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

Molecularly Responsive Aptamer-Functionalized Hydrogel for Continuous Plasmonic Biomonitoring

Continuous in vivo monitoring of small molecule biomarkers requires biosensors with reversibility, sensitivity in physiologically relevant ranges, and biological stability. Leveraging the real-time, label-free detection capability of surface plasmon resonance (SPR) technology, a molecularly responsive hydrogel film is introduced to enhance small molecule sensitivity. This advanced biosensing platform utilizes split-aptamer-cross-linked hydrogels (aptagels) engineered using 8-arm poly(ethylene glycol) macromers, capable of directly and reversibly detecting vancomycin. Investigation through SPR and optical waveguide mode, along with quartz crystal microbalance with dissipation (QCM-D) monitoring, reveals that the reversible formation of analyte-induced ternary molecular complexes leads to aptagel contraction and significant refractive index changes. Optimization of aptamer cross-link distribution and complementarity of split-aptamer pairs maximizes conformational changes of the aptagel, demonstrating a detection limit of 160-250 nM for vancomycin (6-9 fold improvement over monolayer counterpart) with a broad linear sensing range up to 1 mM. The aptagel maintains stability over 24 h in blood serum and 5 weeks in diluted blood plasma (mimicking interstitial fluid). This structurally responsive aptagel platform with superior stability and sensitivity offers promising avenues for continuous in vivo monitoring of small molecules.

Direct detection of doxorubicin in whole blood using a hydrogel-protected electrochemical aptamer-based biosensor

Electrochemical aptamer-based biosensors (EABs) have been developed for multiple important biomarkers for their convenient and real-time features. However, the application of EABs in complex biological fluids has been limited by the rapid loss of sensitivity and selectivity due to inactivation and biofouling of aptamer probes and electrodes. To address this issue, we report the preparation of a simple hydrogel-protected aptamer-based biosensor (HP-EAB) for direct detection of Doxorubicin (DOX) in whole blood. The aptamer provides excellent selectivity for the electrochemical sensor, allowing the prepared sensor to accurately detect DOX in a 50-fold diluted whole blood sample. The agarose hydrogel coating on the electrode surface allows the passage of small molecules while hindering the adsorption of biomolecules from the whole blood matrix to the electrode surface. The experimental results show that the prepared HP-EAB has high stability compared with the unprotected EAB, and the HP-EAB maintains excellent detection performance after 7 days of storage. The hydrogel coating can effectively reduce the non-specific response to the whole blood matrix and prolong the life-time of the sensor. When used to detect DOX in rabbit whole blood, the HP-EAB exhibited excellent detection performance with a detection limit of 25.9 nM (S/N = 3) and a detection range of 0.1 μM-50 μM. The developed HP-EAB provides an excellent platform for the rapid and accurate determination of important analytes in complex biological fluids.

From signal-off to signal-on: polyT linker alters signal response mode and enhances signal change of aptamer beacon probe

A molecular beacon is an oligonucleotide hybridization probe that can report the presence of specific nucleic acids in homogeneous solutions. Using an aptamer has allowed an aptamer-based molecular beacon-aptamer beacon to be developed, which has shown advantages of simplicity, rapidity, and sensitivity in imaging and sensing non-nucleic acid substances. However, due to requirement for a deliberate DNA hairpin structure for the preparation of a molecular beacon, not any given aptamer is suitable for designing an aptamer beacon probe. This paper provides a general design strategy for the preparation of an aptamer beacon probe, which theoretically can be used for any given aptamer. Through coupling an aptamer and a short complementary DNA into one DNA molecule via a rational poly thymidine (T) linker, novel molecular beacon probes are successfully prepared and used for the detection of targets (aflatoxin B1 and ochratoxin A). The working mechanism of this aptamer beacon probe is based on intramolecular hybridization/dehybridization, which is more efficient than commonly aptasensor strategies based on intermolecular reactions. This aptamer beacon probe shows advantages of low background, a signal-on response, a large signal change, as well as simplicity and rapidity of analysis, which have promising application potential.

