Review: Electrochemical DNA sensing – Principles, commercial systems, and applications

Simplified Electrochemical Approach for End-Point Yet Quantitative Detection of Nucleic Acids in Resource-Limited Settings

Nucleic acid detection plays a crucial role in various aspects of health care, necessitating accessible and reliable quantification methods, especially in resource-limited settings. This work presents a simplified electrochemical approach for end-point yet quantitative nucleic acid detection. By elevating the concentration of redox species and choosing potential as the signals, we achieved enhanced signal robustness, even in the presence of interfering substances. Leveraging this robustness, we accurately measured pH-induced redox potential changes in methylene blue solution for end-point nucleic acid detection after loop-mediated isothermal amplification (LAMP). Our method demonstrated quantitative detection of the SARS-CoV-2 N gene and human ATCB gene and successful discrimination of the human BRAF V600E mutation, comparable in sensitivity to commercial kits. The developed user-friendly electrochemical method offers a simplified and reliable approach for end-point yet quantitative detection of nucleic acids, potentially expanding the benefits of nucleic acid testing in resource-limited settings.

May DNA analyses be biased by hidden oxidative damage? Voltammetric study of temperature and oxidation stress effect

The analysis of nucleic acids is one of the fundamental parts of modern molecular biology and molecular diagnostics. The information collected predominantly depends on the condition of the genetic material. All potential damage induced by oxidative stress may affect the final results of the analysis of genetic material obtained using commonly used techniques such as polymerase chain reaction or sequencing. The aim of this work was to evaluate the effects of high temperature and pH on DNA structure in the context of the occurrence of oxidative damage, using square-wave voltammetry and two independent research protocols. We resulted in visible oxidation damage registered in acidic conditions after the thermal denaturation process (pH 4.7) with changes in the intensity of guanine and adenine signals. However, using phosphate buffer (pH 7.0) for DNA denaturation negatively affected the DNA structure, but without any oxidized derivatives present. This leads to the conclusion that oxidation occurring in the DNA melting process results in the formation of various derivatives of nucleobases, both electrochemically active and inactive. These derivatives may distort the results of molecular tests due to the possibility of forming complementary bonds with various nucleobases. For example, 8-oxoguanine can form pairs with both cytosine and adenine.

Combining recombinase polymerase amplification with tyrosine modified 2'-deoxyuridine-5'-triphosphate for direct voltammetric detection of double-stranded DNA: Application to potato pathogen Dickeya solani

The approach based on a combination of isothermal recombinase polymerase amplification (RPA), 2'-deoxyuridine-5'-triphosphate modified with tyrosine aromatic group (dUTP-Y1), and direct voltammetric detection of RPA product carrying electroactive labels was successfully applied to the potato pathogen Dickeya solani. The artificial nucleotide dUTP-Y1 demonstrated a good compatibility with RPA, enabling by targeting a section of D. solani genome with a unique sequence to produce the full-size modified products at high levels of substitution of dTTP by dUTP-Y1 (up to 80-90 %) in the reaction mixture. The optimized procedure of square wave voltammetry allowed to reliably detect the product generated by RPA at 80 % substitution of dTTP by dUTP-Y1 (dsDNA-Y1) in microliter sample volumes on the surface of disposable carbon screen printed electrodes at the potential of about 0.6 V. The calibration curve for the amplicon detection was linear in coordinates 'Ip, A vs. Log (c, M)' within the 0.05-1 μM concentration range. The limit of detection for dsDNA-Y1 was estimated as 8 nM. The sensitivity of the established electrochemical approach allowed to detect amplicons generated in a single standard 50 μL RPA reaction after their purification with silica-coated magnetic beads. The overall detectability of D. solani with the suggested combination of RPA and voltammetric registration of dsDNA-Y1 can be as low as a few copies of bacterial genome per standard reaction. In total, amplification, purification, and electrochemical detection take about 120-150 min. Considering the potential of direct electrochemical analysis for miniaturization, as well as compliance with low-cost and low-power requirements, the findings provide grounds for future development of microfluidic devices integrating isothermal amplification, amplicon purification and detection based on the tyrosine modified nucleotide for the purpose of 'on-site' detection of various pathogens.

Electrochemical Paper-Based Microfluidics: Harnessing Capillary Flow for Advanced Diagnostics

Electrochemical paper-based microfluidics has attracted much attention due to the promise of transforming point-of-care diagnostics by facilitating quantitative analysis with low-cost and portable analyzers. Such devices harness capillary flow to transport samples and reagents, enabling bioassays to be executed passively. Despite exciting demonstrations of capillary-driven electrochemical tests, conventional methods for fabricating electrodes on paper impede capillary flow, limit fluidic pathways, and constrain accessible device architectures. This account reviews recent developments in paper-based electroanalytical devices and offers perspective by revisiting key milestones in lateral flow tests and paper-based microfluidics engineering. The study highlights the benefits associated with electrochemical sensing and discusses how the detection modality can be leveraged to unlock novel functionalities. Particular focus is given to electrofluidic platforms that embed electrodes into paper for enhanced biosensing applications. Together, these innovations pave the way for diagnostic technologies that offer portability, quantitative analysis, and seamless integration with digital healthcare, all without compromising the simplicity of commercially available rapid diagnostic tests.

Organometallic modification confers oligonucleotides new functionalities

To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.

