Harnessing Effective Molarity to Design an Electrochemical DNA‐based Platform for Clinically Relevant Antibody Detection

Unleashing inkjet-printed nanostructured electrodes and battery-free potentiostat for the DNA-based multiplexed detection of SARS-CoV-2 genes

Following the global COVID-19 pandemic triggered by SARS-CoV-2, the need for rapid, specific and cost-effective point-of-care diagnostic solutions remains paramount. Even though COVID-19 is no longer a public health emergency, the disease still poses a global threat leading to deaths, and it continues to change with the risk of new variants emerging causing a new surge in cases and deaths. Here, we address the urgent need for rapid, cost-effective and point-of-care diagnostic solutions for SARS-CoV-2. We propose a multiplexed DNA-based sensing platform that utilizes inkjet-printed nanostructured gold electrodes and an inkjet-printed battery-free near-field communication (NFC) potentiostat for the simultaneous quantitative detection of two SARS-CoV-2 genes, the ORF1ab and the N gene. The detection strategy based on the formation of an RNA-DNA sandwich structure leads to a highly specific electrochemical output. The inkjet-printed nanostructured gold electrodes providing a large surface area enable efficient binding and increase the sensitivity. The inkjet-printed battery-free NFC potentiostat enables rapid measurements and real-time data analysis via a smartphone application, making the platform accessible and portable. With the advantages of speed (5 min), simplicity, sensitivity (low pM range, ∼450% signal gain) and cost-effectiveness, the proposed platform is a promising alternative for point-of-care diagnostics and high-throughput analysis that complements the COVID-19 diagnostic toolkit.

Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing

The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.

Synthetic Antigen-Conjugated DNA Systems for Antibody Detection and Characterization

Antibodies are among the most relevant biomolecular targets for diagnostic and clinical applications. In this Perspective, we provide a critical overview of recent research efforts focused on the development and characterization of devices, switches, and reactions based on the use of synthetic antigen-conjugated DNA strands designed to be responsive to specific antibodies. These systems can find applications in sensing, drug-delivery, and antibody-antigen binding characterization. The examples described here demonstrate how the programmability and chemical versatility of synthetic nucleic acids can be used to create innovative analytical tools and target-responsive systems with promising potentials.

Detection of E.coli 23S rRNA by electrocatalytic "off-on" DNA beacon assay with femtomolar sensitivity

Prevention of food spoilage, environmental bio-contamination, and pathogenic infections requires rapid and sensitive bacterial detection systems. Among microbial communities, the bacterial strain of Escherichia coli is most widespread, with pathogenic and non-pathogenic strains being biomarkers of bacterial contamination. Here, we have developed a fM-sensitive, simple, and robust electrocatalytically-amplified assay facilitating specific detection of E.coli 23S ribosomal rRNA, in the total RNA sample, after its site-specific cleavage by RNase H enzyme. Gold screen-printed electrodes (SPE) were electrochemically pre-treated to be productively modified with a methylene-blue (MB) - labelled hairpin DNA probes, which hybridization with the E. coli-specific DNA placed MB in the top region of the DNA duplex. The formed duplex acted as an electrical wire, mediating electron transfer from the gold electrode to the DNA-intercalated MB, and further to ferricyanide in solution, enabling its electrocatalytic reduction otherwise impeded on the hairpin-modified SPEs. The assay facilitated 20 min 1 fM detection of both synthetic E. coli DNA and 23S rRNA isolated from E.coli (equivalent to 15 CFU mL^-1), and can be extended to fM analysis of nucleic acids isolated from any other bacteria.

Tailoring electrode surface charge to achieve discrimination and quantification of chemically similar small molecules with electrochemical aptamers

Electrochemical biosensors based on structure-switching aptamers offer many advantages because they can operate directly in complex samples and offer the potential to integrate with miniaturized electronics. Unfortunately, these biosensors often suffer from cross-reactivity problems when measuring a target in samples containing other chemically similar molecules, such as precursors or metabolites. While some progress has been made in selecting highly specific aptamers, the discovery of these reagents remains slow and costly. In this work, we demonstrate a novel strategy to distinguish molecules with miniscule difference in chemical composition (such as a single hydroxyl group) - with cross reactive aptamer probes - by tuning the charge state of the surface on which the aptamer probes are immobilized. As an exemplar, we show that our strategy can distinguish between DOX and many structurally similar analytes, including its primary metabolite doxorubicinol (DOXol). We then demonstrate the ability to accurately quantify mixtures of these two molecules based on their differential response to sensors with different surface-charge properties. We believe this methodology is general and can be extended to a broad range of applications.

