Single-Step Incubation Determination of miRNAs in Cancer Cells Using an Amperometric Biosensor Based on Competitive Hybridization onto Magnetic Beads

Smartphone-based device for rapid and single-step detection of piRNA-651 using anti-DNA:RNA hybrid antibody and enzymatic signal amplification

P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs/piRs) are a class of small noncoding RNAs that play a crucial role in regulating various biological processes, including carcinogenesis. One specific piRNA, piR-651, has been reported to be overexpressed in both human blood serum and solid cancer tissues, that can be used a viable biomarker in cancer diagnosis. Early diagnosis of cancer can help reduce the burden of the disease and improve survival rates. In the present work, we report for the first time a smartphone-based colorimetric biosensor for highly sensitive and specific detection of piR-651 thanks to an enzymatic signal amplification, which yielded high colorimetric intensities. Indeed, a heteroduplex DNA:RNA was formed in the presence of piR-651 with the capture DNA probe immobilized on the magnetic beads for easy magnetic separation. Then, a HRP tethered to anti-DNA:RNA (S9.6) was used to reveal the DNA-RNA heteroduplex formed by catalyzing the oxidation of TMB substrate into colorimetric TMBox, which absorbs at 630 nm. The absorbance is positively proportional to the piR-651 concentrations. On the other hand, the colorimetric product of the assay can be photographed with a smartphone camera and analyzed using ImageJ software. Using a smartphone and under optimal conditions, the biosensor responded linearly to the logarithm of piRNA-651 from 8 fM to 100 pM with a detection limit of 2.3 fM and discriminates against other piRNAs. It was also successfully applied to the determination of piRNA-651 levels in spiked human serum.

Enhanced sensitivity in electrochemical detection of ochratoxin A within food samples using ferrocene- and aptamer-tethered gold nanoparticles on disposable electrodes

Ensuring food security is crucial for public health, and the presence of mycotoxins, produced by fungi in improperly stored processed or unprocessed food, poses a significant threat. This research introduces a novel approach - a disposable aptasensing platform designed for the detection of ochratoxin A (OTA). The platform employs gold-nanostructured screen-printed carbon electrodes functionalized with a ferrocene derivative, serving as an integrated faradaic transducing system, and an anti-OTA aptamer as a bioreceptor site. Detection relies on the ferrocene electrochemical signal changes induced by the aptamer folding in the presence of the target molecule. Remarkably sensitive, the platform detects OTA within the range of 0.5 to 70 ng mL-1 and a detection limit of 11 pg mL-1. This limit is approximately 200 times below the levels stipulated by the European Commission for agricultural commodities. Notably, the sensing device exhibits efficacy in detecting OTA in complex media, such as roasted coffee beans and wine, without the need for sample pretreatment, yielding accurate recoveries. Furthermore, while label-free electrochemical aptasensors have proliferated, this study addresses a gap in understanding the binding mechanisms of some aptasensors. To enhance the experimental findings, a theoretical study was conducted to underscore the specificity of the anti-OTA aptamer as a donor for OTA detection. The molecular docking technique was employed to unveil the key binding region of the aptamer, providing valuable insights into the aptasensor specificity.

A highly sensitive colorimetric DNA sensor for MicroRNA-155 detection: leveraging the peroxidase-like activity of copper nanoparticles in a double amplification strategy