Biosensing of DNA through difference in interaction between microparticle and glass plate based on particle dissociation in a coupled acoustic-gravitational field

A novel approach for detecting DNA without labeling the target DNA was developed based on the particle dissociation behavior in a combined acoustic-gravitational field. The particles, which are tethered on a glass plate via intermolecular interactions (Fbind), are dissociated by the resultant force of the acoustic radiation force (Fac), which is a function of the applied voltage (V), and the sedimentation force. In this system, V required for particle dissociation is dependent on Fbind. The differences in Fbind were exploited for detecting the target DNA. A glass plate and polystyrene (PS) particles were respectively modified with anchor and capture DNAs. The target DNA induces immobilization of the PS particles on the glass plate through sandwich hybridization, with a large accompanying Fbind. In the absence of the target DNA, the anchor DNA on the glass plate interacted weakly with the capture DNA on the PS particles via direct binding (small Fbind). The particle dissociation behavior varies based on the concentration of the target DNA due to changes in the ratio of the PS particles tethered through direct binding and sandwich hybridization. Target DNA with a length exceeding 12 base pairs (bps) can be detected on the picomolar scale at concentrations of 10-12 to 10-5 M. This detection scheme was applied to a specific sequence of HIV-2 with 20 bps, achieving a picomolar detection limit.

Microarray-Based Electrochemical Biosensing

Microarrays are widely utilized in bioanalysis. Electrochemical biosensing techniques are often applied in microarray-based assays because of their simplicity, low cost, and high sensitivity. In such systems, the electrodes and sensing elements are arranged in arrays, and the target analytes are detected electrochemically. These sensors can be utilized for high-throughput bioanalysis and the electrochemical imaging of biosamples, including proteins, oligonucleotides, and cells. In this chapter, we summarize recent progress on these topics. We categorize electrochemical biosensing techniques for array detection into four groups: scanning electrochemical microscopy, electrode arrays, electrochemiluminescence, and bipolar electrodes. For each technique, we summarize the key principles and discuss the advantages, disadvantages, and bioanalysis applications. Finally, we present conclusions and perspectives about future directions in this field.

Electroanalysis in Pharmacogenomic Studies: Mechanisms of Drug Interaction with DNA

The review discusses electrochemical methods for analysis of drug interactions with DNA. The electroanalysis method is based on the registration of interaction-induced changes in the electrochemical oxidation potential of heterocyclic nitrogenous bases in the DNA molecule and in the maximum oxidation current amplitude. The mechanisms of DNA-drug interactions can be identified based on the shift in the electrooxidation potential of heterocyclic nitrogenous bases toward more negative (cathodic) or positive (anodic) values. Drug intercalation into DNA shifts the electrochemical oxidation potential to positive values, indicating thermodynamically unfavorable process that hinders oxidation of nitrogenous bases in DNA. The potential shift toward the negative values indicates electrostatic interactions, e.g., drug binding in the DNA minor groove, since this process does not interfere with the electrochemical oxidation of bases. The concentration-dependent decrease in the intensity of electrochemical oxidation of DNA bases allows to quantify the type of interaction and calculate the binding constants.

Electrochemical nucleic acid sensors: Competent pathways for mobile molecular diagnostics

Electrochemical nucleic acid biosensor has demonstrated great promise in clinical diagnostic tests, mainly because of its flexibility, high efficiency, low cost, and easy integration for analytical applications. Numerous nucleic acid hybridization-based strategies have been developed for the design and construction of novel electrochemical biosensors for diagnosing genetic-related diseases. This review describes the advances, challenges, and prospects of electrochemical nucleic acid biosensors for mobile molecular diagnosis. Specifically, the basic principles, sensing elements, applications in diagnosis of cancer and infectious diseases, integration with microfluidic technology and commercialization are mainly included in this review, aiming to provide new insights and directions for the future development of electrochemical nucleic acid biosensors.

DNA intercalation makes possible superior-gain organic photoelectrochemical transistor detection

DNA intercalation has increasingly been studied for various scenario implementations due to the diverse functions of DNA/intercalators. Nascent organic photoelectrochemical transistor (OPECT) biosensing taking place in organic electronics and photoelectrochemical bioanalysis represents a promising technological frontier in the arena. In this work, we first devise DNA intercalation-enabled OPECT for miRNA detection with a superior gain up to 17100. Intercalation of [Ru(bpy)2dppz]2+ within the miRNA-initiated hybrid chain reaction (HCR)-derived duplex DNA is realized for producing anodic photocurrent upon light stimulation, causing the corresponding target-dependent alternation in gate voltage (VG) and hence the modulated channel current (IDS) of poly (3,4-ethylenedioxythiophene) doped with poly (styrene sulfonate) (PEDOT:PSS) under specific drain voltage (VDS) for quantitative miRNA-21 analysis, which shows a wide linear relationship and a low detection limit of 5.5 × 10-15 mol L-1. This study features the DNA intercalation-enabled organic electronics with superior gain and is envisaged to attract more attention to explore DNA adducts for innovative bioelectronics and biosensing, given the diverse DNA binders with multiple functions.

Facile Strategy to Output Fluorescein from Nucleic Acid Interactions

Biomolecular operations, which involve the conversion of molecular signals or interactions into specific functional outputs, are fundamental to the field of biology and serve as the important foundation for the design of diagnostic and therapeutic systems. To maximize their functionalities and broaden their applicability, it is crucial to develop novel outputs and facile chemical transformation methods. With this aim, in this study, we present a straightforward method for converting nucleic acid signals into fluorescein outputs that exhibit a wide range of functionalities. This operation is designed through a DNA-templated reaction based on riboflavin-photocatalyzed oxidation of dihydrofluorescein, which is readily prepared by simple NaBH4 reduction of the fluorescein with no complicated chemical caging steps. The templated photooxidation exhibits high efficiency (kapp = 2.7 × 10-3/s), generating a clear fluorescein output signal distinguishable from a low background, originating from the high stability of the synthesized dihydrofluorescein. This facile and efficient operation allows the nucleic acid-initiated activation of various fluorescein functions, such as fluorescence and artificial oxidase activity, which are applied in the design of novel bioanalytical systems, including fluorescent and colorimetric DNA sensors. The operation presented herein would expand the scope of biomolecular circuit systems for diagnostic and therapeutic applications.

