Chip-Based and Wearable Tools for Isothermal Amplification and Electrochemical Analysis of Nucleic Acids

The determination of nucleic acids has become an analytical diagnostic method with many applications in fields such as biomedical sciences, environmental monitoring, forensic identification, and food safety. Among the different methods for nucleic acid analysis, those based on the polymerase chain reaction (PCR) are nowadays considered the gold standards. Isothermal amplification methods are an interesting alternative, especially in the design of chip-based architectures. Biosensing platforms hold great promise for the simple and rapid detection of nucleic acids since they can be embedded in lab-on-a-chip tools to perform nucleic acid extraction, amplification, and detection steps. Electrochemical transduction schemes are particularly interesting in the design of small and portable devices due to miniaturization, low-energy consumption, and multianalyte detection capability. The aim of this review is to summarize the different applications of isothermal amplification methods combined with electrochemical biosensing techniques in the development of lab-on-a-chip tools and wearable sensors. Different isothermal amplification methods are revised, and examples of different applications are discussed. Finally, a discussion on patented devices is also included.

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.

Electrochemical Beacon Method to Quantify 10 Attomolar Nucleic Acids with a Semilog Dynamic Range of 7 Orders of Magnitude

Change in the dynamics of single-stranded DNA or RNA probes tethered to an Au electrode on immunospecific binding to the analyte is a versatile approach to quantify a variety of molecules, such as heavy metal ions, pesticides, proteins, and nucleic acids (NAs). A widely studied approach is the electrochemical beacon method where the redox of a dye attached to the probe decreases as its proximity to the underlying electrode changes on binding. The limit of quantification (LOQ) defined by the semilog dependence of the signal on target concentration is in the picomolar range. Here, a method was studied where, by differential reflectivity, multiple reactions were measured on a monolith electrode. An alternative contrast mechanism was discovered, which led to an approach to enhance the LOQ to 10 aM and increase the dynamic range to 7 orders of magnitude using similar probes and binding conditions. Quantitative analysis on sequences with the G-C fraction ranging from 37 to 72% was performed. The approach will allow for the development of a label-free, enzyme-free microarray to detect biomolecules including NAs and proteins on a single electrode at quantification from 10 aM to 0.1 nM with high specificity.

Improved Thermal Stability and Homogeneity of Low Probe Density DNA SAMs Using Potential-Assisted Thiol-Exchange Assembly Methods

Methods for producing DNA SAM-based sensors with improved thermal stability and control over the homogeneity of low DNA probe density will enable advanced sensor development. The thermal stability of low-coverage DNA SAMs was studied for surfaces prepared using potential-assisted thiol exchange (E_dep) and compared to DNA SAMs prepared without control over the substrate potential (OCP_dep). Both surface preparation methods were studied using in situ fluorescence microscopy and electrochemistry with fluorophore or redox-modified DNA SAMs on a single-crystal gold bead electrode. Fluorescence microscopy showed that the influence of the underlying surface crystallography was important in both cases. The highest thermal stability was realized for square or rectangular surface atomic structure (e.g., surfaces from 110 to 100). The 111 and related surfaces were the least thermally stable. The low DNA coverage surfaces prepared by E_dep had better thermal stability and higher DNA probe mobility as compared to OCP_dep-prepared surfaces with the similar coverage. These results were correlated with methylene blue redox-tagged DNA probes, which directly measured the average DNA coverage. Both methods indicated that E_dep DNA SAMs were more uniformly distributed across the electrode surface, while the surfaces prepared via OCP_dep assembled into clusters with reduced mobility. The potential-assisted thiol-exchange approach to preparing low-coverage DNA SAMs was shown to quickly create modified surfaces that were consistent, had mobility characteristics which should yield superior DNA hybridization efficiencies, and having greater thermal stability which will translate into a longer shelf-life.

The Role of Aryldiazonium Chemistry in Designing Electrochemical Aptasensors for the Detection of Food Contaminants

Food safety monitoring assays based on synthetic recognition structures such as aptamers are receiving considerable attention due to their remarkable advantages in terms of their ability to bind to a wide range of target analytes, strong binding affinity, facile manufacturing, and cost-effectiveness. Although aptasensors for food monitoring are still in the development stage, the use of an electrochemical detection route, combined with the wide range of materials available as transducers and the proper immobilization strategy of the aptamer at the transducer surface, can lead to powerful analytical tools. In such a context, employing aryldiazonium salts for the surface derivatization of transducer electrodes serves as a simple, versatile and robust strategy to fine-tune the interface properties and to facilitate the convenient anchoring and stability of the aptamer. By summarizing the most important results disclosed in the last years, this article provides a comprehensive review that emphasizes the contribution of aryldiazonium chemistry in developing electrochemical aptasensors for food safety monitoring.

