Electrochemical quantitation of DNA immobilized on gold

Solution-phase nucleic acid reaction weaves interfacial barriers on unmodified electrodes: Just-in-time generation of sensor interface for convenient and highly sensitive bioassays

Electrochemical bioassays that rely on sensor interfaces based on immobilized DNA probes often encounter challenges such as complex fabrication processes and limited binding efficiency. In this study, we developed a novel electrochemical bioassay that bypasses the need for probe immobilization by employing a solution-phase nucleic acid reaction to create interfacial barriers on unmodified electrodes, enabling rapid, just-in-time sensor interface formation. Specifically, a 3'-phosphorylated recognition probe was used to identify the target microRNA-21 (miR-21), followed by target recycling facilitated by duplex-specific nuclease (DSN), which resulted in extensive hydrolysis of the recognition probe into DNA fragments with 3'-hydroxyl ends. These fragments were then extended by terminal deoxynucleotidyl transferase (TdT) to form long poly(A) tails. The extended products hybridized with a thiolated assembly probe rich in thymine bases and subsequently assembled on the unmodified gold electrode (AuE) surface, creating a "barrier effect" that hindered the adsorption of streptavidin-HRP (SA-HRP) on the AuE, generating a detectable electrochemical signal. This method demonstrated excellent analytical performance, with a linear detection range from 10 fM to 10 nM and a detection limit as low as 4.3 fM. Moreover, the assay was successfully applied to detect miR-21 in real biological samples, including cell lines and bladder urothelial carcinoma surgical resection specimens, showing strong concordance with RT-qPCR results. The developed method offers a new approach for establishing electrochemical bioassays without the need for pre-immobilization of probes and with minimal reagent use, presenting a promising tool for clinical diagnostics and cancer research.

Detection of HPV 16 and 18 L1 genes by a nucleic acid amplification-free electrochemical biosensor powered by CRISPR/Cas9

Cervical cancer, closely linked to Human Papillomavirus (HPV) infection, remains a significant health threat for women worldwide. Conventional HPV detection methods, such as reverse transcription polymerase chain reaction (RT-PCR), rely on nucleic acid amplification (NAA), which can be costly and time-consuming. This study introduces an NAA-free electrochemical Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based biosensor designed to detect HPV 16 and HPV 18 L1 genes simultaneously. The system utilizes a Cas9-single guided RNA complex to initiate a selective cleavage reaction, releasing Methylene blue or Ferrocene-labeled fragments correlate to L1 gene concentrations. These fragments then interact with modified gold electrodes immobilized with a complementary probe, allowing precise electrochemical signal measurement during hybridization. The biosensor offers a wide detection range from 1 fM to 10 nM, with detection limits as low as 0.4 fM for HPV 16 L1 and 0.51 fM for HPV 18 L1, providing a sensitive and efficient solution for L1 gene detection. Additionally, its specificity and sensitivity closely match RT-PCR results in clinical testing, highlighting its potential for molecular diagnostics and point-of-care applications.

Using Disulfide DNA to Enhance Control over DNA Self-Assembled Monolayer Surface Coverage and Reduce Impedance Signal Drift

Thiolated DNA biopolymer probes are widely used for their spontaneous interactions with gold electrodes to achieve self-assembled monolayers (SAMs) of DNA. This offers an attractive class of bio-interfaces for developing point-of-care (POC) diagnostics. However, SAMs are prone to structural instability and can be challenging to reproducibly fabricate for probes of different sizes and shapes. Among methods of studying SAMs, electrochemical impedance spectroscopy (EIS) has attracted a lot of attention for its extremely high sensitivity to surface electrostatics and its label-free operation. However, the strong interfacial sensitivity also brings about susceptibility to unstable and drifting impedance signals due to the disorganization of the SAM, which has thwarted the development of EIS analytical methods. Here, we combine EIS and chronocoulometry (CC) to investigate the formation of DNA SAMs created via different methods and demonstrate the impact on the quality of SAMs via background signal drifts and DNA density fixation. Specifically, we find that enhancing stability and suppressing background drift require maximizing the density of upright DNA probes. This understanding led us to develop a protocol in which thiolated DNA probes are delivered to gold surfaces in the form of disulfide dimers. This approach not only enhances the surface density by pairwise delivery but also results in controllable probe density, and it may also intrinsically favor probes binding in the stable upright position, thereby eliminating a key obstacle for creating DNA monolayers adsorbed onto gold surfaces.

Tuning Ion Current Rectifying Nanopipettes for Sensitive Detection of Methicillin-Resistant Staphylococcus aureus

Infectious diseases pose a growing challenge in healthcare, with the increasing rate of antimicrobial resistance limiting therapeutic options available for treatment. Rapid detection of infections at the earliest opportunity can significantly improve patient outcomes. In this report, ion current rectifying quartz nanopipettes with ca. 109 nm orifices were utilized for the label-free detection of DNA indicative of methicillin-resistant Staphylococcus aureus (MRSA). By immobilizing probe DNA complementary to the mecA gene on the internal walls of the nanopipette, the detection was achieved by monitoring changes in ion current rectification (ICR) following probe-target hybridization. We demonstrate enhanced sensitivity by controlling the surface probe density, resulting in a tunable, sensitive sensor technology with a detection limit as low as 0.35 pM. Finite element simulations are used to support our experimental findings, revealing that to maximize target-induced changes to ICR, the probe surface density must be minimized. This sensitive and label-free methodology was integrated with the polymerase chain amplification reaction to achieve selective identification of this pathogen from laboratory-grown cultures, highlighting that ion current rectifying nanopipette sensors offer the potential to be a cost-effective and rapid tools for infectious disease detection.

Programming the Dynamic Range of Nanochannel Biosensors for MicroRNA Detection Through Allosteric DNA Probes

Solid-state nanochannel biosensors are extensively utilized for microRNA (miRNA) detection owing to their high sensitivity and rapid response. However, conventional nanochannel biosensors face limitations in their fixed dynamic range, restricting their versatility and efficacy. Herein, we introduce tunable triblock DNA probes with varying affinities for target miRNA to engineer solid-state nanochannel biosensors capable of customizable dynamic range adjustment. The triblock DNA architecture comprises a poly-adenine (polyA) block for adjustable surface density anchoring, alongside stem and loop blocks for modulating structural stability. Through systematic manipulation of these blocks, we demonstrate the ability to achieve diverse target binding affinities and detection limits, achieving an initial 81-fold dynamic range. By combining probes with various affinities, we extend this dynamic range significantly to 10,900-fold. Furthermore, by implementing a sequestration mechanism, the effective dynamic range of the nanochannel biosensor is narrowed to only a 3-fold span of target concentrations. The customizable dynamic range of these advanced nanochannel biosensors makes them highly promising for a broad spectrum of biomedical and clinical applications.

A Truncated Multi-Thiol Aptamer-Based SARS-CoV-2 Electrochemical Biosensor: Towards Variant-Specific Point-of-Care Detection with Optimized Fabrication

With the goal of fast and accurate diagnosis of infectious diseases, this study presents a novel electrochemical biosensor that employs a refined aptamer (C9t) for the detection of spike (S) protein SARS-CoV-2 variants in a flexible multielectrode aptasensor array with PoC capabilities. Two aptamer modifications were employed: removing the primer binding sites and including two dithiol phosphoramidite anchor molecules. Thus, reducing fabrication time from 24 to 3 h and increasing the stability and sparseness for multi-thiol aptasensors compared to a standard aptasensor using single thiols, without a reduction in aptamer density. The biosensor fabrication, optimization, and detection were verified in detail by electrochemistry, QCM-D, SPR, and XPS. The analyte-receptor binding was further confirmed spectroscopically at the level of individual molecules by AFM-IR. The aptasensor possesses a low limit of detection (8.0 fg/mL), the highest sensitivity reported for S protein (209.5 signal per concentration decade), and a wide dynamic detection range (8.0 fg/mL-38 ng/mL) in nasopharyngeal samples, covering the clinically relevant range. Furthermore, the C9t aptasensor showed high selectivity for SARS-CoV-2 S proteins over biomarkers for MERS-CoV, RSV, and Influenza. Even more, it showed a three times higher sensitivity for the Omicron in comparison to the Wuhan strain (wild type), alpha, and beta variants of the SARS-CoV-2 virus. Those results demonstrate the creation of an affordable and variant-selective refined C9t aptasensor that outperformed current rapid diagnosis tests.