In vitro allosteric transcription factor-based biosensing

A biosensor is an analytical device that converts a biological response into a measurable output signal. Bacterial allosteric transcription factors (aTFs) have been utilized as a novel class of recognition elements for in vitro biosensing, which circumvents the limitations of aTF-based whole-cell biosensors (WCBs) and helps to meet the increasing requirement of small-molecule biosensors for diverse applications. In this review, we summarize the recent advances related to the configuration of aTF-based biosensors in vitro. Particularly, we evaluate the advantages of aTFs for in vitro biosensing and highlight their great potential for the establishment of robust and easy-to-implement biosensing strategies. We argue that key technical innovations and generalizable workflows will enhance the pipeline for facile construction of diverse aTF-based small-molecule biosensors.

Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules

Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.

FRET Imaging of Nonuniformly Distributed DNA SAMs on Gold Reveals the Role Played by the Donor/Acceptor Ratio and the Local Environment in Measuring the Rate of Hybridization

Mixed DNA SAMs labeled with a fluorophore (either AlexaFluor488 or AlexaFluor647) were prepared on a single crystal gold bead electrode using potential-assisted thiol exchange and studied using Förster resonance energy transfer (FRET). A measure of the local environment of the DNA SAM (e.g., crowding) was possible using FRET imaging on these surfaces since electrodes prepared this way have a range of surface densities (Γ_DNA). The FRET signal was strongly dependent on Γ_DNA and on the ratio of AlexaFluor488 to AlexaFluor647 used to make the DNA SAM, which were consistent with a model of FRET in 2D systems. FRET was shown to provide a direct measure of the local DNA SAM arrangement on each crystallographic region of interest providing a direct assessment of the probe environment and its influence on the rate of hybridization. The kinetics of duplex formation for these DNA SAMs was also studied using FRET imaging over a range of coverages and DNA SAM compositions. Hybridization of the surface-bound DNA increased the average distance between the fluorophore label and the gold electrode surface and decreased the distance between the donor (D) and acceptor (A), both of which result in an increase in FRET intensity. This increase in FRET was modeled using a second order Langmuir adsorption rate equation, reflecting the fact that both D and A labeled DNA are required to become hybridized to observe a FRET signal. The self-consistent analysis of the hybridization rates on low and high coverage regions on the same electrode showed that the low coverage regions achieved full hybridization 5× faster than the higher coverage regions, approaching rates typically found in solution. The relative increase in FRET intensity from each region of interest was controlled by manipulating the donor to acceptor composition of the DNA SAM without changing the rate of hybridization. The FRET response can be optimized by controlling the coverage and the composition of the DNA SAM sensor surface and could be further improved with the use of a FRET pair with a larger (e.g., > 5 nm) Förster radius.

Catalytically synthesized Prussian Blue nanozymes as labels for electrochemical DNA/RNA sensors

We propose catalytically synthesized nanozymes based on Prussian Blue (PB) and azidomethyl-substituted poly (3,4-ethylenedioxythiophene) (azidomethyl-PEDOT) as novel electrocatalytic labels for DNA/RNA sensors. Catalytic approach allowed to synthesize highly redox and electrocatalytically active Prussian Blue nanoparticles functionalized with azide groups that enable 'click' conjugation with alkyne-modified oligonucleotides. Both competitive and sandwich-type schemes were realized. As the sensor response the direct (mediator-free) electrocatalytic current of H₂O₂ reduction can be measured, which is proportional to the concentration of the hybridized labeled sequences. The current of H₂O₂ electrocatalytic reduction is only 3-8 times increased in the presence of the freely diffusing mediator catechol, which indicates high efficiency of direct electrocatalysis with the elaborated labels. Electrocatalytic amplification of the signal allows robust detection of (63-70)-base target sequences with concentrations below 0.2 nM in blood serum within an hour. We believe, the use of advanced Prussian Blue based electrocatalytic labels sets new avenues for point-of-care DNA/RNA sensing.

A plug-and-play aptamer diagnostic platform based on linear dichroism spectroscopy

A plug-and-play sandwich assay platform for the aptamer-based detection of molecular targets using linear dichroism (LD) spectroscopy as a read-out method has been demonstrated. A 21-mer DNA strand comprising the plug-and-play linker was bioconjugated onto the backbone of the filamentous bacteriophage M13, which gives a strong LD signal due to its ready alignment in linear flow. Extended DNA strands containing aptamer sequences that bind the protein thrombin, TBA and HD22, were then bound to the plug-and-play linker strand via complementary base pairing to generate aptamer-functionalised M13 bacteriophages. The secondary structure of the extended aptameric sequences required to bind to thrombin was checked using circular dichroism spectroscopy, with the binding confirmed using fluorescence anisotropy measurements. LD studies revealed that this sandwich sensor design is very effective at detecting thrombin down to pM levels, indicating the potential of this plug-and-play assay system as a new label-free homogenous detection system based on aptamer recognition.

Functional Nanomaterials Enhancing Electrochemical Biosensors as Smart Tools for Detecting Infectious Viral Diseases

Electrochemical biosensors are known as analytical tools, guaranteeing rapid and on-site results in medical diagnostics, food safety, environmental protection, and life sciences research. Current research focuses on developing sensors for specific targets and addresses challenges to be solved before their commercialization. These challenges typically include the lowering of the limit of detection, the widening of the linear concentration range, the analysis of real samples in a real environment and the comparison with a standard validation method. Nowadays, functional nanomaterials are designed and applied in electrochemical biosensing to support all these challenges. This review will address the integration of functional nanomaterials in the development of electrochemical biosensors for the rapid diagnosis of viral infections, such as COVID-19, middle east respiratory syndrome (MERS), influenza, hepatitis, human immunodeficiency virus (HIV), and dengue, among others. The role and relevance of the nanomaterial, the type of biosensor, and the electrochemical technique adopted will be discussed. Finally, the critical issues in applying laboratory research to the analysis of real samples, future perspectives, and commercialization aspects of electrochemical biosensors for virus detection will be analyzed.

Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification

Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.

Recent Developments in Electrochemical Sensors for the Detection of Antibiotic-Resistant Bacteria

The development of efficient point-of-care (POC) diagnostic tools for detecting infectious diseases caused by destructive pathogens plays an important role in clinical and environmental monitoring. Nevertheless, evolving complex and inconsistent antibiotic-resistant species mire their drug efficacy. In this regard, substantial effort has been expended to develop electrochemical sensors, which have gained significant interest for advancing POC testing with rapid and accurate detection of resistant bacteria at a low cost compared to conventional phenotype methods. This review concentrates on the recent developments in electrochemical sensing techniques that have been applied to assess the diverse latent antibiotic resistances of pathogenic bacteria. It deliberates the prominence of biorecognition probes and tailor-made nanomaterials used in electrochemical antibiotic susceptibility testing (AST). In addition, the bimodal functional efficacy of nanomaterials that can serve as potential transducer electrodes and the antimicrobial agent was investigated to meet the current requirements in designing sensor module development. In the final section, we discuss the challenges with contemporary AST sensor techniques and extend the key ideas to meet the demands of the next POC electrochemical sensors and antibiotic design modules in the healthcare sector.

A Highly Integrated and Diminutive Fluorescence Detector for Point-of-Care Testing: Dual Negative Feedback Light-Emitting Diode (LED) Drive and Photoelectric Processing Circuits Design and Implementation

As an important detection tool in biochemistry, fluorescence detection has wide applications. Quantitative detection can be achieved by detecting fluorescence signals excited by excitation light at a specific wavelength range. Therefore, the key to fluorescence detection is the stable control of the excitation light and the accurate acquisition of weak photoelectric signals. Moreover, to improve portability and instantaneity, devices are developing in miniaturization and integration. As the core of such devices, fluorescence detectors should also have these features. Under this circumstance, we designed a highly integrated and diminutive fluorescence detector and focused on its excitation light driving and photoelectric signal processing. A current–light dual negative feedback light-emitting diode (LED) driving circuit was proposed to obtain constant current and luminance. In addition, a silicon photodiode (PD) was used to receive and convert the fluorescence signal to an electric signal. Then, amplifying, filtering, and analog-to-digital (A/D) converting were applied to make the detection of weak fluorescence signals possible. The test results showed that the designed circuit has wonderful performance, and the detector shows good linearity (R² = 0.9967) and sensitivity (LOD = 0.077 nM) in the detection of fluorescein sodium solution. Finally, a real-time fluorescence polymerase chain reaction (real-time PCR) of Legionella pneumophila was carried out on a homemade platform equipped with this detector, indicating that the detector met the requirements of real-time PCR detection.

Sensitive Electrochemical Biosensor for Rapid Screening of Tumor Biomarker TP53 Gene Mutation Hotspot

Rapid and sensitive detection of cancer biomarkers is crucial for cancer screening, early detection, and improving patient survival rate. The present study proposes an electrochemical gene-sensor capable of detecting tumor related TP53 gene mutation hotspots by self-assembly of sulfhydryl ended hairpin DNA probes tagged with methylene blue (MB) onto a gold electrode. By performing a hybridization reaction with the target DNA sequence, the gene-sensor can rearrange the probe’s structure, resulting in significant electrochemical signal differences by differential pulse voltammetry. When the DNA biosensor is hybridized with 1 μM target DNA, the peak current response signal can decrease more than 60%, displaying high sensitivity and specificity for the TP53 gene. The biosensor achieved rapid and sensitive detection of the TP53 gene with a detection limit of 10 nmol L⁻¹, and showed good specific recognition ability for single nucleotide polymorphism (SNP) and base sequence mismatches in the TP53 gene affecting residue 248 of the P53 protein. Moreover, the biosensor demonstrated good reproducibility, repeatability, operational stability, and anti-interference ability for target DNA molecule in the complex system of 50% fetal bovine serum. The proposed biosensor provides a powerful tool for the sensitive and specific detection of TP53 gene mutation hotspot sequences and could be used in clinical samples for early diagnosis and detection of cancer.

Recent Advances in Electrochemical Sensing Strategies for Food Allergen Detection

Food allergy has been indicated as the most frequent adverse reaction to food ingredients over the past few years. Since the only way to avoid the occurrence of allergic phenomena is to eliminate allergenic foods, it is essential to have complete and accurate information on the components of foodstuff. In this framework, it is mandatory and crucial to provide fast, cost-effective, affordable, and reliable analysis methods for the screening of specific allergen content in food products. This review reports the research advancements concerning food allergen detection, involving electrochemical biosensors. It focuses on the sensing strategies evidencing different types of recognition elements such as antibodies, nucleic acids, and cells, among others, the nanomaterial role, the several electrochemical techniques involved and last, but not least, the ad hoc electrodic surface modification approaches. Moreover, a selection of the most recent electrochemical sensors for allergen detection are reported and critically analyzed in terms of the sensors’ analytical performances. Finally, advantages, limitations, and potentialities for practical applications of electrochemical biosensors for allergens are discussed.