A novel and highly sensitive colorimetric DNA sensor for determination of miRNA-155 at attomolar levelsis presented that combines the peroxidase-like activity of copper nanoparticles (CuNPs) with the hybridization chain reaction (HCR) . The utilization of CuNPs offers advantages such as strong interaction with double-stranded DNA, excellent molecular recognition, and mimic catalytic activity. Herein, a capture probe DNA (P1) was immobilized on carboxylated magnetic beads (MBs), allowing for amplified immobilization due to the 3D surface. Subsequently, the presence of the target microRNA-155 led to the formation of a sandwich structure (P2/microRNA-155/P1/MBs) when P2 was introduced to the modified P1/MBs. The HCR reaction was then triggered by adding H1 and H2 to create a super sandwich (H1/H2)n. Following this, Cu2+ ions were attracted to the negatively charged phosphate groups of the (H1/H2)n and reduced by ascorbic acid, resulting in the formation of CuNPs, which were embedded into the grooves of the (H1/H2)n. The peroxidase-like activity of CuNPs catalyzed the oxidation reaction of 3,3',5,5'-Tetramethylbenzidine (TMB), resulting in a distinct blue color measured at 630 nm. Under optimal conditions, the colorimetric biosensor exhibited a linear response to microRNA-155 concentrations ranging from 80 to 500 aM, with a detection limit of 22 aM, and discriminate against other microRNAs. It was also successfully applied to the determination of microRNA-155 levels in spiked human serum.

A Magnetoelectrochemical Bioassay for Highly Sensitive Sensing of Point Mutations in Interleukin-6 Gene Using TMB as a Hybridization Intercalation Indicator

Point mutations are common in the human DNA genome and are closely related to higher susceptibility to cancer diseases. Therefore, suitable methods for their sensing are of general interest. In this work, we report on a magnetic electrochemical bioassay using DNA probes tethered to streptavidin magnetic beads (strep-MBs) to detect T > G single nucleotide polymorphism (SNP) within the inteleukin-6 (IL6) gene in human genomic DNA. In the presence of the target DNA fragment and tetramethylbenzidine (TMB), the electrochemical signal related to the oxidation of TMB is observed, which is much higher than the one obtained in the absence of the target. The key parameters affecting the analytical signal, such as the concentration of the biotinylated probe, its incubation time with strep-MBs, DNA hybridization time, and TMB loading, were optimized using the electrochemical signal intensity and signal-to-blank (S/B) ratio as selection criteria. Using spiked buffer solutions, the bioassay can detect the mutated allele in a wide range of concentrations (over six decades) with a low detection limit (7.3 fM). Furthermore, the bioassay displays a high specificity with high concentrations of the major allele (one mismatched), and two mismatched and non-complementary DNA. More importantly, the bioassay can detect the variation in scarcely diluted human DNA, collected from 23 donors, and can reliably distinguish between heterozygous (TG genotype) and homozygous (GG genotype) in respect to the control subjects (TT genotype), where the differences are statistically highly significant (p-value < 0.001). Thus, the bioassay is useful for cohort studies targeting one or more mutations in human DNA.

Sensitive electrochemical detection of polymorphisms in IL6 and TGFβ1 genes from ovarian cancer DNA patients using EcoRI and DNA hairpin-modified gold electrodes

Two electrochemical bioplatforms were prepared based on thiolated hairpin DNA probes tethered to AuNP-modified screen-printed electrodes to detect T > G and T > C polymorphisms, namely rs1880269 and rs1800469, present the interleukin-6 (IL6) and transforming growth factor β1 (TGFβ1) genes. The electrochemical readout was ensured by the detection of the double-stranded DNA using methylene blue as a redox probe after treatment by EcoRI restrictase. The main parameters influencing the analytical response such as the thiolated DNA probe concentration, incubation time with electrode, DNA hybridization time, EcoRI enzyme load, and its cleavage time were optimized based on the current intensity and signal-to-blank (S/B) ratio as selection criteria. Using spiked buffer solutions, the IL6 and TGFβ1 E-bioplatforms display wide ranges of linearity (1 × 10²-1 × 10⁸ fM and 5 × 10¹-1 × 10⁵ fM, respectively) and limits of detection (47.9 fM and 16.6 fM, respectively). The two bioelectrodes have also good discrimination toward 1-mismatched, two mismatched, and non-complementary sequences, when they were used 30-fold higher than the target sequences. More importantly, the two bioplatforms successfully detected the single nucleotide polymorphisms (SNPs) in scarcely diluted genomic DNA, collected from 52 donors, and showed they can reliably distinguish between heterozygous (TG and TC genotypes) and homozygous (GG and CC genotypes) patients with  respect to the control subjects (TT genotype), where the differences are statistically highly significant (p-value < 0.0001). Thus, the designed devices could be used to conduct large cohort studies targeting these mutations or extended to other SNPs.