PNA-functionalized magnetic microbeads as substrates for enzyme-labelled voltammetric genoassay for DNA sensing applied to identification of GMO in food

A novel enzyme-labelled voltammetric magnetogenoassay for DNA sensing based on the use of carboxyl-surface coated magnetic microbeads functionalized with PNA probes and subsequent read-out on screen-printed electrode (SPE) substrates was developed. The assay was validated for determination of non-amplified genomic DNA from genetically modified Roundup Ready soy. Outstanding performance with respect to other genoassays requiring preliminary amplification of target DNA via PCR was demonstrated. The analytical performance was also improved compared to previous methods based on the immobilization of the same PNA probes on SPE substrates, since the method was found capable of achieving LOD and LOQ of 415 fM and 995 fM, respectively. The ability of the magnetogenoassay to detect the presence of Roundup Ready soy DNA sequence was tested on genomic DNA extract from European Reference Material soy flours, demonstrating the capability of the method to match the European Union regulation for labelling of food containing a percentage of GM products greater than 0,9%.

Tailoring the performance of electrochemical biosensors based on carbon nanomaterials via aryldiazonium electrografting

Carbon nanomaterials (CNs) offer some of the most valuable properties for electrochemical biosensing applications, such as good electrical conductivity, wide electrochemical stability, high specific surface area, and biocompatibility. Regardless the envisioned sensing application, endowing CNs with specific functions through controlled chemical functionalization is fundamental for promoting the specific binding of the analyte. As a versatile and straightforward method of surface functionalization, aryldiazonium chemistry have been successfully used to accommodate in a stable and reproducible way different functionalities, while the electrochemical route has become the favourite choice since the deposition conditions can be readily controlled and adapted to the substrate. In particular, the modification of CNs by electrochemical reduction of aryl diazonium salts is established as a powerful tool which allows tailoring the chemical and electronic properties of the sensing platform. By outlining the stimulating results disclosed in the last years, this article provides not only a comprehensively review, but also a rational assessment on contribution of aryldiazonium electrografting in developing CNs-based electrochemical biosensors. Furthermore, some of the emerging challenges to be surpassed to effectively implement this methodology for in vivo and point of care analysis are also highlighted.

Interplay of Effective Surface Area, Mass Transport, and Electrochemical Features in Nanoporous Nucleic Acid Sensors

Electrochemical biosensors transduce biochemical events (e.g., DNA hybridization) to electrical signals and can be readily interfaced with electronic instrumentation for portability. Nanostructuring the working electrode enhances sensor performance via augmented effective surface area that increases the capture probability of an analyte. However, increasing the effective surface area via thicker nanostructured electrodes hinders the analyte's permeation into the nanostructured volume and limits its access to deeper electrode surfaces. Here, we use nanoporous gold (np-Au) with various thicknesses and pore morphologies coupled with a methylene blue (MB) reporter-tagged DNA probe for DNA target detection as a model system to study the influence of electrode features on electrochemical sensing performance. Independent of the DNA target concentration, the hybridization current (surrogate for detection sensitivity) increases with the surface enhancement factor (EF), until an EF of ∼5, after which the sensor performance deteriorates. Electrochemical and fluorometric quantification of a desorbed DNA probe suggest that DNA permeation is severely limited for higher EFs. In addition, undesirable capacitive currents disguise the faradaic currents from the MB reporter at larger EFs that require higher square wave voltammetry (SWV) frequencies. Finally, a real-time hybridization study reveals that expanding the effective surface area beyond EFs of ∼5 decreases sensor performance.

Enlightening the advancements in electrochemical bioanalysis for the diagnosis of Alzheimer's disease and other neurodegenerative disorders

Neurodegenerative disorders (NDD), and particularly Alzheimer's disease (AD), are one of the greatest challenges facing our current medicine and society because of its increasing incidence and the high burden imposed both on patients' families and health systems. Despite this, their accurate diagnosis, mostly conducted by cerebrospinal fluid (CSF) analysis or neuroimaging techniques, costly, time-consuming, and unaffordable for most of the population, remains a complex task. In this situation, electrochemical biosensors are flourishing as promising alternative tools for the simple, fast, and low-cost diagnosis of NDD/AD. This review article provides the relevant clinical details of NDD/AD along with the closely related genetic (genetic mutations, polymorphisms of ApoE and specific miRNAs) and proteomic (amyloid-β peptides, total and phosphorylated tau protein) biomarkers circulating mostly in CSF. In addition, the article systematically enlightens a general view of the electrochemical affinity biosensors (mostly aptasensors and immunosensors) reported in the past two years for the determination of such biomarkers. The different developed strategies, analytical performances and applications are comprehensively discussed. Recent advancements in signal amplification methodologies involving smart designs and the use of nanomaterials and rational surface chemistries, as well as the challenges that must be struggled and the prospects in electrochemical affinity biosensing to bring more accessibility to NDD/AD diagnosis, prognosis, and follow-up, are also pointed out.