A highly-efficient 3D DNAzyme motor for sensitive biosensing analysis

Herein, driven by the need of highly-efficient DNAzyme-amplified detection strategy, a novel 3D DNAzyme motor was designed as a biosensor platform for realizing sensitive detection of target DNA. The 3D DNAzyme motor was composed of target-activated DNAzyme nanowires and substrates H1-Fc that co-immobilized on Au@Fe₃O₄ nanoparticles (Au@Fe₃O₄NP_S) surface, possessing high local concentration of DNA reactants and shortened distance between DNAzyme and substrates for enhancing electrochemical signal. Compared with traditional DNAzyme-powered machines, the target-activated DNAzyme nanowires of 3D DNAzyme motor had greater flexibility and more powerful cleavage capability without troublesome sequence optimization, which overcame the space limitation and simultaneously interacted with adjacent and distant substrates H1-Fc to output a large amount of cleavage products with high signal response. Therefore, on account of the above-mentioned merits of nanoparticles localization DNA design and DNAzyme nanowires, the reported 3D DNAzyme motor ingeniously overcame many defects existing in traditional DNAzyme-amplified detection strategies such as low reactants concentration, limited flexibility of DNAzyme and small DNAzyme swing range, realizing the sensitive detection of target DNA with a detection limit of 1.7 fM ranging from 5 fM to 50 nM. Impressively, the 3D DNAzyme motor here presented a new strategy to achieve effective DNAzyme signal amplification and provided a reference for the assembly of various and functional 3D DNA machines in the future.

DNAzyme-Immobilizing Microgel Magnetic Beads Enable Rapid, Specific, Culture-Free, and Wash-Free Electrochemical Quantification of Bacteria in Untreated Urine

Rapid, ultrasensitive, and specific detection and identification of bacteria in unprocessed clinical specimens is critically needed to enable point-of-care diagnosis of infectious diseases. However, existing systems require sample processing and/or analyte enrichment for direct bacterial analysis in clinical samples, which significantly adds to the assay time and complexity. Herein, we integrate RNA-cleaving DNAzymes specific to Escherichia coli (E. coli) and programmed for electrochemical signal transduction, multifunctional microgel magnetic beads for immobilizing the DNAzyme into a hydrated and three-dimensional scaffold, and hierarchical electrodes for ultrasensitive electrochemical readout to achieve rapid bacterial analysis in undiluted and unprocessed urine collected from symptomatic patients suspected of having urinary tract infections (UTIs). The microgel magnetic bead assay enables highly efficient conjugation and hydration of the immobilized DNAzymes, resulting in low limits-of-detection of 6 CFU/mL in buffer and 138 CFU/mL in unprocessed urine with high specificity against multiple urinary pathogens within a 1 hour assay time. The assay successfully identifies which patients are infected with E. coli as the causative organism for their UTI symptoms, indicating the clinical relevance of this assay.

Impedance Technique-Based Label-Free Electrochemical Aptasensor for Thrombin Using Single-Walled Carbon Nanotubes-Casted Screen-Printed Carbon Electrode

An impedance technique-based aptasensor for the detection of thrombin was developed using a single-walled carbon nanotube (SWCNT)-modified screen-printed carbon electrode (SPCE). In this work, a thrombin-binding aptamer (TBA) as probe was used for the determination of thrombin, and that was immobilized on SWCNT through π-π interaction. In the presence of thrombin, the TBA on SWCNT binds with target thrombin, and the amount of TBA on the SWCNT surface decreases. The detachment of TBA from SWCNT will be affected by the concentration of thrombin and the remaining TBA on the SWCNT surface can be monitored by electrochemical methods. The TBA-modified SWCNT/SPCE sensing layer was characterized by cyclic voltammetry (CV). For the measurement of thrombin, the change in charge-transfer resistance (R_ct) of the sensing interface was investigated using electrochemical impedance spectroscopy (EIS) with a target thrombin and [Fe(CN)₆]^3- as redox maker. Upon incubation with thrombin, a decrease of R_ct change was observed due to the decrease in the repulsive interaction between the redox marker and the electrode surface without any label. A plot of R_ct changes vs. the logarithm of thrombin concentration provides the linear detection ranges from 0.1 nM to 1 µM, with a ~0.02 nM detection limit.

Hybridization chain reaction for regulating surface capacitance of organic photoelectrochemical transistor toward sensitive miRNA detection

Photon-enabled bioelectronics has long been pursued in modern electronics due to their non-contact, remote-control, and even self-powered function interfacing the biological world with semiconductor devices. The debuting organic photoelectrochemical transistor (OPECT) relies on the photovoltage generated by the semiconductors to modulate the channel conductance, which enables light-fueled operation at zero gate bias. Inspired by the insulating nature of macrobiomolecules and surface capacitance mechanism, herein we demonstrate the biological regulation of the surface capacitance towards new OPECT biodetection, which was exemplified by a CdS quantum dots/TiO₂ nanotubes photoanode accommodating hybridization chain reaction (HCR) amplification with the target of biomarker miRNA-17. Formation of the non-conducting DNA layer from the miRNA-17-oriented HCR could decrease the surface capacitance and increase the corresponding fractional potential drop, shifting the transfer curve horizontally to higher gate voltage and thus producing different drain currents. The OPECT biosensor exhibited a linear relationship with the miRNA-17 concentration on the logarithmic axis in the range from 1 pm. to 10 μm with a detection limit of 1 pm. This work not only represented a generic methodology of miRNA detection, but also provided a universal mechanism for the operation of advanced OPECT bioanalytics.

Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout

Carbon nanotube (CNT)-based electrodes are cheap, highly performing, and robust platforms for the fabrication of electrochemical sensors. Engineering programmable DNA nanotechnologies on the CNT surface can support the construction of new electrochemical DNA sensors providing an amperometric output in response to biomolecular recognition. This is a significant challenge, since it requires gaining control of specific hybridization processes and functional DNA systems at the interface, while limiting DNA physisorption on the electrode surface, which contributes to nonspecific signal. In this study, we provide design rules to program dynamic DNA structures at the surface of single-walled carbon nanotubes electrodes, showing that specific DNA interactions can be monitored through measurement of the current signal provided by redox-tagged DNA strands. We propose the use of pyrene as a backfilling agent to reduce nonspecific adsorption of reporter DNA strands and demonstrate the controlled formation of DNA duplexes on the electrode surface, which we then apply in the design and conduction of programmable DNA strand displacement reactions. Expanding on this aspect, we report the development of novel amperometric hybridization platforms based on artificial DNA structures templated by the small molecule melamine. These platforms enable dynamic strand exchange reactions orthogonal to conventional toehold-mediated strand displacement and may support new strategies in electrochemical sensing of biomolecular targets, combining the physicochemical properties of nanostructured carbon-based materials with programmable nucleic acid hybridization.

