentrations in patient biofluids can significantly improve clinical outcomes while simultaneously minimizing adverse side effects. A model example of this practice is vancomycin dosing in intensive care units. If dosed correctly, vancomycin can effectively treat methicillin-resistant streptococcus aureus (MRSA) infections. However, it can also induce nephrotoxicity or fail to kill the bacteria if dosed too high or too low, respectively. Although undeniably important to achieve effectiveness, therapeutic drug monitoring remains inconvenient in practice due primarily to the lengthy process of sample collection, transport to a centralized facility, and analysis using costly instrumentation. Adding to this workflow is the possibility of backlogs at centralized clinical laboratories, which is not uncommon and may result in additional delays between biofluid sampling and concentration measurement, which can negatively affect clinical outcomes. Here, we explore the possibility of using point-of-care electrochemical aptamer-based (E-AB) sensors to minimize the time delay between biofluid sampling and drug measurement. Specifically, we conducted a clinical agreement study comparing the measurement outcomes of E-AB sensors to the benchmark automated competitive immunoassays for vancomycin monitoring in serum. Our results demonstrate that E-ABs are selective for free vancomycin─the active form of the drug, over total vancomycin. In contrast, competitive immunoassays measure total vancomycin, including both protein-bound and free drug. Accounting for these differences in a pilot study consisting of 85 clinical samples, we demonstrate that the E-AB vancomycin measurement achieved a 95% positive correlation rate with the benchmark immunoassays. Therefore, we conclude that E-AB sensors could provide clinically useful stratification of patient samples at trough sampling to guide effective vancomycin dose recommendations.

Rapid Colloidal Gold Immunoassay for Pharmacokinetic Evaluation of Vancomycin in the Cerebrospinal Fluid and Plasma of Beagle Dogs

Vancomycin (VAN), a glycopeptide antibiotic, is the preferred therapeutic agent for treating Gram-positive bacteria. Rapid and precise quantification of VAN levels in cerebrospinal fluid (CSF) and plasma is crucial for optimized drug administration, particularly among elderly patients. Herein, we introduce a novel clinical test strip utilizing colloidal gold competitive immunoassay technology for the expedient detection of VAN. This test strip enables the detection of VAN concentrations in clinical samples such as plasma within 10 min and has a limit of detection of 10.3 ng/mL, with an inhibitory concentration 50% (IC50) value of 44.5 ng/mL. Furthermore, we used the test strip for pharmacokinetic analysis of VAN in the CSF and plasma of beagle dogs. Our results provide valuable insights into the fluctuations of the drug concentration in the CSF and plasma over a 24 h period after a single intravenous dose of 12 mg/kg. The test strip results were compared with the results obtained via liquid chromatography-mass spectrometry methods, and the measured VAN concentrations in the CSF and plasma via both of the methods showed excellent agreement.

Sensorization of microfluidic brain-on-a-chip devices: Towards a new generation of integrated drug screening systems

Brain-on-a-chip (BoC) devices show typical characteristics of brain complexity, including the presence of different cell types, separation in different compartments, tissue-like three-dimensionality, and inclusion of the extracellular matrix components. Moreover, the incorporation of a vascular system mimicking the blood-brain barrier (BBB) makes BoC particularly attractive, since they can be exploited to test the brain delivery of different drugs and nanoformulations. In this review, we introduce the main innovations in BoC and BBB-on-a-chip models, especially focusing sensorization: electrical, electrochemical, and optical biosensors permit the real-time monitoring of different biological phenomena and markers, such as the release of growth factors, the expression of specific receptors/biomarkers, the activation of immune cells, cell viability, cell-cell interactions, and BBB crossing of drugs and nanoparticles. The recent improvements in signal amplification, miniaturization, and multiplication of the sensors are discussed in an effort to highlight their benefits versus limitations and delineate future challenges in this field.