Electrochemical DNA Scaffold-Based Sensing Platform for Multiple Modes of Protein Assay and a Keypad Lock System

Development of a flexible, easy-to-use, and well-controllable DNA-based sensing platform would provide enormous opportunities to boost molecular diagnosis and signal transduction or information processing. Herein, a duplex DNA scaffold containing a bulge was deployed for the fabrication of a simple and general DNA-based electrochemical sensing platform. It could be harnessed for different signal output behaviors (one signal-off and two signal-on modes) toward a single-step analysis of the target protein. The detection limit toward the target protein could reach about 0.1 nM. Also, it could be used as a streamlined electrochemical workflow for the successive monitoring of protein binding. Furthermore, such an electrochemical sensing platform could be explored for the operation of the concatenated AND logic gates as a molecular keypad lock system. The current sensing platform based on only one duplex DNA scaffold presented features such as simple biosensor design and fabrication, flexible operation for different signal outputs, sensitive and selective protein detection, and expandable logic operation. It thus would pave a broad road toward the development of high-performance biosensors or logic devices to be applied for molecular diagnosis or computing.

Programmable Cell-Free Transcriptional Switches for Antibody Detection

We report here the development of a cell-free in vitro transcription system for the detection of specific target antibodies. The approach is based on the use of programmable antigen-conjugated DNA-based conformational switches that, upon binding to a target antibody, can trigger the cell-free transcription of a light-up fluorescence-activating RNA aptamer. The system couples the unique programmability and responsiveness of DNA-based systems with the specificity and sensitivity offered by in vitro genetic circuitries and commercially available transcription kits. We demonstrate that cell-free transcriptional switches can efficiently measure antibody levels directly in blood serum. Thanks to the programmable nature of the sensing platform, the method can be adapted to different antibodies: we demonstrate here the sensitive, rapid, and cost-effective detection of three different antibodies and the possible use of this approach for the simultaneous detection of two antibodies in the same solution.

Flow-homogeneous electrochemical sensing system based on 2D metal-organic framework nanozyme for successive microRNA assay

Considering DNA-based homogeneous electrochemical assay allows identification of targets to be carried out in a homogeneous solution, it would be of significance to develop the successive homogeneous assay system in dynamic solution for rapid disease diagnosis and high-throughput bioanalysis. In homogeneous assay, the work electrodes generally have capability of DNA capture but lack signal amplification, restricting its sensitivity. Here, a flow-homogeneous sensing system was proposed to realize the successive assay of microRNA, a model biomarker. Ultrathin 2D metal-organic framework (MOF) nanozymes with thickness of about 1 nm were facilely prepared by ultrasonic approach. Due to the excellent enzyme-like activity and adsorption capacity towards single-strand DNA (ssDNA), MOF nanozymes adsorbed on electrode simultaneously played two roles of ssDNA collector and signal-amplifier. To adapt the recoverable electrode to on-line monitoring, duplex-specific nuclease-assisted circle reaction was conducted to produce the turn-on amplified signal. Flow injection device was employed to realize the recycling of electrodes and the successive microRNA assay. The assay strategy showed low limit of detection (0.12 pM, S/N = 3) for microRNA, excellent renewability and acceptable reliability for real sample assay. The established system exerts the advantages of DNA-based homogeneous electrochemical sensing strategy. This work would not only expand homogeneous electrochemical assay to successive bioassay, but also provide the possibility for practical application of homogeneous sensing strategy.