Rapid and direct detection of m6A methylation by DNAzyme-based and smartphone-assisted electrochemical biosensor

m6A methylation detection is crucial for understanding RNA functions, revealing disease mechanisms, guiding drug development and advancing epigenetics research. Nevertheless, high-throughput sequencing and liquid chromatography-based traditional methods still face challenges to rapid and direct detection of m6A methylation. Here we report a DNAzyme-based and smartphone-assisted electrochemical biosensor for rapid detection of m6A. We initially identified m6A methylation-sensitive DNAzyme mutants through site mutation screening. These mutants were then combined with tetrahedral DNA to modify the electrodes, creating a 3D sensing interface. The detection of m6A was accomplished by using DNAzyme to capture and cleave the m6A sequence. The electrochemical biosensor detected the m6A sequence at nanomolar concentrations with a low detection limit of 0.69 nM and a wide detection range from 10 to 104 nM within 60 min. As a proof of concept, the 3'-UTR sequence of rice was selected as the m6A analyte. Combined with a smartphone, our biosensor shows good specificity, sensitivity, and easy-to-perform features, which indicates great prospects in the field of RNA modification detection and epigenetic analysis.

Pathogen-Specific Electrochemical Real-Time LAMP Detection Using Universal Solid-Phase Probes on Carbon Electrodes

Epidemic infections and spreading antibiotic resistance require diagnostic tests that can be rapidly adopted. To reduce the usually time-consuming adaptation of molecular diagnostic tests to changing targets, we propose the novel approach of a repurposable sensing electrode functionalization with a universal, target-independent oligonucleotide probe. In the liquid phase covering the electrode, the target sequence is amplified by MD LAMP (mediator-displacement loop-mediated isothermal amplification) releasing a generic methylene blue-labeled mediator, which specifically hybridizes to the solid-phase probe. To demonstrate the universality of the approach, two different pathogens, Staphylococcus aureus (crude lysate) and Treponema pallidum, are detected using the same solid-phase probe. The reactions reach a limit of detection of 1 × 103 and 4 × 102 copies per reaction within 30 min, respectively. The solid-phase probes carry a carboxymethyl aniline modification to form covalent C-C bonds on low-cost carbon electrodes. Maximum surface coverage and maximum hybridization signals are observed at grafting concentrations of ≥2 μM solid-phase probes. Successful detection of spiked target DNA in real swab samples and with three different commercial amplification buffers proved the broad applicability of this assay approach. The electrochemical MD LAMP is fast, compatible with dsDNA targets, and requires only minimal adaptation of an established amplification method. It is easily transferable to existing analytical electrochemical platforms, allowing the consumable to be synergistically used for different targets. The suggested approach of repurposable functionalized electrodes can also be considered to increase the preparedness for future epidemic or pandemic outbreaks as well as rapidly evolving resistance patterns or variants.

Optimizing Tris(2-Carboxyethyl)phosphine and Mercaptohexanol Concentrations for Thiolated Oligonucleotide Immobilization on Platinum Electrodes in Microfluidic Platforms

In this study, we propose a strategy to explore the impact of the proportion of tris(2-carboxyethyl)phosphine (TCEP) and 6-mercaptohexanol (MCH) on the efficiency of oligonucleotide functionalization on PDMS microfluidic channels equipped with pairs of homemade microfabricated platinum microelectrodes. We identified an optimal concentration of these compounds that enables the effective orientation and distribution of probes, thereby facilitating subsequent target hybridization. The experiment included optimizing sample injection into microfluidic channels. We used TCEP as a reducing agent to help the DNA probes adhere to the channel electrode better. This stopped the formation of disulfide bonds during the probe immobilization step. We found the optimal TCEP/MCH mixture ratio (5 mM TCEP and 50 mM MCH), which led to a more uniform distribution and orientation of the DNA probes on the platinum electrode. These optimized conditions resulted in a more compact DNA monolayer and enhanced detection capabilities. The biosensor's performance was evaluated by the detection of the hybridization of complementary DNA sequences in the presence of equimolar Fe(CN)63-/Fe(CN)64-. The detection of the synthetic GP8 resistance gene is facilitated by a measurable decrease in the electron transfer rate, which is directly proportional to its concentration. Under the optimized conditions, the DNA biosensor showed excellent sensitivity (with a detection limit of 10-17 M) and high specificity when tested against noncomplementary DNA strands.

Hybridization-driven synchronous regeneration of biosensing interfaces for Listeria monocytogenes based on recognition of fullerol to single- and double-stranded DNA

A novel sensitive and reusable electrochemical biosensor for Listeria monocytegenes DNA has been constructed based on the recognition of water-soluble hydroxylated fullerene (fullerol) to single- and double-stranded DNA. First, the fullerol was electrodeposited on glassy carbon electrode (GCE), acting as a matrix for non-covalent adsorption of single-stranded probe DNA. Upon hybridization with the target DNA, the double helix structure was formed and desorbed from the electrode surface, driving synchronous regeneration of the biosensing interfaces. The biosensor showed a probe DNA loading density of 144 pmol∙cm-2 with the hybridization efficiency of 72.2%. The biosensor is applicable for the analysis of target DNA in actual milk samples with recoveries between 101.0% and 104.0%. This sensing platform provides a simple method for the construction of sensitive and reusable biosensor to monitor Listeria monocytogenes-related food pollution.

Variable gain DNA nanostructure charge amplifiers for biosensing

Electronic measurements of engineered nanostructures comprised solely of DNA (DNA origami) enable new signal conditioning modalities for use in biosensing. DNA origami, designed to take on arbitrary shapes and allow programmable motion triggered by conjugated biomolecules, have sufficient mass and charge to generate a large electrochemical signal. Here, we demonstrate the ability to electrostatically control the DNA origami conformation, and thereby the resulting signal amplification, when the structure binds a nucleic acid analyte. Critically, unlike previous studies that employ DNA origami to amplify an electrical signal, we show that the conformation changes under an applied field are reversible. This applied field also simultaneously accelerates structural transitions above the rate determined by thermal motion. We tuned this property of the structures to achieve a response that was ≈2 × 104 times greater (i.e., a gain or amplification) than the value from DNA hybridization under similar conditions. Because this signal amplification is independent of DNA origami-analyte interactions, our approach is agnostic of the end application. Furthermore, since large signal changes are only triggered in response to desirable interactions, we minimize the deleterious effects of non-specific binding. The above benefits of self-assembled DNA origami make them ideally suited for multiplexed biosensing when paired with highly parallel electronic readout.

Electrochemically modulated surface plasmon waves for characterization and interrogation of DNA-based sensors

This work reports on a comparative analysis of electrical and optical measurements for structural characterization and for assessing signal transduction performance of a redox-labeled DNA-based sensing platform. We conducted complementary investigations employing conventional electrochemical techniques with electric current measurements in cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) and confronted those results with optical measurements using surface plasmon waves while the redox assembly was undergoing similar electrochemical modulation as in the electrical CV and EIS measurements. The specific sensor configuration deployed here was composed of a methylene blue (MB)-modified single-stranded DNA (ssDNA) signaling probe and an unlabeled capture ssDNA probe that complements the signaling probe. Two types of signaling probes were employed: one with MB attached to the 3' end, which positions the redox marker closer to the electrode surface upon hybridization with the capture probe, and the other with MB attached to the 5' end, which places the redox marker farther from the electrode surface. For each molecular assembly and for each electrochemical modulation protocol, both the electrical and optical experimental data were quantitatively analyzed to determine the surface density of electro-active species and the rate of electron transfer between the redox marker and the electrode surface. Our experimental results highlight the consistency of the confronted methodologies and indicate that optical impedance spectroscopy utilizing electrochemically modulated surface plasmon waves, which is a transduction protocol immune from non-faradaic interferents that invariably are present in the electrical methodology, can provide a powerful route for developing a redox-labeled DNA-hybridization biosensing strategy.