Single DNA Origami Detection by Nanoimpact Electrochemistry

DNA has emerged as the material of choice for producing supramolecular building blocks of arbitrary geometry from the 'bottom up'. Characterisation of these structures via electron or atomic force microscopy usually requires their surface immobilisation. In this work, we developed a nanoimpact electrochemistry platform to detect DNA self-assembled origami structures in solution, using the intercalator methylene blue as a redox probe. Here, we report the electrochemical detection of single DNA origami collisions at Pt microelectrodes. Our work paves the way towards the characterisation of DNA nanostructures in solution via nanoimpact electrochemistry.

Electrochemical Impedance Spectroscopy in the Characterisation and Application of Modified Electrodes for Electrochemical Sensors and Biosensors

Electrochemical impedance spectroscopy is finding increasing use in electrochemical sensors and biosensors, both in their characterisation, including during successive phases of sensor construction, and in application as a quantitative determination technique. Much of the published work continues to make little use of all the information that can be furnished by full physical modelling and analysis of the impedance spectra, and thus does not throw more than a superficial light on the processes occurring. Analysis is often restricted to estimating values of charge transfer resistances without interpretation and ignoring other electrical equivalent circuit components. In this article, the important basics of electrochemical impedance for electrochemical sensors and biosensors are presented, focussing on the necessary electrical circuit elements. This is followed by examples of its use in characterisation and in electroanalytical applications, at the same time demonstrating how fuller use can be made of the information obtained from complete modelling and analysis of the data in the spectra, the values of the circuit components and their physical meaning. The future outlook for electrochemical impedance in the sensing field is discussed.

Electrochemical Sensors for Antibiotic Susceptibility Testing: Strategies and Applications

Increasing awareness of the impacts of infectious diseases has driven the development of advanced techniques for detecting pathogens in clinical and environmental settings. However, this process is hindered by the complexity and variability inherent in antibiotic-resistant species. A great deal of effort has been put into the development of antibiotic-resistance/susceptibility testing (AST) sensors and systems to administer proper drugs for patient-tailored therapy. Electrochemical sensors have garnered increasing attention due to their powerful potential to allow rapid, sensitive, and real-time monitoring, alongside the low-cost production, feasibility of minimization, and easy integration with other techniques. This review focuses on the recent advances in electrochemical sensing strategies that have been used to determine the level of antibiotic resistance/susceptibility of pathogenic bacteria. The recent examples of the current electrochemical AST sensors discussed here are classified into four categories according to what is detected and quantitated: the presence of antibiotic-resistant genes, changes in impedance caused by cell lysis, current response caused by changes in cellular membrane properties, and changes in the redox state of redox molecules. It also discusses potential strategies for the development of electrochemical AST sensors, with the goal of broadening their practical applications across various scientific and technological fields.

Electrochemical Detection Platform Based on RGO Functionalized with Diazonium Salt for DNA Hybridization

In this paper, we propose an improved electrochemical platform based on graphene for the detection of DNA hybridization. Commercial screen-printed carbon electrodes (SPCEs) were used for this purpose due to their ease of functionalization and miniaturization opportunities. SPCEs were modified with reduced graphene oxide (RGO), offering a suitable surface for further functionalization. Therefore, aryl-carboxyl groups were integrated onto RGO-modified electrodes by electrochemical reduction of the corresponding diazonium salt to provide enough reaction sites for the covalent immobilization of amino-modified DNA probes. Our final goal was to determine the optimum conditions needed to fabricate a simple, label-free RGO-based electrochemical platform to detect the hybridization between two complementary single-stranded DNA molecules. Each modification step in the fabrication process was monitored by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) using [Fe(CN)6]3-/4- as a redox reporter. Although, the diazonium electrografted layer displayed the expected blocking effect of the charge transfer, the next steps in the modification procedure resulted in enhanced electron transfer properties of the electrode interface. We suggest that the improvement in the charge transfer after the DNA hybridization process could be exploited as a prospective sensing feature. The morphological and structural characterization of the modified electrodes performed by scanning electron microscopy (SEM) and Raman spectroscopy, respectively, were used to validate different modification steps in the platform fabrication process.

Biosensors for the Determination of SARS-CoV-2 Virus and Diagnosis of COVID-19 Infection

Monitoring and tracking infection is required in order to reduce the spread of the coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To achieve this goal, the development and deployment of quick, accurate, and sensitive diagnostic methods are necessary. The determination of the SARS-CoV-2 virus is performed by biosensing devices, which vary according to detection methods and the biomarkers which are inducing/providing an analytical signal. RNA hybridisation, antigen-antibody affinity interaction, and a variety of other biological reactions are commonly used to generate analytical signals that can be precisely detected using electrochemical, electrochemiluminescence, optical, and other methodologies and transducers. Electrochemical biosensors, in particular, correspond to the current trend of bioanalytical process acceleration and simplification. Immunosensors are based on the determination of antigen-antibody interaction, which on some occasions can be determined in a label-free mode with sufficient sensitivity.