Dual-Aptamer Drift Canceling Techniques to Improve Long-Term Stability of Real-Time Structure-Switching Aptasensors

This paper presents a dual-aptamer scheme to mitigate signal drifts caused by structure-switching aptamers during long-term monitoring. Electrochemical aptamer-based (E-AB) biosensors have recently shown great potential for continuous in vivo monitoring. However, the accuracy of detection is often limited by signaling drifts. Traditional approaches rely on kinetic differential measurements (KDM) coupled with square-wave voltammetry to eliminate these drifts. Yet, we have discovered that KDM does not apply universally to all aptamers, as their responses at different SWV frequencies heavily rely on their structure-switching characteristics and the electron transfer (ET) kinetics of the redox reporters. In light of this, we propose a "dual-aptamer" scheme that utilizes two aptamers, each responding differently to the same target molecule to cancel out drift. These paired aptamers are identified through (1) screening from an existing pool of aptamers and (2) engineering the signaling behavior of the redox reporters. We demonstrate the differential signaling of the aptamer pair in the presence of ampicillin and ATP molecules and show that the pair exhibits similar drifts in undiluted goat serum. By implementing drift cancelation, sensor drift is reduced by a factor of 370. Additionally, the differential signaling enables an increased recording throughput by leveraging differential readout electronics. The authors believe that the proposed technique holds significant benefits for long-term in vivo monitoring.

Revolutionizing Precision Medicine: Exploring Wearable Sensors for Therapeutic Drug Monitoring and Personalized Therapy

Precision medicine, particularly therapeutic drug monitoring (TDM), is essential for optimizing drug dosage and minimizing toxicity. However, current TDM methods have limitations, including the need for skilled operators, patient discomfort, and the inability to monitor dynamic drug level changes. In recent years, wearable sensors have emerged as a promising solution for drug monitoring. These sensors offer real-time and continuous measurement of drug concentrations in biofluids, enabling personalized medicine and reducing the risk of toxicity. This review provides an overview of drugs detectable by wearable sensors and explores biosensing technologies that can enable drug monitoring in the future. It presents a comparative analysis of multiple biosensing technologies and evaluates their strengths and limitations for integration into wearable detection systems. The promising capabilities of wearable sensors for real-time and continuous drug monitoring offer revolutionary advancements in diagnostic tools, supporting personalized medicine and optimal therapeutic effects. Wearable sensors are poised to become essential components of healthcare systems, catering to the diverse needs of patients and reducing healthcare costs.

Continuous Molecular Monitoring in the Body via Nucleic Acid-based Electrochemical Sensors: The Need for Statistically-powered Validation

Nucleic acid-based electrochemical (NBE) sensors offer real-time and reagent-free sensing capabilities that overcome limitations of target-specific reactivity via affinity-based molecular detection. By leveraging affinity probes, NBE sensors become modular and versatile, allowing the monitoring of a variety of molecular targets by simply swapping the recognition probe without the need to change their sensor architecture. However, NBE sensors have not been rigorously validated in vivo in terms of analytical performance and clinical agreement relative to benchmark methods. In this article, we highlight reports from the past three years that evaluate NBE sensors performance in vivo. We hope this discussion will inspire future translational efforts with statistically robust experimental design, thus enabling real-world clinical applications and commercial development of NBE sensors.

Expanding the Monolayer Scope for Nucleic Acid-Based Electrochemical Sensors Beyond Thiols on Gold: Alkylphosphonic Acids on ITO

Electrochemical biosensors are a powerful and rapidly evolving molecular monitoring technology. Evidenced by the success of the continuous glucose monitor in managing Type 1 Diabetes, these sensors are capable of precise, accurate measurements in unprocessed biological environments. Nucleic acid-based electrochemical sensors (NBEs) are a specific type of biosensor that employs the target binding and conformational dynamics of nucleic acids for signal transduction. Currently, the vast majority of NBEs are fabricated via self-assembly of alkylthiols on Au electrodes. However, this architecture is limited in scope, as Au electrodes are not universally deployable for all potential NBE applications. Here, to expand the repertoire of materials on which NBEs can be made, we describe the multistep procedure for creating sensing monolayers of alkylphosphonic acids on a conductive oxide surface. Using such monolayers on indium tin oxide (ITO)-coated glass slides, we couple redox reporter-modified nucleic acids and demonstrate signaling of procaine-binding NBE sensors in buffer and human serum. We investigate the operational stability of these NBE sensors to reveal faster signal loss relative to benchmark thiol-on-gold sensing layers, a result that arises due to poor stability of the underlying ITO. Finally, we discuss future directions to continue expansion of NBE sensor materials and 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.