A Comparison of DNA-DNA Hybridization Kinetics in Complex Media on Planar and Nanostructured Electrodes

A comprehensive investigation into how nanostructures alter real-time DNA hybridization kinetics in both buffer and complex media and under a wide range of probe and target concentrations is currently lacking. In response, we use a real-time, wash-free, and in situ assay to study DNA hybridization kinetics by performing continuous electrochemical measurements in different media. We investigated the differences in hybridization kinetics under three regimes of probe density (low, medium, and high) and over three orders of magnitude of target concentrations (0.01-1 μM). Additionally, we compared the performance of planar and nanostructured electrodes in buffer, blood, urine, and saliva. Our experiments indicate that adding nanostructures to the transducer surface is only effective under a specific probe/target concentration regime. Additionally, we found that direct electrochemical readout is possible in the examined physiological media, with measurements in blood showing the highest and saliva showing the lowest signal magnitudes compared to buffer.

Investigation of G-Quadruplex DNA-Mediated Charge Transport for Exploring DNA Oxidative Damage in Telomeres

The human telomeric DNA 3' single-stranded overhang comprises tandem repeats of the sequence d(TTAGGG), which can fold into the stable secondary structure G-quadruplex (G4) and is susceptible to oxidative damage due to the enrichment of G bases. 8-Oxoguanine (8-oxoG) formed in telomeric DNA destabilizes G4 secondary structures and then inhibits telomere functions such as the binding of G4 proteins and the regulation of the length of telomeres. In this work, we developed a G4-DNA self-assembled monolayer electrochemical sensing interface using copper-free click chemistry based on the reaction of dibenzocyclooctyl with azide, resulting in a high yield of DNA tethers with order and homogeneity surfaces, that is more suitable for G-quadruplex DNA charge transport (CT) research. At high DNA coverage density surfaces, G-quadruplex DNA is 4 times more conductive than double-stranded DNA owing to the well-stacked aromatic rings of G-quartets acting as good charge transfer channels. The effect of telomeric oxidative damage on G-quadruplex-mediated CT is investigated. The accommodation of 8-oxoG at G sites originally in the syn or anti conformation around the glycosyl bond in the nonsubstituted hTel G-quadruplex causes structural perturbation and a conformational shift, which disrupts the π-stack, affecting the charge transfer and attenuating the electrochemical signal. The current intensity was found to correlate with the amount of 8-oxodG, and the detection limit was estimated to be approximately one lesion in 286 DNA bases, which can be converted into 64.7 fmol on the basis of the total surface DNA coverage. The improved G4-DNA order and homogeneity sensing interface represent a major step forward in this regard, providing a reliable and controlled electrochemical platform for the accurate measurement and diagnosis of G4-DNA oxidative damage.

Ratiometric electrochemical aptasensor with strand displacement for insulin detection in blood samples

BACKGROUND

Diabetes patients suffer either from insulin deficiency or resistance with a high risk of severe long-term complications, thus the quantitative assessment of insulin level is highly desired for diabetes surveillance and management. Utilizing insulin-capturing aptamers may facilitate the development of affordable biosensors however, their rigid G-quadruplex structures impair conformational changes of the aptamers and diminish the sensor signals.

RESULTS

Here we report on a ratiometric, electrochemical insulin aptasensor which is achieved by hybridization of an insulin-capturing aptamer and a partially complementary ssDNA to break the rigid G-quadruplex structures. To improve the durability of the aptasensor, the capturing aptamer was immobilized on gold electrodes via two dithiol-phosphoramidite functional groups while methoxy-polyethylene glycol thiol was used as a blocking molecule. The exposure of the sensor to insulin-containing solutions induced the dissociation of the hybridized DNA accompanied by a conformational rearrangement of the capturing aptamer back into a G-quadruplex structure. The reliability of sensor readout was improved by the adoption of an AND logic gate utilizing anthraquinone and methylene blue redox probes associated to the aptamer and complementary strand, respectively. Our aptasensor possessed an improved detection limit of 0.15 nM in comparison to aptasensors without strand displacement.

SIGNIFICANCE

The sensor was adapted for detection in real blood and is ready for future PoC diagnostics. The capability of monitoring the insulin level in an affordably manner can improve the treatment for an increasing number of patients in developed and developing nations. The utilization of low-cost and versatile aptamer receptors together with the engineering of ratiometric electrochemical signal recording has the potential to considerably advance the current insulin detection technology toward multi-analyte diabetes sensors.

Interferon gamma (IFN-γ)-sensitive TB aptasensor based on novel chitosan-indium nano-kesterite (χtCITS)-labeled DNA aptamer hairpin technology

There has been increasing interest in the use of biosensors for diagnosis of infectious diseases such as tuberculosis (TB) due to their simplicity, affordability, and potential for point-of-care application. The incorporation of aptamer molecules and nanomaterials in biosensor fabrication explores the advantages of high-binding affinity and low immunogenicity of aptamers as well as the high surface-to-volume ratio of nanomaterials, for increased aptasensor performance. In this work, we employed a novel microwave-synthesized copper indium tin sulfide (CITS) substituted-kesterite nanomaterial, together with a natural biopolymer (chitosan), for signal amplification and increased loading of aptamer molecules. Study of the optical properties of CITS nanomaterials showed strong absorption in the UV region characteristic of kesterite semiconductor nanomaterials. X-ray diffraction analysis confirmed the presence of the kesterite phase with average crystallite size of 6.188 nm. Fabrication of interferon-gamma (IFN-γ) TB aptasensor with a chitosan-CITS nanocomposite (χtCITS) increased the aptasensor's electrochemical properties by 77.5 % and improved aptamer loading by 73.7 %. The aptasensor showed excellent sensitivity to IFN-γ concentrations with limit of detection of 6885 fg/mL (405 fM) and linear range of 850-17000 fg/mL (50 - 1000 fM). The aptasensor also exhibited excellent storage and electrochemical stability, with good selectivity towards IFN-γ and possible real sample application.

Magnetic metal-organic frameworks as sensitive aptasensors for coronavirus spike protein

Electrochemical biosensors, known for their low cost, sensitivity, selectivity, and miniaturization capabilities, are ideal for point-of-care devices. The magnetic metal-organic framework (MMOF), synthesized using the in-situ growth method, consists of ferric salt, magnetic nanoparticles, histidine, and benzene tetracarboxylic acid. MMOF was sequentially modified with aptamer-biotin and streptavidin-horseradish peroxidase, serving as a detector for spike protein and a transducer converting electrochemical signals using H2O2-hydroquinone on a screen-printed electrode. MMOF facilitates easy washing and homogeneous deposition on the working electrode with a magnet, enhancing sensitivity and reducing noise. The physical and electrochemical properties of the modified MMOFs were thoroughly characterized using various analytical techniques. The aptasensors' performance achieved a detection limit of 6 pM for voltammetry and 5.12 pM for impedance spectroscopy in human serum samples. This cost-effective, portable MMOF platform is suitable for rapid point-of-care testing for SARS-CoV-2 spike proteins.