Electrochemical Sensing of Interactions between DNA and Charged Macrocycles

In this work, we investigated aggregation of native DNA and thiacalix[4]arene derivative bearing eight terminal amino groups in cone configuration using various redox probes on the glassy carbon electrode. It was shown that sorption transfer of the aggregates on the surface of the electrode covered with carbon black resulted in changes in electrostatic interactions and diffusional permeability of the surface layer. Such changes alter the signals of ferricyanide ion, methylene green and hydroquinone as redox probes to a degree depending on their specific interactions with DNA and own charge. Inclusion of DNA in the surface layer was independently confirmed by scanning electron microscopy, electrochemical impedance spectroscopy and experiments with doxorubicin as a model intercalator. Thermal denaturing of DNA affected the charge separation on the electrode interface and the signals of redox probes. Using hydroquinone, less sensitive to electrostatic interactions, made it possible to determine from 10 pM to 1.0 nM doxorubicin (limit of detection 3 pM) after 10 min incubation. Stabilizers present in the commercial medications did not alter the signal. The DNA sensors developed can find future application in the assessment of the complexes formed by DNA and macrocycles as delivery agents for small chemical species.

A Homogeneous Label-Free Electrochemical microRNA Biosensor Coupling With G-Triplex/Methylene Blue Complex and λ-Exonuclease-Assisted Recycling Amplification

A novel homogeneous label-free electrochemical biosensor using G-triplex/methylene blue (G3/MB) complex as the signal generator together with an amplification assisted by the λ-exonuclease (λ-Exo) has been successfully constructed for ultrasensitive microRNA (miRNA) detection. An integrated microelectrode was designed to realize the miniaturization of the homogeneous electrochemical assay. Taking advantage of G3, that can specifically bind with MB and decrease its diffusion current, a single-stranded functional DNA hairpin structure was designed as the bio-recognition probe. The probe consisted of G3, eight bases to block G3, and the complementary sequences of the target miRNA. Here we chose miRNA141—a potentially diagnostic biomarker of prostate cancer as the model target. The presence of miRNA141 could hybridize with the probe DNA to form a double-stranded structure with a 5′-phosphorylated terminus. Then λ-Exo was adopted to digest mononucleotides from the 5′-end, leading to the release of G3 part and miRNA141. The released miRNA could hybridize with another probe to trigger the cycling process, while the released G3 could therefore interact with MB to cause a detectable decrease of diffusion current. The proposed strategy showed a low detection limit of 16 fM and an excellent specificity to discriminate single-base mismatches. Furthermore, this sensor was applied to detect miRNA141 from diluted human serum samples, indicating that it has great potential in the application of nucleic acid detection in real samples.

Electrochemical DNA Sensor Based on Acridine Yellow Adsorbed on Glassy Carbon Electrode

Electrochemical DNA sensors offer unique opportunities for the sensitive detection of specific DNA interactions. In this work, a voltametric DNA sensor is proposed on the base of glassy carbon electrode modified with carbon black, adsorbed acridine yellow and DNA for highly sensitive determination of doxorubicin antitumor drug. The signal recorded by cyclic voltammetry was attributed to irreversible oxidation of the dye. Its value was altered by aggregation of the hydrophobic dye molecules on the carbon black particles. DNA molecules promote disaggregation of the dye and increased the signal. This effect was partially suppressed by doxorubicin compensate for the charge of DNA in the intercalation. Sensitivity of the signal toward DNA and doxorubicin was additionally increased by treatment of the layer with dimethylformamide. In optimal conditions, the linear range of doxorubicin concentrations determined was 0.1 pM–1.0 nM, and the detection limit was 0.07 pM. No influence of sulfonamide medicines and plasma electrolytes on the doxorubicin determination was shown. The DNA sensor was tested on two medications (doxorubicin-TEVA and doxorubicin-LANS) and showed recoveries of 102–105%. The DNA sensor developed can find applications in the determination of drug residues in blood and for the pharmacokinetics studies.

Highly selective and sensitive detection of glutamate by an electrochemical aptasensor

An electrochemical aptamer-based sensor was developed for glutamate, the major excitatory neurotransmitter in the central nervous system. Determining glutamic acid release and glutamic acid levels is crucial for studying signal transmission and for diagnosing pathological conditions in the brain. Glutamic acid-selective oligonucleotides were isolated from an ssDNA library using the Capture-SELEX protocol in complex medium. The selection permitted the isolation of an aptamer 1d04 with a dissociation constant of 12 µM. The aptamer sequence was further used in the development of an electrochemical aptamer sensor. For this purpose, a truncated aptamer sequence named glu1 was labelled with a ferrocene redox tag at the 3'-end and immobilized on a gold electrode surface via Au-thiol bonds. Using 6-mercapto-1-hexanol as the backfill, the sensor performance was characterized by alternating current voltammetry. The glu1 aptasensor showed a limit of detection of 0.0013 pM, a wide detection range between 0.01 pM and 1 nM, and good selectivity for glutamate in tenfold diluted human serum. With this enzyme-free aptasensor, the highly selective and sensitive detection of glutamate was demonstrated, which possesses great potential for implementation in microelectrodes and for in vitro as well as in vivo monitoring of neurotransmitter release.

Antifouling lipid membrane coupled with silver nanoparticles for electrochemical detection of nucleic acids in biological fluids

Electrochemical method capable of detecting specific nucleic acids in complex fluid will undoubtedly advance the diagnosis of many kinds of diseases. Herein, by coupling lipid membrane with silver nanoparticles (AgNPs), we develop a new electrochemical method for sensitive and reliable detection of nucleic acids in biological fluids. The advantages of lipid membrane especially its excellent antifouling ability is employed to enhance the applicability of the method in complex environment; while the significant solid-state Ag/AgCl response of AgNPs is used to ensure the detection sensitivity of the method. The core of this method's workflow is the target-induced Y-shape structure formation, which results in the recruitment of AgNPs to the electrode surface, producing considerable electrochemical responses used for target nucleic acid detection. Taking highly upregulated in liver cancer (HULC), a liver cancer-related long non-coding RNA as a model target, the method exhibits high sensitivity, specificity, and reproducibility with a detection limit of 0.42 fM. Moreover, the method displays desirable usability in biological fluids such as serum, which will be of great potential in clinical diagnosis.