Genosensing Applications of Glassy Carbon Electrodes Modified with Multi-Walled Carbon Nanotubes Non-Covalently Functionalized with Polyarginine

We report the advantages of glassy carbon electrodes (GCE) modified with multi-walled carbon nanotubes (MWCNTs) non-covalently functionalized with polyarginine (PolyArg) for the adsorption and electrooxidation of different DNAs and the analytical applications of the resulting platform. The presence of the carbon nanostructures, and mainly the charge of the PolyArg that supports them, facilitates the adsorption of calf-thymus and salmon sperm double-stranded DNAs and produces an important decrease in the overvoltages for the oxidation of guanine and adenine residues and a significant enhancement in the associated currents. As a proof-of-concept of possible GCE/MWCNTs-PolyArg biosensing applications, we develop an impedimetric genosensor for the quantification of microRNA-21 at femtomolar levels, using GCE/MWCNTs-PolyArg as a platform for immobilizing the DNA probe, with a detection limit of 3fM, a sensitivity of 1.544 × 10³ Ω M^-1, and a successful application in enriched biological fluids.

Screen-printed electrode-based biosensors modified with functional nucleic acid probes and their applications in this pandemic age: a review

Electrochemical methodology has probably been the most used sensing platform in the past few years as they provide superior advantages. In particular, screen-printed electrode (SPE)-based sensing applications stand out as they provide extraordinary miniaturized but robust and user-friendly detection system. In this context, we are focusing on the modification of SPE with functional nucleic acid probes and nanostructures to improve the electrochemical detection performance in versatile sensing applications, particularly in the fight against the COVID-19 pandemic. Aptamers are immobilized on the electrode surface to detect non-nucleic acid targets and complementary probes to recognize and capture nucleic acid targets. In a step further, SPE-based biosensors with the modification of self-assembled DNA nanostructures are emphasized as they offer great potential for the interface engineering of the electrode surface and promote the excellent performance of various interface reactions. By equipping with a portable potentiostat and a smartphone monitoring device, the realization of this SPE-based miniaturized diagnostic system for the further requirement of fast and POC detection is revealed. Finally, more novel and excellent works are previewed and future perspectives in this field are mentioned.

Sandwich-Based Immunosensor for Dual-Mode Detection of Pathogenic F17-Positive Escherichia coli Strains

Bacterial diseases cause tremendous economic losses due to high morbidity and mortality in livestock animals. F17A protein, the major subunit of F17 fimbriae, is one of the most prevalent and crucial virulence factors among the pathogenic Escherichia coli (E. coli) isolated from diarrheic and septicemic animals of various species. Purification and detection of this protein is regarded as an interesting field of investigation due to its important role as a therapeutic target, such as vaccines, and as a diagnostic tool. In this context, polyclonal rabbit antibodies recognizing F17A protein (anti−F17A antibody) were developed and used for its detection. In fact, sandwich biosensor using anti−F17A/gold nanoparticles conjugates as capture probe and anti−F17A antibody labelled with horseradish peroxidase as signal amplification probe was developed for electrochemical and fluorescent detection of purified F17A protein and live F17–positive E. coli bacteria. Good specificity and sensitivity for detection of F17–positive E. coli strains were obtained. The dynamic range for the biosensor varies from 1 × 10² to 1 × 10⁹ CFU·mL⁻¹ (R² = 0.998) and the detection limit (LOD) and the IC₅₀ value were estimated to be 37 CFU·mL⁻¹ and 75 CFU·mL⁻¹, respectively.