Laser-induced graphene interdigitated electrodes for label-free or nanolabel-enhanced highly sensitive capacitive aptamer-based biosensors

Highly porous laser-induced graphene (LIG) is easily generated in complex electrode configurations such as interdigitated electrodes (IDEs). Here, we demonstrate that their superior capacitive response at low frequencies can be exploited in affinity biosensors using thrombin aptamers as model biorecognition elements. Of specific interest was the effect of electrode surface area on capacitance detection, and the comparison between a label-free format and enhancement strategies afforded by carboxy group bearing polymeric nanoparticles or liposomes. Electrochemical impedance spectroscopy (EIS) was used to investigate the LIG performance and optimize the biosensor design. Interestingly, the label-free strategy performed extremely well and additional labels decreased the limit of detection or increased the sensitivity only minimally. It is assumed that the highly porous nature of the LIG structures dominates the capacitive response so that labels removed from the surface have only limited influence Also, while slight performance changes can be observed for smaller vs. larger electrode structures, the performance of a LIG IDE is reasonably independent of its size. In the end, a dynamic range of 5 orders of magnitude was obtained (0.01 nM-1000 nM) with a limit of detection as low as 0.12 pM. When measured in serum, this increased to 1.3 pM. The good reproducibility (relative standard deviation (RSD), 4.90%) and repeatability (RSD, 2.59%) and good long-term stability (>7 weeks at 4 °C) prove that a LIG-based capacitance sensor is an excellent choice for affinity-based biosensor. The ease-of-production, the simplicity of modification and the superior performance even in a label-free format indicate that LIG-based biosensors should be considered in point-of-care diagnostics in the future.

DNA framework-engineered electrochemical biosensors

Self-assembled DNA nanostructures have shown remarkable potential in the engineering of biosensing interfaces, which can improve the performance of various biosensors. In particular, by exploiting the structural rigidity and programmability of the framework nucleic acids with high precision, molecular recognition on the electrochemical biosensing interface has been significantly enhanced, leading to the development of highly sensitive and specific biosensors for nucleic acids, small molecules, proteins, and cells. In this review, we summarize recent advances in DNA framework-engineered biosensing interfaces and the application of corresponding electrochemical biosensors.

Cutting-Edge Advances in Electrochemical Affinity Biosensing at Different Molecular Level of Emerging Food Allergens and Adulterants

The presence of allergens and adulterants in food, which represents a real threat to sensitized people and a loss of consumer confidence, is one of the main current problems facing society. The detection of allergens and adulterants in food, mainly at the genetic level (characteristic fragments of genes that encode their expression) or at functional level (protein biomarkers) is a complex task due to the natural interference of the matrix and the low concentration at which they are present. Methods for the analysis of allergens are mainly divided into immunological and deoxyribonucleic acid (DNA)-based assays. In recent years, electrochemical affinity biosensors, including immunosensors and biosensors based on synthetic sequences of DNA or ribonucleic acid (RNA), linear, aptameric, peptide or switch-based probes, are gaining special importance in this field because they have proved to be competitive with the methods commonly used in terms of simplicity, test time and applicability in different environments. These unique features make them highly promising analytical tools for routine determination of allergens and food adulterations at the point of care. This review article discusses the most significant trends and developments in electrochemical affinity biosensing in this field over the past two years as well as the challenges and future prospects for this technology.

Electrochemical biosensing to move forward in cancer epigenetics and metastasis: A review