Wash-Free, Sandwich-Type Protein Detection Using Direct Electron Transfer and Catalytic Signal Amplification of Multiple Redox Labels

Direct electron transfer (DET) between a redox label and an electrode has been used for sensitive and selective sandwich-type detection without a wash step. However, applying DET is still highly challenging in protein detection, and a single redox label per probe is insufficient to obtain a high electrochemical signal. Here, we report a wash-free, sandwich-type detection of thrombin using DET and catalytic signal amplification of multiple redox labels. The detection scheme is based on (i) the redox label-catalyzed oxidation of a reductant, (ii) the conjugation of multiple redox labels per probe using a poly-linker, (iii) the low nonspecific adsorption of the conjugated poly-linker due to uncharged, reduced redox labels, and (iv) a facile DET using long, flexible poly-linker and spacer DNA. Amine-reactive phenazine ethosulfate and NADH were used as the redox label and reductant, respectively. N₃-terminated polylysine was used as the poly-linker for the conjugation between an aptamer probe and multiple redox labels. Approximately 11 redox labels per probe and rapid catalytic NADH oxidation enable high signal amplification. Thrombin in urine could be detected without a wash step with a detection limit of ∼50 pM, which is practically promising for point-of-care testing of proteins.

Accelerated Electron Transfer in Nanostructured Electrodes Improves the Sensitivity of Electrochemical Biosensors

Electrochemical biosensors hold the exciting potential to integrate molecular detection with signal processing and wireless communication in a miniaturized, low-cost system. However, as electrochemical biosensors are miniaturized to the micrometer scale, their signal-to-noise ratio degrades and reduces their utility for molecular diagnostics. Studies have reported that nanostructured electrodes can improve electrochemical biosensor signals, but since the underlying mechanism remains poorly understood, it remains difficult to fully exploit this phenomenon to improve biosensor performance. In this work, electrochemical aptamer biosensors on nanoporous electrode are optimized to achieve improved sensitivity by tuning pore size, probe density, and electrochemical measurement parameters. Further, a novel mechanism in which electron transfer is physically accelerated within nanostructured electrodes due to reduced charge screening, resulting in enhanced sensitivity is proposed and experimentally validated. In concert with the increased surface areas achieved with this platform, this newly identified effect can yield an up to 24-fold increase in signal level and nearly fourfold lower limit of detection relative to planar electrodes with the same footprint. Importantly, this strategy can be generalized to virtually any electrochemical aptamer sensor, enabling sensitive detection in applications where miniaturization is a necessity, and should likewise prove broadly applicable for improving electrochemical biosensor performance in general.

Aptamer-based biosensors and application in tumor theranostics

An aptamer is a short oligonucleotide chain that can specifically recognize targeting analytes. Due to its high specificity, low cost, and good biocompatibility, aptamers as the targeting elements of biosensors have been applied widely in non-invasive tumor imaging and treatment in situ to replace traditional methods. In this review, we will summarize recent advances in using aptamer-based biosensors in tumor diagnosis. After a brief introduction of the advantage of aptamers compared with enzyme sensors and immune sensors, the different sensing designs and mechanisms based on 3 signal transduction modes will be reviewed to cover different kinds of analytical methods, including: electrochemistry analysis, colorimetry analysis, and fluorescence analysis. Finally, the prospective advantages of aptamer-based biosensors in tumor theranostics and post-treatment monitoring are also evaluated in this review.

Carbon Dots/α-Fe2O3-Fe3O4 nanocomposite: Efficient synthesis and application as a novel electrochemical aptasensor for the ultrasensitive determination of aflatoxin B1

Developing an effective method for the detection of aflatoxin B1 (AFB1) remains an arduous task due to the high toxicity of AFB1 to a health concern. In this study, a sensitive and reliable electrochemical aptasensor based on carbon dots/α-Fe₂O₃-Fe₃O₄ nanocomposite (CDs/α-Fe₂O₃-Fe₃O₄) is constructed for the determination of AFB1. The CDs have good electrical conductivity and large specific surface areas to improve the aptasensor's sensitivity. The α-Fe₂O₃-Fe₃O₄ can not only improve the catalytic performance of the aptasensor but also have magnetism, which can realize the recovery of CDs/α-Fe₂O₃-Fe₃O₄ to avoid material waste and environmental pollution. This electrochemical aptasensor can achieve a good linear (0.001-100.0 nM) and excellent detection limit (0.5 pM) for the determination of AFB1. In addition, the aptasensor was also applied to determine AFB1 in beer, rice, and peanuts, all results were in good agreement with HPLC, indicating that the electrochemical aptasensor has a broad application prospect.