Site-Directed Electrochemical Grafting for Amplified Detection of Antibody Pharmaceuticals

Antibody pharmaceuticals have become the most popular immunotherapeutic drugs and are often administered with low serum drug dosages. Hence, the development of a highly sensitive method for the quantitative assay of antibody levels is of great importance to individualized therapy. On the basis of the dual signal amplification by the glycan-initiated site-directed electrochemical grafting of polymer chains (glyGPC), we report herein a novel strategy for the amplified electrochemical detection of antibody pharmaceuticals. The target of interest was affinity captured by a DNA aptamer ligand, and then the glycans of antibody pharmaceuticals were decorated with the alkyl halide initiators (AHIs) via boronate cross-linking, followed by the electrochemical grafting of the ferrocenyl polymer chains from the glycans of antibody pharmaceuticals through the electrochemically controlled atom transfer radical polymerization (eATRP). As the glycans can be decorated with multiple AHIs and the grafted polymer chains are composed of tens to hundreds of electroactive tags, the glyGPC-based strategy permits the dually amplified electrochemical detection of antibody pharmaceuticals. In the presence of trastuzumab (Herceptin) as the target, the glyGPC-based strategy achieved a detection limit of 71.5 pg/mL. Moreover, the developed method is highly selective, and the results of the quantitative assay of trastuzumab levels in human serum are satisfactory. Owing to its uncomplicated operation and cost-effectiveness, the glyGPC-based strategy shows great promise in the amplified electrochemical detection of antibody pharmaceuticals.

Strategy, Design, and Fabrication of Electrochemical Biosensors: A Tutorial

Advanced healthcare requires novel technologies capable of real-time sensing to monitor acute and long-term health. The challenge relies on converting a real-time quantitative biological and chemical signal into a desired measurable output. Given the success in detecting glucose and the commercialization of glucometers, electrochemical biosensors continue to be a mainstay of academic and industrial research activities. Despite the wealth of literature on electrochemical biosensors, reports are often specific to a particular application (e.g., pathogens, cancer markers, glucose, etc.), and most fail to convey the underlying strategy and design, and if it is transferable to detection of a different analyte. Here we present a tutorial review for those entering this research area that summarizes the basic electrochemical techniques utilized as well as discusses the designs and optimization strategies employed to improve sensitivity and maximize signal output.

A target-triggered ultra-sensitive aptasensor for simultaneous detection of Cd2+ and Hg2+ using MWCNTs-Au NPs modified electrode

A sensitive electrochemical assay for simultaneously detecting cadmium ion (Cd2+) and mercury ion (Hg2+) with the aptamer as recognition unit was established, in which methylene blue (MB) and target-triggered in-situ generated Ag nanoclusters (Ag NCs) were identified as signal reporters. Multi-walled carbon nanotubes and gold nanoparticles composites were prepared with polyethyleneimine to amplify electrical signals of screen-printed electrodes. Due to the particular base sequences, MB labeled Cd2+ aptamer paired with ssDNA through T-Hg-T structure with Hg2+. Notably, the C-rich structure in ssDNA acted as a template for the generation of Ag NCs, which could induce differential pulse voltammetry signals corresponding to Hg2+ concentrations. This electrochemical aptasensor exhibited detection limits of 94.01 pg/mL and 15.74 pg/mL for Cd2+ and Hg2+, respectively. The developed aptasensor allowed for practical application to tea and vegetable samples with satisfactory accuracy. This work possesses potential in developing biosensing technologies for simultaneous determination of multiple heavy metals.

Sensitive electrochemical sensor for Cd2+ with engineered short high-affinity aptamer undergoing large conformation change

Cadmium ion (Cd2+) is a highly toxic heavy metal ion that threatens the environment and human health. To achieve rapid and sensitive detection of Cd2+, here we developed a reagent-less aptamer electrochemical sensor by immobilizing an engineered high-affinity DNA aptamer with a redox tag of methylene blue (MB) on the gold electrode. After testing a series of engineered aptamer sequences, we employed an optimal and new 15-mer aptamer with a short 3-bp stem for sensor fabrication, which underwent large conformation change upon Cd2+ binding. This aptamer retained high affinity with a Kd about 360 nM, verified by isothermal titration calorimetry (ITC) analysis. In the presence of Cd2+, this aptamer folded into a stem-loop structure, drawing the MB into a close proximity to the electrode surface and generating enhanced current in square wave voltammetry (SWV). Under the optimized conditions, this aptamer sensor enabled us to sensitively detect Cd2+ in a wide concentration range from 0.5 nM to 4 μM, and the detection limit was 90 pM. The developed electrochemical aptasensor has the advantages in easy preparation, rapid response, high stability, high selectivity and easy regeneration and reuse, showing the potential for Cd2+ detection in broad applications.

Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering

DNA monolayers with inherent chirality play a pivotal role across various domains including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), often lack structural orderliness and design flexibility at the interface. Structural DNA nanotechnology has emerged as a promising solution to tackle these challenges. In this study, we present a strategy for crafting highly adaptable twisted DNA origami-based chiral monolayers. These structures exhibit distinct interfacial assembly characteristics and effectively mitigate the structural disorder of dsDNA monolayers, which is constrained by a limited persistence length of ∼50 nm of dsDNA. We highlight the spin-filtering capabilities of seven representative DNA origami-based chiral monolayers, demonstrating a maximal one-order-of-magnitude increase in spin-filtering efficiency per unit area compared with conventional dsDNA chiral monolayers. Intriguingly, our findings reveal that the higher-order tertiary chiral structure of twisted DNA origami further enhances the spin-filtering efficiency. This work paves the way for the rational design of DNA chiral monolayers.

Electrochemical detection of glutathione based on accelerated CRISPR/Cas12a trans-cleavage with MnO2 nanosheets

The CRISPR/Cas12a system is accelerated by glutathione-mediated reduction of MnO2 nanosheets. By monitoring the trans-cleavage of the DNA probe, an electrochemical method for glutathione assay is fabricated, with the detection limit of 3.5 pM. It provides a promising tool for plasma analysis with satisfactory performance, indicating the broad application prospects of this glutathione assay.

Electrochemically assisted DNA and thioaromatic assembly as sensing and antifouling interface for food allergens

Food allergies have become a global issue and are estimated to affect approximately 220 million people worldwide. Allergy to peanuts can easily become life-threatening and induce anaphylactic reactions. Mislabeling and cross-contamination during food processing can occur in the frame of world population growth and pose a serious health issue. As the mandatory allergen list is not uniform worldwide, the development of routine analytical strategies with high specificity and sensitivity is a demanding task to aid in the rapid identification of allergenic foods. In this work, an electrochemical aptasensor for Ara h1 peanut allergen was developed by immobilizing the specific aptamer by the inserting method. First, a layer of p-aminothiophenol (p-ATP) was immobilized on the gold surface of screen-printed electrodes (GSPE) to improve the aptamer insertion and reduce the fouling effects at the electrode surface. The grafting of the p-ATP and Ara h1 aptamer on the GSPE surface was monitored by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The resulting disposable aptasensor allowed for indirect electrochemical detection of Ara h1 protein in the presence of 5 mM ferro/ferricyanide as a redox probe. The electrochemical response upon aptamer-target interaction was monitored in the concentration range 1-250 nM, and two limits of detection in the nanomolar range were estimated based on DPV (2.78 nM Ara h1) and EIS (0.82 nM Ara h1) measurements. The aptasensor was successfully applied to real sample analysis.

DNA Polymerase-Steered Self-Propelled and Self-Enhanced DNA Walker for Rapid and Distinctly Amplified Electrochemical Sensing

The development of a simple, rapid, easy-to-operate, and ultrasensitive DNA walker-based sensing system is challenging but would be very intriguing for the enormous applications in biological analysis and disease monitoring. Herein, a new self-propelled and self-enhanced DNA walking strategy was developed on the basis of a simple DNA polymerase-steered conversion from a typical alternate DNA assembly process. The sensing platform was fabricated easily by immobilizing only one hairpin probe (H1) and the sensing process was based on a simple one-step mixing with another hairpin-like DNA probe (H2) and DNA polymerase. The DNA polymerization could achieve target recycling and successive DNA walking steps. Interestingly, along with each DNA walking step, the new DNA walker sequence could be autonomously accumulated for a self-enhanced DNA walking effect. This provided a multilevel signal amplification ability for the ultrasensitive detection of the target with a low detection limit of 0.18 fM. Moreover, it could greatly reduce the reaction time with the sensing process finished within 1 h. The detection selectivity and the applicative potential in a complicated biological matrix were also demonstrated. Furthermore, the flexible control of sensing modes (self-enhanced DNA walking or the alternate DNA assembly) by using DNA polymerase or not offered a powerful means for sensing performance modulation. It thus opens a new avenue toward the development of a DNA walker-based sensing platform with both rapid and ultrasensitive features and might hold a huge potential for point-of-care diagnostic applications.