Engineered Aptamer-Derived Fluorescent Aptasensor: the Label-Free, Single-Step, Rapid Detection of Vancomycin in Clinical Samples

Currently, the reported vancomycin (VCM) aptamers, including the 3- (Kd  =  9.13 × 10-6 m) and 4-truncated variants (Kd = 45.5 × 10-6 m), are engineered via stem truncation of the VCM parent aptamer, which inevitably compromises their affinities, thus affecting their clinical application within the VCM therapeutic window of 6.9-13.8 × 10-6 m. Herein, the binding pocket of the VCM parent aptamer is elucidated for the first time and we implemented the Post-SELEX modification strategy involving truncation and mutagenesis to refined the VCM parent aptamer. This yielded a VCM aptamer (ABC20-11) with an intramolecular G-triplex, an enhanced thioflavin T (ThT) fluorescence intensity, and an improved affinity (Kd = 0.591 × 10-6 m) and specificity (one-methyl level) for VCM. Utilizing a portable fluorescence detector specifically designed for rapidly detecting VCM concentration and leveraging the competitive binding between VCM and ThT to ABC20-11, a label-free fluorescent aptasensor is developed. This aptasensor exhibits exceptional analytical performances across various clinical samples (serum, cerebrospinal fluid, and joint fluid), with corresponding linear ranges of 0.5-50, 0.5-40, and 0.5-50 × 10-6 m and detection limits at 0.11, 0.12, and 0.16 × 10-6 m, respectively. Consequently, the proposed VCM aptasensor displays considerable clinical value and potential for use in rapid VCM detection.

Ferrocenyl Compounds as Alternative Redox Labels for Robust and Versatile Electrochemical Aptamer-Based Sensors

This study explores the potential of seven ferrocenyl (Fc) compounds with cross-linking groups as alternative redox labels to methylene blue (MB) for electrochemical aptamer-based (E-AB) sensors. The cross-linking efficiency, formal potential (E0'), and electrochemical durability of these compounds were evaluated. Compound Fc1a-X exhibited superior performance, characterized by efficient cross-linking, a moderate and pH-insensitive E0', and enhanced durability during repeated potential scans. The attachment of Fc1a-X, which includes a 3-carbon chain spacer and an N-hydroxysuccinimide-ester cross-linking group, to an amine-terminated monolayer on a Au electrode demonstrated high cross-linking efficiency, which is critical for achieving high sensitivity. The E0' of Fc1a-X attached to the aptamer monolayer was 0.14 V, which is within the optimal range of -0.2 to 0.2 V vs Ag/AgCl. Square wave voltammetry showed that the peak potential and current of Fc1a-X are pH-insensitive, which is critical for versatile use. In serum, Fc1a-X maintained stable peak current levels without a gradual decrease after an initial rapid decrease during the first 2 h with considerably less reduction over 12 h compared to MB. Using Fc1a-X as the redox label, an E-AB sensor effectively detected doxorubicin in serum, covering the clinical range. These findings suggest Fc1a-X as a promising candidate for developing robust, versatile, and sensitive E-AB sensors.

Aptamer-Mediated Electrochemical Detection of SARS-CoV-2 Nucleocapsid Protein in Saliva

Gold standard detection of SARS-CoV-2 by reverse transcription quantitative PCR (RT-qPCR) can achieve ultrasensitive viral detection down to a few RNA copies per sample. Yet, the lengthy detection and labor-intensive protocol limit its effectiveness in community screening. In view of this, a structural switching electrochemical aptamer-based biosensor (E-AB) targeting the SARS-CoV-2 nucleocapsid (N) protein was developed. Four N protein-targeting aptamers were characterized on an electrochemical cell configuration using square wave voltammetry (SWV). The sensor was investigated in an artificial saliva matrix optimizing the aptamer anchoring orientation, SWV interrogation frequency, and target incubation time. Rapid detection of the N protein was achieved within 5 min at a low nanomolar limit of detection (LOD) with high specificity. Specific N protein detection was also achieved in simulated positive saliva samples, demonstrating its feasibility for saliva-based rapid diagnosis. Further research will incorporate novel signal amplification strategies to improve sensitivity for early diagnosis.

A novel and sensitive electrochemical aptasensor for sulfadimethoxine detection based on the triple helix/exonuclease I-assisted double-amplification strategy

In this paper, a novel and sensitive electrochemical aptasensor for sulfadimethoxine (SDM) detection has been designed based on the triple helix structure/exonuclease I (Exo I)-assisted double signal amplification strategy. The aptamer probe (Apt) hybridizes with the signal transduction probe (STP) on the electrode to form a rigid double-stranded DNA (dsDNA) structure, so that the STP remains upright and methylene blue (MB) on the STP is far away from the electrode surface, resulting in a delicate current signal. In the presence of SDM, the SDM and Apt combine into a complex, leading to the transfer of the Apt and the exposure of the STP. Meanwhile, the added Exo I can digest the Apt to realize the cyclic amplification of SDM. After the addition of the signal probe (SP), a triple helix structure between the SP and STP is formed under acidic conditions, and MB on the STP and SP collide with the electrode surface to generate a strong electrochemical signal. The proposed aptasensor combines the features of the triple helix structure and Exo I to achieve double signal amplification for the sensitive detection of SDM with a wide linear range of 0.05-1000 ng mL-1 and a low detection limit of 0.02 ng mL-1. Furthermore, it has been successfully used to detect SDM in milk and lake water samples.