Two-Step Competitive Hybridization Assay: A Method for Analyzing Cancer-Related microRNA Embedded in Extracellular Vesicles

With an increased understanding of the role of microRNAs (miRNAs) in cancer evolution, there is a growing interest in the use of these non-coding nucleic acids in cancer diagnosis, prognosis, and treatment monitoring. miRNAs embedded in extracellular vesicles (EVs) are of particular interest given that circulating EVs carry cargo that are strongly correlated to their cells of origin such as tumor cells while protecting them from degradation. As such, there is a tremendous interest in new simple-to-operate vesicular microRNA analysis tools for widespread use in performing liquid biopsies. Herein, we present a two-step competitive hybridization assay that is rationally designed to translate low microRNA concentrations to large electrochemical signals as the measured signal is inversely proportional to the microRNA concentration. Using this assay, with a limit-of-detection of 122 aM, we successfully analyzed vesicular miRNA 200b from prostate cancer cell lines and human urine samples, demonstrating the expected lower expression levels of miRNA 200b in the EVs from prostate cancer cells and in the prostate cancer patient's urine samples compared to healthy patients and non-tumorigenic cell lines, validating the suitability of our approach for clinical analysis.

A gold nanoparticle-dye/poly(3-aminobenzylamine)/two dimensional MoSe2/graphene oxide electrode towards label-free electrochemical biosensor for simultaneous dual-mode detection of cancer antigen 15-3 and microRNA-21

A dual-mode electrochemical biosensor is successfully developed for simultaneous detection of two different kinds of breast cancer biomarkers, namely cancer antigen 15-3 (CA 15-3) and microRNA-21 (miRNA-21), for the first time. The sensor composes of a poly(3-aminobenzylamine)/two-dimensional (2D) molybdenum selenide/graphene oxide nanocomposite modified two-screen-printed carbon electrode array (dual electrode), functionalized individually with 2,3-diaminophenazine-gold nanoparticles and toluidine blue-gold nanoparticles. Both kinds of the redox probe-gold nanoparticles are employed as signaling molecules and supports for immobilization of anti-CA 15-3 antibodies and capture DNA-21 probes, respectively. Due to the good conductivity and high surface-to-volume ratio of the nanocomposite, high amount of the antibodies and capture probes can be immobilized on the modified dual-electrode, giving the efficient duplex detection. Consequently, the biosensor provides good selectivity, and high sensitivity for the dual target analyte detection. The experimental results show that this label-free biosensor exhibits good linear responses to the concentrations of both target analytes with the limits of detection (LODs) of 0.14 U mL^-1 and 1.2 fM for CA 15-3 and miRNA-21, respectively. This assay strategy has a great potential to be further developed for the simultaneous detection of a variety of miRNAs and protein biomarkers for point-of-care (POC) diagnostic applications.

Magnetic nanoparticles in developing electrochemical sensors for pharmaceutical and biomedical applications

A revolutionary impact on the pharmaceutical and biomedical applications has been arisen in the few years to come as a result of the advances made in magnetic nanoparticles (MNPs) research. The use of MNPs opens wide opportunities in diagnostics, drug and gene delivery, in vivo imaging, magnetic separation, and hyperthermia therapy, etc. Besides, their possible integration in sensors makes them an ideal essential element of innovative pharmaceutical and biomedical applications. Nowadays, MNPs-based electrochemical sensors have attracted great attention to pharmaceutical and biomedical applications owing to their high sensitivity, stability. Selectivity towards the target as well as their simplicity of manufacture. Therefore, this review focus on recent advances with cutting-edge approaches dealing with the synthesis, design, and advantageous analytical performance of MNPs in the electrochemical sensors utilized for pharmaceutical and biomedical applications between 2015 and 2020. The challenges existing in this research area and some potential strategies/future perspectives for the rational design of electrochemical sensors are also outlined.

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.