A highly sensitive and robust electrochemical biosensor for microRNA detection based on PNA-DNA hetero-three-way junction formation and target-recycling catalytic hairpin assembly amplification

Robust and sensitive methods for the detection of microRNAs (miRNAs) are crucial in the clinical diagnosis of cancers. In this study, a novel electrochemical biosensor with high sensitivity for miRNA-21 detection is developed, which relies on the formation of a peptide nucleic acid (PNA)-DNA hetero-three-way junction (H3WJ) and target-recycling catalytic hairpin assembly (CHA) amplification. The electroneutral PNA probes are initially immobilized onto a gold electrode to construct the sensor. Upon introduction of miRNA-21, target-recycling CHA is initiated, resulting in abundant double-stranded CHA products. Subsequently, association between the PNA probes and these products leads to the formation of PNA-DNA H3WJs. Consequently, the electrode surface is densely populated with numerous electroactive Ferrocene (Fc) groups, resulting in a significantly amplified current response for highly sensitive detection of miRNA-21 at concentrations as low as 0.15 fM. This approach demonstrates remarkable specificity towards target miRNAs and can be utilized for quantitative monitoring of miRNA-21 expression in human cancer cells. More importantly, the sensor exhibits exceptional stability and shows a significant reduction in background noise during miRNA detection, making this method a highly promising sensing platform for monitoring various miRNA biomarkers to facilitate the diagnosis of diverse cancers.

Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution

Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.

Aptamer-Based Fentanyl Detection in Biological Fluids

Fentanyl is a widely abused analgesic and anesthetic drug with a narrow therapeutic window that creates easy opportunities for overdose and death. Rapid, accurate, and sensitive fentanyl detection in biosamples is crucial for therapeutic drug monitoring and overdose diagnosis. Unfortunately, current methods are limited to either sophisticated laboratory-based tests or antibody-based immunoassays, which are prone to false results and are mainly used with urine samples. Here, we have utilized library-immobilized SELEX to isolate new aptamers─nucleic acid-based bioreceptors that are well-suited for biosensing─that can specifically bind fentanyl under physiological conditions. We isolated multiple aptamers with nanomolar affinity and excellent specificity against dozens of interferents and incorporated one of these into an electrochemical aptamer-based sensor that can rapidly detect fentanyl at clinically relevant concentrations in 50% diluted serum, urine, and saliva. Given the excellent performance of these sensors, we believe that they could serve as the basis for point-of-care devices for monitoring fentanyl during medical procedures and determining fentanyl overdose.

Highly Uniform DNA Monolayers Generated by Freezing-Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood

Assembling DNA on solid surfaces is fundamental to surface-based DNA technology. However, precise control over DNA conformation and organization at solid-liquid interfaces remains a challenge, resulting in limited stability and sensitivity in biosensing applications. We herein communicate a simple and robust method for creating highly uniform DNA monolayers on gold surfaces by a freeze-thawing process. Using Raman spectroscopy, fluorescent imaging, and square wave voltammetry, we demonstrate that thiolated DNA is concentrated and immobilized on gold surfaces with an upright conformation. Moreover, our results reveal that the freezing-induced DNA surfaces are more uniform, leading to improved DNA stability and target recognition. Lastly, we demonstrate the successful detection of a model drug in undiluted whole blood while mitigating the effects of biofouling. Our work not only provides a simple approach to tailor the DNA-gold surface for biosensors but also sheds light on the unique behavior of DNA oligonucleotides upon freezing on the liquid-solid interface.

A sensitive and rapid electrochemical biosensor for sEV-miRNA detection based on domino-type localized catalytic hairpin assembly

Small extracellular-vesicule-associated microRNA (sEV-miRNA) is an important biomarker for cancer diagnosis. However, rapid and sensitive detection of low-abundance sEV-miRNA in clinical samples is challenging. Herein, a simple electrochemical biosensor that uses a DNA nanowire to localize catalytic hairpin assembly (CHA), also called domino-type localized catalytic hairpin assembly (DT-LCHA), has been proposed for sEV-miRNA1246 detection. The DT-LCHA offers triple amplification, (i). CHA system was localized in DNA nanowire, which shorten the distance between hairpin substrate, inducing the high collision efficiency of H1 and H2 and domino effect. Then, larger numbers of CHAs were triggered, capture probe bind DT-LCHA by exposed c sites. (ii) The DNA nanowire can load large number of electroactive substance RuHex as amplified electrochemical signal tags. (iii) multiple DT-LCHA was carried by the DNA nanowire, only one CHA was triggered, the DNA nanowire was trapped by the capture probe, which greatly improve the detection sensitivity, especially when the target concentration is extremely low. Owing to the triple signal amplification in this strategy, sEV-miRNA at a concentration of as low as 24.55 aM can be detected in 20 min with good specificity. The accuracy of the measurements was also confirmed using reverse transcription quantitative polymerase chain reaction. Furthermore, the platform showed good performance in discriminating healthy donors from patients with early gastric cancer (area under the curve [AUC]: 0.96) and was equally able to discriminate between benign gastric tumors and early cancers (AUC: 0.77). Thus, the platform has substantial potential in biosensing and clinical diagnosis.

Label-Free DNA Biosensor Based on Reduced Graphene Oxide and Gold Nanoparticles

Currently available DNA detection techniques frequently require compromises between simplicity, speed, accuracy, and cost. Here, we propose a simple, label-free, and cost-effective DNA detection platform developed at screen-printed carbon electrodes (SPCEs) modified with reduced graphene oxide (RGO) and gold nanoparticles (AuNPs). The preparation of the detection platform involved a two-step electrochemical procedure based on GO reduction onto SPCEs followed by the electrochemical reduction of HAuCl4 to facilitate the post-grafting reaction with AuNPs. The final sensor was fabricated by the simple physical adsorption of a single-stranded DNA (ssDNA) probe onto a AuNPs-RGO/SPCE electrode. Each preparation step was confirmed by morphological and structural characterization using scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy, respectively. Furthermore, the electrochemical properties of the modified electrodes have been investigated by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The results demonstrated that the introduction of AuNPs onto RGO/SPCEs led to an enhancement in surface conductivity, a characteristic that favored an increased sensitivity in detection. The detection process relied on the change in the electrochemical signal induced by the binding of target DNA to the bioreceptor and was particularly monitored by the change in the charge transfer resistance of a [Fe(CN)6]4-/3- redox couple added in the test solution.

Strategies in the optimization of DNA hybridization conditions and its role in electrochemical detection of dengue virus (DENV) using response surface methodology (RSM)

In recent years, limited research has been conducted on enhancing DNA hybridization-based biosensor approaches using statistical models. This study explores the application of response surface methodology (RSM) to improve the performance of a DNA hybridization biosensor for dengue virus (DENV) detection. The biosensor is based on silicon nanowires decorated with gold nanoparticles (SiNWs/AuNPs) and utilizes methylene blue as a redox indicator. The DNA hybridization process between the immobilized DNA probe and the target DENV gene was monitored using differential pulse voltammetry (DPV) based on the reduction of methylene blue. Fourier-transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS) were employed to confirm successful DNA hybridization events on the modified screen-printed gold electrode (SPGE) surface. Several parameters, including pH buffer, NaCl concentration, temperature, and hybridization time, were simultaneously optimized, with NaCl concentration having the most significant impact on DNA hybridization events. This study enhances the understanding of the role of each parameter in influencing DNA hybridization detection in electrochemical biosensors. The optimized biosensor demonstrated the ability to detect complementary oligonucleotide and amplified DENV gene concentrations as low as 0.0891 ng µL^-1 (10 pM) and 2.8 ng µL^-1, respectively. The developed biosensor shows promise for rapid clinical diagnosis of dengue virus infection.