Recent advances in aptamer-based biosensors for potassium detection

Maintaining a stable level of potassium is crucial for proper bodily function because even a slight imbalance can result in serious disorders like hyperkalemia and hypokalemia. Therefore, detecting and monitoring potassium ion (K+) levels are of utmost importance. Various biosensors have been developed for rapid K+ detection, with aptamer-based biosensors garnering significant attention due to their high sensitivity and specificity. This review focuses on aptamer-based biosensors for K+ detection, providing an overview of their signal generation strategies, including electrochemical, field-effect transistor, nanopore, colorimetric, and fluorescent systems. The analytical performance of these biosensors is evaluated comprehensively. In addition, factors that affect their efficiency, such as their physicochemical properties, regeneration for reusability, and linkers/spacers, are listed. Lastly, this review examines the major challenges faced by aptamer-based biosensors in K+ detection and discusses potential future developments.

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.

Continuous Square Wave Voltammetry for High Information Content Interrogation of Conformation Switching Sensors

Square wave voltammetry (SWV) is a voltammetric technique for measuring Faradaic current while minimizing contributions from non-Faradaic processes. In square wave voltammetry, the potential waveform applied to a working electrode and the current sampling protocols followed are designed to minimize contributions from non-Faradaic processes (i.e., double layer charging) to improve voltammetric sensitivity. To achieve this, the current is measured at the end of each forward and reverse potential pulse after allowing time for non-Faradaic currents to decay exponentially. A consequence of sampling current at the end of a potential pulse is that the current data from the preceding time of the potential pulse are discarded. These discarded data can provide information about the non-Faradaic contributions as well as information about the redox system including charge transfer rates. In this paper, we introduce continuous square wave voltammetry (cSWV), which utilizes the continuous collection of current to maximize the information content obtainable from a single voltammetry sweep eliminating the need for multiple scans. cSWV enables acquiring a multitude of voltammograms corresponding to various frequencies and, thus, different scan rates from a single sweep. An application that benefits significantly from cSWV is conformation switching, functional nucleic acid sensors. We demonstrate the utility of cSWV on two representative small molecules targeting electrochemical, aptamer-based sensors. Moreover, we show that cSWV provides comparable results to those obtained from traditional square wave voltammetry, but with cSWV, we are able to acquire dynamic information about the sensor surfaces enabling rapid calibration and optimization of sensing performance. We also demonstrate cSWV on soluble redox markers. cSWV can potentially become a mainstay technique in the field of conformation switching sensors.

Os(II/III) complex supports pH-insensitive electrochemical DNA-based sensing with superior operational stability than the benchmark methylene blue reporter

DNA-based electrochemical sensors use redox reporters to transduce affinity events into electrical currents. Ideally, such reporters must be electrochemically reversible, chemically stable for thousands of redox cycles, and tolerant to changing chemical environments. Here we report the first use of an Os(II/III) complex in DNA-based sensors, which undergoes pH-insensitive electron transfer with 35% better operational stability relative to the benchmark methylene blue, making it a promising reporter for continuous molecular monitoring applications where pH fluctuates with time.

Finding the Lost Dissociation Constant of Electrochemical Aptamer-Based Biosensors