Early detection and effective treatment are crucial to reduce the physical, emotional, and financial pressure exerted by growing cancer burden on individuals, families, communities, and health systems. Currently, it is clear that the accurate analysis of emerging cancer epigenetic and metastatic-related biomarkers at different molecular levels is envisaged as an exceptional solution for early and reliable diagnosis and the improvement of therapy efficiency through personalized treatments. Within this field, electrochemical biosensing has demonstrated to be competitive over other emerging and currently used methodologies for the determination of these biomarkers accomplishing the premises of user-friendly, multiplexing ability, simplicity, reduced costs and decentralized analysis, demanded by clinical oncology, thus priming electrochemical biosensors to spark a diagnostic revolution for cancer prediction and eradication. This review article critically discusses the main characteristics, opportunities and versatility exhibited by electrochemical biosensing, through highlighting representative examples published during the last two years, for the reliable determination of these emerging biomarkers, with great diagnostic, predictive and prognostic potential. Special attention is paid on electrochemical affinity biosensors developed for the single or multiplexed determination of methylation events, non-coding RNAs, ctDNA features and metastasis-related protein biomarkers both in liquid and solid biopsies of cancer patients. The main challenges to which further work must be addressed and the impact of these advances should have in the clinical acceptance of these emerging biomarkers are also discussed which decisively will contribute to understand the molecular basis involved in the epigenetics and metastasis of cancer and to apply more efficient personalized therapies.

Imbibition of Femtoliter-Scale DNA-Rich Aqueous Droplets into Porous Nylon Substrates by Molecular Printing

This work presents the first reported imbibition mechanism of femtoliter (fL)-scale droplets produced by microchannel cantilever spotting (μCS) of DNA molecular inks into porous substrates (hydrophilic nylon). Differently from macroscopic or picoliter droplets, the downscaling to the fL-size leads to an imbibition process controlled by the subtle interplay of evaporation, spreading, viscosity, and capillarity, with gravitational forces being quasi-negligible. In particular, the minimization of droplet evaporation, surface tension, and viscosity allows for a reproducible droplet imbibition process. The dwell time on the nylon surface permits further tuning of the droplet lateral size, in accord with liquid ink diffusion mechanisms. The functionality of the printed DNA molecules is demonstrated at different imbibed oligonucleotide concentrations by hybridization with a fluorolabeled complementary sequence, resulting in a homogeneous coverage of DNA within the imbibed droplet. This study represents a first step toward the μCS-enabled fabrication of DNA-based biosensors and microarrays into porous substrates.

Pushing the limits of electrochemistry toward challenging applications in clinical diagnosis, prognosis, and therapeutic action

Constant progress in the identification of biomarkers at different molecular levels in samples of different natures, and the need to conduct routine analyses, even in limited-resource settings involving simple and short protocols, are examples of the growing current clinical demands not satisfied by conventional available techniques. In this context, the unique features offered by electrochemical biosensors, including affordability, real-time and reagentless monitoring, simple handling and portability, and versatility, make them especially interesting for adaptation to the increasingly challenging requirements of current clinical and point-of-care (POC) diagnostics. This has allowed the continuous development of strategies with improved performance in the clinical field that were unthinkable just a few years ago. After a brief introduction to the types and characteristics of clinically relevant biomarkers/samples, requirements for their analysis, and currently available methodologies, this review article provides a critical discussion of the most important developments and relevant applications involving electrochemical biosensors reported in the last five years in response to the demands of current diagnostic, prognostic, and therapeutic actions related to high prevalence and high mortality diseases and disorders. Special attention is paid to the rational design of surface chemistry and the use/modification of state-of-the-art nanomaterials to construct electrochemical bioscaffolds with antifouling properties that can be applied to the single or multiplex determination of biomarkers of accepted or emerging clinical relevance in particularly complex clinical samples, such as undiluted liquid biopsies, whole cells, and paraffin-embedded tissues, which have scarcely been explored using conventional techniques or electrochemical biosensing. Key points guiding future development, challenges to be addressed to further push the limits of electrochemical biosensors towards new challenging applications, and their introduction to the market are also discussed.

Antifouling (Bio)materials for Electrochemical (Bio)sensing

(Bio)fouling processes arising from nonspecific adsorption of biological materials (mainly proteins but also cells and oligonucleotides), reaction products of neurotransmitters oxidation, and precipitation/polymerization of phenolic compounds, have detrimental effects on reliable electrochemical (bio)sensing of relevant analytes and markers either directly or after prolonged incubation in rich-proteins samples or at extreme pH values. Therefore, the design of antifouling (bio)sensing interfaces capable to minimize these undesired processes is a substantial outstanding challenge in electrochemical biosensing. For this purpose, efficient antifouling strategies involving the use of carbon materials, metallic nanoparticles, catalytic redox couples, nanoporous electrodes, electrochemical activation, and (bio)materials have been proposed so far. In this article, biomaterial-based strategies involving polymers, hydrogels, peptides, and thiolated self-assembled monolayers are reviewed and critically discussed. The reported strategies have been shown to be successful to overcome (bio)fouling in a diverse range of relevant practical applications. We highlight recent examples for the reliable sensing of particularly fouling analytes and direct/continuous operation in complex biofluids or harsh environments. Opportunities, unmet challenges, and future prospects in this field are also pointed out.