Novel electrochemiluminescence biosensor of fumonisin B1 detection using MWCNTs-PDMS flexible bipolar electrode

A novel portable and disposable bipolar electrode (BPE)-electrochemiluminescence (ECL) device was fabricated for fumonisin B₁ (FB₁) detection. BPE was fabricated by using MWCNTs and polydimethylsiloxane (PDMS) due to their excellent electrical conductivity and good mechanical stiffness. After the deposition of Au NPs on the cathode of BPE, the ECL signal could be improved 89-fold. Then a specific aptamer-based sensing strategy was constructed by grafting capture DNA on Au surface, followed by hybridizing with aptamer. Meanwhile, an excellent catalyst, Ag NPs was labeled on aptamer to activate oxygen reduction reaction, leading to a 13.8-fold enhancement in ECL signal at the anode of BPE. Under the optimal conditions, the biosensor exhibited a wide linear range of 0.10 pg/mL to 10 ng/mL for FB₁ detection. Meanwhile, it demonstrated satisfactory recoveries for real sample detection with good selectivity, making it to be a convenient and sensitive device for mycotoxin assay.

Design of a novel aptamer/molecularly imprinted polymer hybrid modified Ag-Au@Insulin nanoclusters/Au-gate-based MoS2 nanosheet field-effect transistor for attomolar detection of BRCA1 gene

Early detection of breast cancer, the first main cause of death in women, with robust assay platforms using appropriate biomarkers is of great importance for diagnosis and follow-up of the disease progression. This paper introduces an extra selective and sensitive label-free aptasensor for the screening of BRCA1 gene biomarker by taking advantage of a gate modified with aptamer and molecularly imprinted polymer hybrid (MIP) as a new synthetic receptor film coupled with an electrolyte-gated molybdenum disulfide (MoS2) field-effect transistor (FET). The Au gate surface of FET was modified with insulin stabilized bimetallic Ag-Au@nanoclusters (Ag-Au@InsNCs), after which, the immobilization of the hybridized aptamer and o-phenylenediamine was electropolymerized to form an aptamer-MIP hybrid receptor. The output characteristics of Apta-MIP hybrid modified Au gate MoS2 FET device were followed as a result of change in electrical double layer capacitance of electrolye-gate interface. The magnitude of decrease in the drain current showed a linear response over a wide concentration range of 10 aM to 1 nM of BRCA1 ssDNA with a sensitivity as high as 0.4851 μA/decade of concentration and a limit of detection (LOD) of 3.0 aM while very low responses observed for non-imprinted polymer. The devised aptasensor not only was capable to the discrimination of the complementary versus one-base mismatch BRCA1 ssDNA sequence, but also it could detect the complementary BRCA1 ssDNA in spiked human serum samples over a wide concentration range of 10 aM to 1.0 nM with a low LOD of 6.4 aM and a high sensitivity 0.3718 μA/decade.

DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging

By using AFM as a nanografting tool, we grafted micrometer-sized DNA platforms into inert alkanethiol SAMs. Tuning the grafting conditions (surface density of grafting lines and scan rate) allowed us to tailor the molecular density of the DNA platforms. Following the nanografting process, AFM was operated in the low perturbative Quantitative Imaging (QI) mode. The analysis of QI AFM images showed the coexistence of molecular domains of different heights, and thus different densities, within the grafted areas, which were not previously reported using contact AFM imaging. Thinner domains corresponded to low-density DNA regions characterized by loosely packed, randomly oriented DNA strands, while thicker domains corresponded to regions with more densely grafted DNA. Grafting with densely spaced and slow scans increased the size of the high-density domains, resulting in an overall increase in patch height. The structure of the grafted DNA was compared to self-assembled DNA, which was assessed through nanoshaving experiments. Exposing the DNA patches to the target sequence produced an increase in the patch height, indicating that hybridization was accomplished. The relative height increase of the DNA patches upon hybridization was higher in the case of lower density patches due to hybridization leading to a larger molecular reorganization. Low density DNA patches were therefore the most suitable for targeting oligonucleotide sequences.

Suite of Aptamer-Based Sensors for the Detection of Fentanyl and Its Analogues

Fentanyl and its analogues are potent synthetic opioids that are commonly abused and are currently the number one cause of drug overdose death in the United States. The ability to detect fentanyl with simple, rapid, and low-cost tools is crucial for forensics, medical care, and public safety. Conventional on-site testing options for fentanyl detection─including chemical spot tests, lateral-flow immunoassays, and portable Raman spectrometers─each have their own unique flaws that limit their analytical utility. Here, we have developed a series of new aptamer-based assays and sensors that can detect fentanyl as well as several of its analogues in a reliable, accurate, rapid, and economic manner. These include colorimetric, fluorescent, and electrochemical sensors, which can detect and quantify minute quantities of fentanyl and many of its analogues with no response to other illicit drugs, cutting agents, or adulterants─even in interferent-ridden binary mixtures containing as little as 1% fentanyl. Given the high performance of these novel analytical tools, we foresee the potential for routine use by medical and law enforcement personnel as well as the general public to aid in rapid and accurate fentanyl identification.

An enzyme-responsive electrochemical DNA biosensor achieving various dynamic range by using only-one immobilization probe

Developing a simple and easy-to-operate biosensor with tunable dynamic range would provide enormous opportunities to promote the diagnostic applications. Herein, an enzyme-responsive electrochemical DNA biosensor is developed by using only-one immobilization probe. The immobilization probe was designed with a two-loop hairpin-like structure that contained the mutually independent target recognition and enzyme (EcoRI restriction endonuclease) responsive domains. The target recognition was based on a toehold-mediated strand displacement reaction strategy. The toehold region was initially caged in the loop of the immobilization probe and showed a relatively low binding affinity with target, which was improved via EcoRI cleavage of immobilization probe to liberate the toehold region. The EcoRI cleavage operation for immobilization probe demonstrated the well regulation ability in detection performance. It showed a largely extended dynamic range, a significantly lowered detection limit and better discrimination ability toward the mismatched sequences whether in two buffers (with high or low salt concentrations) or in the serum system. The advantages also includes simplicity in probe design, and facile biosensor fabrication and operation. It thus opens a new avenue for the development of the modulated DNA biosensor and hold a great potential for the diagnostic applications and drug monitoring.

Amplification-free electrochemical biosensor detection of circulating microRNA to identify drug-induced liver injury

Drug-induced liver injury (DILI) is a major challenge in clinical medicine and drug development. There is a need for rapid diagnostic tests, ideally at point-of-care. MicroRNA 122 (miR-122) is an early biomarker for DILI which is reported to increase in the blood before standard-of-care markers such as alanine aminotransferase activity. We developed an electrochemical biosensor for diagnosis of DILI by detecting miR-122 from clinical samples. We used electrochemical impedance spectroscopy (EIS) for direct, amplification free detection of miR-122 with screen-printed electrodes functionalised with sequence specific peptide nucleic acid (PNA) probes. We studied the probe functionalisation using atomic force microscopy and performed elemental and electrochemical characterisations. To enhance the assay performance and minimise sample volume requirements, we designed and characterised a closed-loop microfluidic system. We presented the EIS assay's specificity for wild-type miR-122 over non-complementary and single nucleotide mismatch targets. We successfully demonstrated a detection limit of 50 pM for miR-122. Assay performance could be extended to real samples; it displayed high selectivity for liver (miR-122 high) comparing to kidney (miR-122 low) derived samples extracted from murine tissue. Finally, we successfully performed an evaluation with 26 clinical samples. Using EIS, DILI patients were distinguished from healthy controls with a ROC-AUC of 0.77, a comparable performance to qPCR detection of miR-122 (ROC-AUC: 0.83). In conclusion, direct, amplification free detection of miR-122 using EIS was achievable at clinically relevant concentrations and in clinical samples. Future work will focus on realising a full sample-to-answer system which can be deployed for point-of-care testing.