A profile of the binx health io® molecular point-of-care test for chlamydia and gonorrhea in women and men

Introduction: Point-of-care (POC) tests for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are urgently needed to control the STI epidemic in order to offer patients an immediate diagnoses and accurate treatment before they leave a clinical encounter and thus reduce transmission and sequelae. Nucleic acid amplification tests (NAATs) have increased sensitivity and specificity, but very few POC assays can provide results of such tests within the usual time of the patient visit.Areas covered: This review describes the technology and performance characteristics of the binx health io® [Boston, MA] (binx io) CT/NG assay, a new rapid molecular POC assay. The assay is compared to other available molecular POC tests. We also describe the importance of time to results and assay performance for this POC assay.Expert opinion: The binx io CT/NG assay offers the ability to incorporate the use of POC tests to identify and immediately treat chlamydia and gonococcal infections into the clinical visit, which will provide improved outcomes for patients. Additional implementation studies are needed to optimize the adoption of this new test.

Hybridization Chain Reaction-Amplified Electrochemical DNA-Based Sensors Enable Calibration-Free Measurements of Nucleic Acids Directly in Whole Blood

Hybridization chain reaction (HCR) amplification strategy has been extensively explored for the application of electrochemical DNA-based sensors. Despite the enhancement in its sensitivity using the HCR, such sensor platform exhibited significant sensor-to-sensor variations in current due to variations in probe counts and lengths. To circumvent this, we are developing here a calibration-free "O-N" approach to generate a ratiometric, unitless value that is independent of these variations. Specifically, this approach employs two types of redox reporters, denoted as "One reporter" and "N reporters", with the former attached on the capture DNA and the latter on H1 and H2 strands. By optimizing the attachment sites of these reporters onto DNA strands, we demonstrate a significantly enhanced sensitivity of such sensor platform by four orders of magnitude, achieving accurate, calibration-free measurement of nucleic acids including ctDNA directly in undiluted whole blood without the requirement to calibrate each individual sensor.

One-pot colorimetric detection of molecules based on proximity proteolysis reaction

Various types of molecules serve as biomarkers of diseases, and numerous methods have been reported to detect and quantify them. Recently, research efforts have been made to develop point-of-care (POC) tests, which contribute to early diagnoses of diseases, particularly in resource-limited settings. An assay performed in a homogeneous phase is an obvious route to develop these methods. Here, simple homogeneous methods based on proximity proteolysis reactions (PPR) are reported to detect biological molecules. A typical PPR system has been designed such that the proteolysis reaction between protease and zymogen is enhanced in the presence of a target analyte. The activated zymogen generates a color signal by hydrolyzing a chromophore. A protease and zymogen are linked to target binders using specific hybridization between complementary single-stranded DNAs, and several molecules, including proteins, antibodies, aptamers, and small molecules, are used as target binders. The developed assay methods successfully detected several kinds of analytes at subnanomolar concentrations with the one-step procedure and color signal. The modular design of the PPR-based assay will enable the development of simple POC diagnostics for various biomarkers.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

CRISPR-Cas12a System for Biosensing and Gene Regulation

Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising technology in the biological world. As one of the CRISPR-associated (Cas) proteins, Cas12a is an RNA-guided nuclease in the type V CRISPR-Cas system, which has been a robust tool for gene editing. In addition, due to the discovery of target-binding-induced indiscriminate single-stranded DNase activity of Cas12a, CRISPR-Cas12a also exhibits great promise in biosensing. This minireview not only gives a brief introduction to the mechanism of CRISPR-Cas12a but also highlights the recent developments and applications in biosensing and gene regulation. Finally, future prospects of the CRISPR-Cas12a system are also discussed. We expect this minireview will inspire innovative work on the CRISPR-Cas12a system by making full use of its features and advantages.

A Label-Free DNA-Immunosensor Based on Aminated rGO Electrode for the Quantification of DNA Methylation

In this work, we developed a sandwich DNA-immunosensor for quantification of the methylated tumour suppressor gene O-6-methylguanine-DNA methyltransferase (MGMT), which is a potential biomarker for brain tumours and breast cancer. The biosensor is based on aminated reduced graphene oxide electrode, which is achieved by ammonium hydroxide chemisorption and anti-5-methylcytosine (anti-5mC) as a methylation bioreceptor. The target single-strand (ss) MGMT oligonucleotide is first recognised by its hybridisation with complementary DNA to form double-stranded (ds) MGMT, which is then captured by anti-5mC on the electrode surface due to the presence of methylation. Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Scanning electron microscopy (SEM) techniques were used to characterise the electrode surface. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used for electrochemical measurements. Under optimised conditions, the proposed biosensor is able to quantify a linear range of concentrations of the MGMT gene from 50 fM to 100 pM with a limit of detection (LOD) of 12 fM. The sandwich design facilitates the simultaneous recognition and quantification of DNA methylation, and the amination significantly improves the sensitivity of the biosensor. This biosensor is label-, bisulfite- and PCR-free and has a simple design for cost-efficient production. It can also be tailor-made to detect other methylated genes, which makes it a promising detection platform for DNA methylation-related disease diagnosis and prognosis.

Electroanalysis of Biomolecules: Rational Selection of Sensor Construction

Methods of electrochemical analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules are presented. Polymer nanocomposite materials that modify electrodes to increase sensitivity of electrochemical events on the surface of electrodes are described. Examples of applications electrochemical biosensors constructed with nanocomposite material for detection of biological molecules are presented, advantages and drawbacks of different applications are discussed.