Ultrasensitive Detection of SARS-CoV-2 Antibody by Graphene Field-Effect Transistors

The fast spread of SARS-CoV-2 has severely threatened the public health. Establishing a sensitive method for SARS-CoV-2 detection is of great significance to contain the worldwide pandemic. Here, we develop a graphene field-effect transistor (g-FET) biosensor and realize ultrasensitive SARS-CoV-2 antibody detection with a limit of detection (LoD) down to 10^-18 M (equivalent to 10^-16 g mL^-1) level. The g-FETs are modified with spike S1 proteins, and the SARS-CoV-2 antibody biorecognition events occur in the vicinity of the graphene surface, yielding an LoD of ∼150 antibodies in 100 μL full serum, which is the lowest LoD value of antibody detection. The diagnoses time is down to 2 min for detecting clinical serum samples. As such, the g-FETs leverage rapid and precise SARS-CoV-2 screening and also hold great promise in prevention and control of other epidemic outbreaks in the future.

Proximity-induced exponential amplification reaction triggered by proteins and small molecules

We proposed a method to regulate nucleic acid polymerization by proximity and designed an ultrasensitive biosensor based on proximity-induced exponential amplification reaction for proximity assay of proteins (streptavidin) and small molecules (adenosine triphosphate), which allows us to detect a variety of interesting targets by simply changing the binding sites of DNA.

DNA-Based Nanoswitches: Insights into Electrochemiluminescence Signal Enhancement

Electrochemiluminescence (ECL) is a powerful transduction technique that has rapidly gained importance as a powerful analytical technique. Since ECL is a surface-confined process, a comprehensive understanding of the generation of ECL signal at a nanometric distance from the electrode could lead to several highly promising applications. In this work, we explored the mechanism underlying ECL signal generation on the nanoscale using luminophore-reporter-modified DNA-based nanoswitches (i.e., molecular beacon) with different stem stabilities. ECL is generated according to the "oxidative-reduction" strategy using tri-n-propylamine (TPrA) as a coreactant and Ru(bpy)₃²⁺ as a luminophore. Our findings suggest that by tuning the stem stability of DNA nanoswitches we can activate different ECL mechanisms (direct and remote) and, under specific conditions, a "digital-like" association curve, i.e., with an extremely steep transition after the addition of increasing concentrations of DNA target, a large signal variation, and low preliminary analytical performance (LOD 22 nM for 1GC DNA-nanoswtich and 16 nM for 5GC DNA-nanoswitch). In particular, we were able to achieve higher signal gain (i.e., 10 times) with respect to the standard "signal-off" electrochemical readout. We demonstrated the copresence of two different ECL generation mechanisms on the nanoscale that open the way for the design of customized DNA devices for highly efficient dual-signal-output ratiometric-like ECL systems.

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

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

An Integrated Multi-Function Heterogeneous Biochemical Circuit for High-Resolution Electrochemistry-Based Genetic Analysis

Modular construction of an autonomous and programmable multi-functional heterogeneous biochemical circuit that can identify, transform, translate, and amplify biological signals into physicochemical signals based on logic design principles can be a powerful means for the development of a variety of biotechnologies. To explore the conceptual validity, we design a CRISPR-array-mediated primer-exchange-reaction-based biochemical circuit cascade, which probes a specific biomolecular input, transform the input into a structurally accessible form for circuit wiring, translate the input information into an arbitrary sequence, and finally amplify the prescribed sequence through autonomous formation of a signaling concatemer. This upstream biochemical circuit is further wired with a downstream electrochemical interface, delivering an integrated bioanalytical platform. We program this platform to directly analyze the genome of SARS-CoV-2 in human cell lysate, demonstrating the capability and the utility of this unique integrated system.