Studies on the application of single-stranded DNA and PNA probes for electrochemical detection of miRNA 141

The abnormal concentration of microRNAs (miRNAs) can be associated with occurrence of various diseases including cancer, cardiovascular and neurodegenerative, hence they can be considered as potential biomarkers. An attractive approach could be the application of electrochemical methods, particularly where hybridization event between single-stranded deoxyribonucleic acid (ssDNA) or peptide-nucleic acid (PNA) with miRNA strand happens. Recently, the use of various nanomaterials such as gold nanoparticles, graphene oxide, quantum dots as well as catalyzed hairpin assembly or hybridization chain reaction were proposed to further enhance the performance of elaborated sensors. Herein, we present the studies on selection of receptor layer composition for detection of miRNA 141. The possibility of formation of receptor layer and further duplex monolayer between ssDNA or PNA with miRNA was analyzed by atomic force microscopy (AFM) technique. The interaction of ssDNA and PNA probes with miRNA was further verified using surface plasmon resonance (SPR) and quartz - crystal microbalance (QCM) techniques. On the basis of impedance spectroscopy it was shown that the use of unlabelled ssDNA as receptor layer provided 0.1 pM detection limit. This shows that proposed biosensor that is simple in preparation and use is an attractive alternative to other recently presented approaches.

Ultrasensitive and amplification-free detection of SARS-CoV-2 RNA using an electrochemical biosensor powered by CRISPR/Cas13a

This study proposed a CRISPR/Cas13a-powered electrochemical multiplexed biosensor for detecting SARS-CoV-2 RNA strands. Current SARS-CoV-2 diagnostic methods, such as reverse transcription PCR (RT-PCR), are primarily based on nucleic acid amplification (NAA) and reverse transcription (RT) processes, which have been linked to significant issues such as cross-contamination and long turnaround times. Using a CRISPR/Cas13a system integrated onto an electrochemical biosensor, we present a multiplexed and NAA-free strategy for detecting SARS-CoV-2 RNA fragments. SARS-CoV-2 S and Orf1ab genes were detected in both synthetic and clinical samples. The CRISPR/Cas13a-powered biosensor achieved low detection limits of 2.5 and 4.5 ag/µL for the S and Orf1ab genes, respectively, successfully meeting the sensitivity requirement. Furthermore, the biosensor's specificity, simplicity, and universality may position it as a potential rival to RT-PCR.

Label-Free Electrogenerated Chemiluminescence Aptasensing Method for Highly Sensitive Determination of Dopamine via Target-Induced DNA Conformational Change

A label-free electrogenerated chemiluminescence (ECL) aptasensing method for highly sensitive determination of dopamine (DA) was developed based on target-induced DNA conformational change. After anti-DA specific aptamer, as molecular recognition element, was hybridized with a capture ss-DNA (complementary with the aptamer), the formed double-strand DNA (ds-DNA) was self-assembled onto the surface of a gold electrode, and then Ru(phen)₃²⁺, as ECL reagent, was intercalated into ds-DNA to form an ECL biosensing platform. In the presence of DA, DA bound with its aptamer and target-induced DNA conformational change occurred, resulting in the dissociation of ds-DNA, the release of intercalated Ru(phen)₃²⁺ from the electrode surface, and the decrease of ECL intensity. For comparison, an ECL aptamer-based biosensing method using an ECL reagent-labeled aptamer was also developed for DA assay based on target-induced DNA conformational change. Because of the increase in the amount of ECL reagent into ds-DNA over that of the single-site ECL reagent-labeled aptamer, an obvious increase of ECL intensity was found at the ds-DNA modified electrode over the aptamer modified electrode. DA can be sensitively detected with a lower detection limit of 0.05 nM in the range from 0.1 to 100 nM. With the recognition of the aptamer for DA, DA can be selectively and sensitively detected in artificial cerebrospinal fluid and serum samples without interference from common small molecules. This work demonstrates that the combination of the direct transduction of specific recognition of DA and its aptamer into an ECL signal with Ru(phen)₃²⁺ intercalated ds-DNA amplification provides a promising strategy for the development of a simple, sensitive, and selective method for DA assay, which is of great importance in neurochemical assays and clinical diagnosis.

Explaining the Decay of Nucleic Acid-Based Sensors under Continuous Voltammetric Interrogation

Nucleic acid-based electrochemical sensors (NBEs) can support continuous and highly selective molecular monitoring in biological fluids, both in vitro and in vivo, via affinity-based interactions. Such interactions afford a sensing versatility that is not supported by strategies that depend on target-specific reactivity. Thus, NBEs have significantly expanded the scope of molecules that can be monitored continuously in biological systems. However, the technology is limited by the lability of the thiol-based monolayers employed for sensor fabrication. Seeking to understand the main drivers of monolayer degradation, we studied four possible mechanisms of NBE decay: (i) passive desorption of monolayer elements in undisturbed sensors, (ii) voltage-induced desorption under continuous voltammetric interrogation, (iii) competitive displacement by thiolated molecules naturally present in biofluids like serum, and (iv) protein binding. Our results indicate that voltage-induced desorption of monolayer elements is the main mechanism by which NBEs decay in phosphate-buffered saline. This degradation can be overcome by using a voltage window contained between -0.2 and 0.2 V vs Ag|AgCl, reported for the first time in this work, where electrochemical oxygen reduction and surface gold oxidation cannot occur. This result underscores the need for chemically stable redox reporters with more positive reduction potentials than the benchmark methylene blue and the ability to cycle thousands of times between redox states to support continuous sensing for long periods. Additionally, in biofluids, the rate of sensor decay is further accelerated by the presence of thiolated small molecules like cysteine and glutathione, which can competitively displace monolayer elements even in the absence of voltage-induced damage. We hope that this work will serve as a framework to inspire future development of novel sensor interfaces aiming to eliminate the mechanisms of signal decay in NBEs.

Signal Amplification in Electrochemical DNA Biosensors Using Target-Capturing DNA Origami Tiles

Electrochemical DNA (e-DNA) biosensors are feasible tools for disease monitoring, with their ability to translate hybridization events between a desired nucleic acid target and a functionalized transducer, into recordable electrical signals. Such an approach provides a powerful method of sample analysis, with a strong potential to generate a rapid time to result in response to low analyte concentrations. Here, we report a strategy for the amplification of electrochemical signals associated with DNA hybridization, by harnessing the programmability of the DNA origami method to construct a sandwich assay to boost charge transfer resistance (R_CT) associated with target detection. This allowed for an improvement in the sensor limit of detection by two orders of magnitude compared to a conventional label-free e-DNA biosensor design and linearity for target concentrations between 10 pM and 1 nM without the requirement for probe labeling or enzymatic support. Additionally, this sensor design proved capable of achieving a high degree of strand selectivity in a challenging DNA-rich environment. This approach serves as a practical method for addressing strict sensitivity requirements necessary for a low-cost point-of-care device.

High-throughput quantitative binding analysis of DNA aptamers using exonucleases

Aptamers are nucleic acid bioreceptors that have been used in various applications including medical diagnostics and as therapeutic agents. Identifying the most optimal aptamer for a particular application is very challenging. Here, we for the first time have developed a high-throughput method for accurately quantifying aptamer binding affinity, specificity, and cross-reactivity via the kinetics of aptamer digestion by exonucleases. We demonstrate the utility of this approach by isolating a set of new aptamers for fentanyl and its analogs, and then characterizing the binding properties of 655 aptamer-ligand pairs using our exonuclease digestion assay and validating the results with gold-standard methodologies. These data were used to select optimal aptamers for the development of new sensors that detect fentanyl and its analogs in different analytical contexts. Our approach dramatically accelerates the aptamer characterization process and streamlines sensor development, and if coupled with robotics, could enable high-throughput quantitative analysis of thousands of aptamer-ligand pairs.