Electrochemical aptamer-based (E-AB) biosensors afford real-time measurements of the concentrations of molecules directly in complex matrices and in the body, offering alternative strategies to develop innovative personalized medicine tools. While different electroanalytical techniques have been used to interrogate E-AB sensors (i.e., cyclic voltammetry, electrochemical impedance spectroscopy, and chronoamperometry) to resolve the change in electron transfer of the aptamer's covalently attached redox reporter, square-wave voltammetry remains a widely used technique due to its ability to maximize the redox reporter's faradic contribution to the measured current. Several E-AB sensors interrogated with this technique, however, show lower aptamer affinity (i.e., μM-mM) even in the face of employing aptamers that have high affinities (i.e., nM-μM) when characterized using solution techniques such as isothermal titration calorimetry (ITC) or fluorescence spectroscopy. Given past reports showing that E-AB sensor's response is dependent on square-wave interrogation parameters (i.e., frequency and amplitude), we hypothesized that the difference in dissociation constants measured with solution techniques stemmed from the electrochemical interrogation technique itself. In response, we decided to compare six dissociation constants of aptamers when characterized in solution with ITC and when interrogated on electrodes with electrochemical impedance spectroscopy, a technique able to, in contrast to square-wave voltammetry, deconvolute and quantify E-AB sensors' contributions to the measured current. In doing so, we found that we were able to measure dissociation constants that were either separated by 2-3-fold or within experimental errors. These results are in contrast with square-wave voltammetry-measured dissociation constants that are at the most separated by 2-3 orders of magnitude from ones measured by ITC. We thus envision that the versatility and time scales covered by electrochemical impedance spectroscopy offer the highest sensitivity to measure target binding in electrochemical biosensors relying on changes in electron-transfer rates.

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

The measurement of serum vancomycin levels at the clinic is critical to optimizing dosing given the narrow therapeutic window of this antibiotic. Current approaches to quantitate serum vancomycin levels are based on immunoassays, which are multistep methods requiring extensive processing of patient samples. As an alternative, vancomycin-binding electrochemical, aptamer-based sensors (E-ABs) were developed to simplify the workflow of vancomycin monitoring. E-ABs enable the instantaneous measurement of serum vancomycin concentrations without the need for sample dilution or other processing steps. However, the originally reported vancomycin-binding E-ABs had a dissociation constant of 45 μM, which is approximately 1 order of magnitude higher than the recommended trough concentrations of vancomycin measured in patients. This limited sensitivity hinders the ability of E-ABs to accurately support vancomycin monitoring. To overcome this problem, here we sought to optimize the length of the vancomycin-binding aptamer sequence to enable a broader dynamic range in the E-AB platform. Our results demonstrate, via isothermal calorimetry and E-AB calibrations in undiluted serum, that superior affinity and near-equal sensor gain in vitro can be achieved using a one-base-pair-longer aptamer than the truncated sequence originally reported. We validate the impact of the improved binding affinity in vivo by monitoring vancomycin levels in the brain cortex of live mice following intravenous administration. While the original sequence fails to resolve vancomycin concentrations from baseline noise (SNR = 1.03), our newly reported sequence provides an SNR of 1.62 at the same dose.

Wearable chemical sensors for biomarker discovery in the omics era

Biomarkers are crucial biological indicators in medical diagnostics and therapy. However, the process of biomarker discovery and validation is hindered by a lack of standardized protocols for analytical studies, storage and sample collection. Wearable chemical sensors provide a real-time, non-invasive alternative to typical laboratory blood analysis, and are an effective tool for exploring novel biomarkers in alternative body fluids, such as sweat, saliva, tears and interstitial fluid. These devices may enable remote at-home personalized health monitoring and substantially reduce the healthcare costs. This Review introduces criteria, strategies and technologies involved in biomarker discovery using wearable chemical sensors. Electrochemical and optical detection techniques are discussed, along with the materials and system-level considerations for wearable chemical sensors. Lastly, this Review describes how the large sets of temporal data collected by wearable sensors, coupled with modern data analysis approaches, would open the door for discovering new biomarkers towards precision medicine.

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.

Aptasensors for the detection of infectious pathogens: design strategies and point-of-care testing

The epidemic of infectious diseases caused by contagious pathogens is a life-threatening hazard to the entire human population worldwide. A timely and accurate diagnosis is the critical link in the fight against infectious diseases. Aptamer-based biosensors, the so-called aptasensors, employ nucleic acid aptamers as bio-receptors for the recognition of target pathogens of interest. This review focuses on the design strategies as well as state-of-the-art technologies of aptasensor-based diagnostics for infectious pathogens (mainly bacteria and viruses), covering the utilization of three major signal transducers, the employment of aptamers as recognition moieties, the construction of versatile biosensing platforms (mostly micro and nanomaterial-based), innovated reporting mechanisms, and signal enhancement approaches. Advanced point-of-care testing (POCT) for infectious disease diagnostics are also discussed highlighting some representative ready-to-use devices to address the urgent needs of currently prevalent coronavirus disease 2019 (COVID-19). Pressing issues in aptamer-based technology and some future perspectives of aptasensors are provided for the implementation of aptasensor-based diagnostics into practical application.