Ultrasensitive electrochemical platform for the p53 gene via molecular beacon-mediated circular strand displacement and terminal deoxynucleotidyl transferase-mediated signal amplification strategy

As an important tumor suppressor gene, the p53 gene is considered to be a typical biomarker for the early diagnosis and prognosis evaluation of severe cancer. Herein, an electrochemical biosensor was proposed for the ultrasensitive detection of the p53 gene based on molecular beacon-mediated circular strand displacement polymerization combined with terminal deoxynucleotide transferase-mediated template-free DNA extension. Firstly, the p53 gene opened the hairpin structure of the molecular beacon, thereby exposing the binding sequence region of the primer DNA. The circular strand displacement polymerization occurred in the presence of the primer DNA and phi29 DNA polymerase, subsequently resulting in the circulation of the p53 gene. With the catalysis of the terminal deoxynucleotide transferase, the 3'-OH terminal sequence of the molecular beacon elongated to produce long single-stranded DNA under the template-free DNA extension. Methylene blue bound with such DNA strands generated a strong differential pulse voltammetry (DPV) signal with a peak potential of -0.28 V. Under the optimal detection conditions, the DPV signal of methylene blue showed good linear relationships with the logarithm value of the p53 gene in two concentration ranges of 0.05 fM to 3 pM and 5 fM to 100 fM, and the detection limit of the p53 gene was as low as 0.018 fM. This electrochemical biosensor possessed high recognition ability for the p53 gene in its analogues and was successfully applied for p53 gene analysis in human serum samples.

Carbon Electrode-Based Biosensing Enabled by Biocompatible Surface Modification with DNA and Proteins

Modification of electrodes with biomolecules is an essential first step for the development of bioelectrochemical systems, which are used in a variety of applications ranging from sensors to fuel cells. Gold is often used because of its ease of modification with thiolated biomolecules, but carbon screen-printed electrodes (SPEs) are gaining popularity due to their low cost and fabrication from abundant resources. However, their effective modification with biomolecules remains a challenge; the majority of work to-date relies on nonspecific adhesion or broad amide bond formation to chemical handles on the electrode surface. By combining facile electrochemical modification to add an aniline handle to electrodes with a specific and biocompatible oxidative coupling reaction, we can readily modify carbon electrodes with a variety of biomolecules. Importantly, both proteins and DNA maintain bioactive conformations following coupling. We have then used biomolecule-modified electrodes to generate microbial monolayers through DNA-directed immobilization. This work provides an easy, general strategy to modify inexpensive carbon electrodes, significantly expanding their potential as bioelectrochemical systems.

Electro-Nano Diagnostic Platform Based on Antibody-Antigen Interaction: An Electrochemical Immunosensor for Influenza A Virus Detection

H1N1 is a kind of influenza A virus that causes serious health issues throughout the world. Its symptoms are more serious than seasonal flu and can sometimes be lethal. For this reason, rapid, accurate, and effective diagnostic tests are needed. In this study, an electrochemical immunosensor for the sensitive, selective, and practical detection of the H1N1 virus was developed. The sensor platform included multi-walled carbon nanotube gold-platinum (MWCNT-Au-Pt) hybrid nanomaterial and anti-hemagglutinin (anti-H1) monoclonal antibody. For the construction of this biosensor, a gold screen-printed electrode (AuSPE) was used as a transducer. Firstly, AuSPE was modified with MWCNT-Au-Pt hybrid nanomaterial via drop casting. Anti-H1 antibody was immobilized onto the electrode surface after the modification process with cysteamine was applied. Then, the effect of the interaction time with cysteamine for surface modification was investigated. Following that, the experimental parameters, such as the amount of hybrid nanomaterial and the concentration of anti-H1 were optimized. Under the optimized conditions, the analytical characteristics of the developed electrochemical immunosensor were investigated for the H1N1 virus by using electrochemical impedance spectroscopy. As a result, a linear range was obtained between 2.5-25.0 µg/mL with a limit of the detection value of 3.54 µg/mL. The relative standard deviation value for 20 µg/mL of the H1N1 virus was also calculated and found as 0.45% (n = 3). In order to determine the selectivity of the developed anti-H1-based electrochemical influenza A immunosensor, the response of this system towards the H3N2 virus was investigated. The matrix effect was also investigated by using synthetic saliva supplemented with H1N1 virus.

Two-Dimensional Non-Carbon Materials-Based Electrochemical Printed Sensors: An Updated Review

Recently, there has been increasing interest in electrochemical printed sensors for a wide range of applications such as biomedical, pharmaceutical, food safety, and environmental fields. A major challenge is to obtain selective, sensitive, and reliable sensing platforms that can meet the stringent performance requirements of these application areas. Two-dimensional (2D) nanomaterials advances have accelerated the performance of electrochemical sensors towards more practical approaches. This review discusses the recent development of electrochemical printed sensors, with emphasis on the integration of non-carbon 2D materials as sensing platforms. A brief introduction to printed electrochemical sensors and electrochemical technique analysis are presented in the first section of this review. Subsequently, sensor surface functionalization and modification techniques including drop-casting, electrodeposition, and printing of functional ink are discussed. In the next section, we review recent insights into novel fabrication methodologies, electrochemical techniques, and sensors' performances of the most used transition metal dichalcogenides materials (such as MoS₂, MoSe₂, and WS₂), MXenes, and hexagonal boron-nitride (hBN). Finally, the challenges that are faced by electrochemical printed sensors are highlighted in the conclusion. This review is not only useful to provide insights for researchers that are currently working in the related area, but also instructive to the ones new to this field.

Target Recognition- and HCR Amplification-Induced In Situ Electrochemical Signal Probe Synthesis Strategy for Trace ctDNA Analysis

An electrochemical-DNA (E-DNA) sensor was constructed by using DNA metallization to produce an electrochemical signal reporter in situ and hybridization chain reaction (HCR) as signal amplification strategy. The cyclic voltammetry (CV) technique was used to characterize the electrochemical solid-state Ag/AgCl process. Moreover, the enzyme cleavage technique was introduced to reduce background signals and further improve recognition accuracy. On the basis of these techniques, the as-prepared E-DNA sensor exhibited superior sensing performance for trace ctDNA analysis with a detection range of 0.5 fM to 10 pM and a detection limit of 7 aM. The proposed E-DNA sensor also displayed excellent selectivity, satisfied repeatability and stability, and had good recovery, all of which supports its potential applications for future clinical sample analysis.

Human Cyclophilin B Nuclease Activity Revealed via Nucleic Acid-Based Electrochemical Sensors

Human cyclophilin B (CypB) is oversecreted by pancreatic cancer cells, making it a potential biomarker for early-stage disease diagnosis. Our group is motivated to develop aptamer-based assays to measure CypB levels in biofluids. However, human cyclophilins have been postulated to have collateral nuclease activity, which could impede the use of aptamers for CypB detection. To establish if CypB can hydrolyze electrode-bound nucleic acids, we used ultrasensitive electrochemical sensors to measure CypB's hydrolytic activity. Our sensors use ssDNA and dsDNA in the biologically predominant d-DNA form, and in the nuclease resistant l-DNA form. Challenging such sensors with CypB and control proteins, we unequivocally demonstrate that CypB can cleave nucleic acids. To our knowledge, this is the first study to use electrochemical biosensors to reveal the hydrolytic activity of a protein that is not known to be a nuclease. Future development of CypB bioassays will require the use of nuclease-resistant aptamer sequences.