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures

One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologues (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under polymerase chain reaction (PCR) conditions. There are a number of SAHs available, and for assay design, it is of great interest to determine as to which SAH will perform the best under assay conditions. Although there are numerous single studies on the characterization of SAHs in solution or selected solid phases, there is no systematic study comparing different SAHs for biomolecule-binding, hybridization, and PCR assays on solid phases. We compared streptavidin, core streptavidin, traptavidin, core traptavidin, neutravidin, and monomeric streptavidin on the surface of microbeads (10-15 μm in diameter) and designed multiplex microbead-based experiments and analyzed simultaneously the binding of biotinylated oligonucleotides and the hybridization of oligonucleotides to complementary capture probes. We also bound comparably large DNA origamis to capture probes on the microbead surface. We used a real-time fluorescence microscopy imaging platform, with which it is possible to subject samples to a programmable time and temperature profile and to record binding processes on the microbead surface depending on the time and temperature. With the exception of core traptavidin and monomeric streptavidin, all other SA/SAHs were suitable for our investigations. We found hybridization efficiencies close to 100% for streptavidin, core streptavidin, traptavidin, and neutravidin. These could all be considered equally suitable for hybridization, PCR applications, and melting point analysis. The SA/SAH-biotin bond was temperature-sensitive when the oligonucleotide was mono-biotinylated, with traptavidin being the most stable followed by streptavidin and neutravidin. Mono-biotinylated oligonucleotides can be used in experiments with temperatures up to 70 °C. When oligonucleotides were bis-biotinylated, all SA/SAH-biotin bonds had similar temperature stability under PCR conditions, even if they comprised a streptavidin variant with slower biotin dissociation and increased mechanostability.

Sensitive and enzyme-free fluorescence polarization detection for miRNA-21 based on decahedral sliver nanoparticles and strand displacement reaction

A highly sensitive method for miRNA-21 detection has been developed, which relied on the principle of strand displacement reaction to achieve asymmetric signal amplification and combined with the enhanced effect of Ag₁₀NPs.

Impact of assay format on miRNA sensing: Electrochemical microfluidic biosensor for miRNA-197 detection

MicroRNAs (miRNAs) are important biomarkers for the early detection of various diseases, especially cancer. Therefore, there is a continuing interest in different biosensing strategies that allow for the point-of-care measurement of miRNAs. Almost all miRNA sensors utilize cross-hybridization of the target miRNA with a capture probe for the recognition, which can be designed in either a sandwich or a competitive format. In this work, we present a low-cost microfluidic biosensor platform for the electrochemical measurement of miRNA-197 (a tumor biomarker candidate) in undiluted human serum samples, operating with very low sample volumes (580 nl) and a sample-to-result time of one hour. For this purpose, different on-chip miRNA bioassays based on sandwich and competitive formats are developed and compared in terms of their sensitivity, dynamic range, selectivity, precision, and simplicity. The obtained results show that, despite having a narrower dynamic range when compared to the competitive format, the sandwich assay has superior performance regarding its sensitivity and selectivity. The lowest limit of detection which can be achieved with the sandwich assay is 1.28 nM (0.74 fmole), while 4.05 nM (2.35 fmole) with the competitive format. Moreover, the sandwich assay proves to have a better distinction against single-base mismatch oligonucleotide sequences compared to the competitive one. Due to its versatility and easy handling, overcoming the issue with the sensitivity, the implemented electrochemical microfluidic biosensor could pave the way for rapid and low-cost on-site miRNA diagnostics.

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.

Enzyme-linked oligonucleotide hybridization assay for direct oligo measurement in blood

Small oligonucleotides (oligos) are increasingly being utilized as diagnostics or treatments for disease. An impediment to broader use is the ability to readily measure oligos in biological fluids. Here, we describe a very straightforward assay with detection in the sub-picomole range that does not require extraction from serum/plasma or polymerization chain reaction amplification. As a result, there are no losses or errors due to sample handling, and the assay can be used to measure oligos modified in a variety of ways that increase therapeutic efficacy. The enzyme-linked oligonucleotide hybridization assay (ELOHA) is based on competition with a detection oligo for hybridization to a capture oligo covalently linked to a solid substrate. The versatility of ELOHAs is demonstrated by application to the measurement of three oligos, including two morpholino-oligos with 3′-octaguanidine derivatization for efficient cell uptake. The third oligo is unmodified and has a DNA sequence equivalent to miR93. The assays have sensitivity as low as 0.28 pmol/sample reaction at 50% hybridization. Adding to clinical utility is the need for only a simple 96-well absorbance plate reader and the finding that neither EDTA nor heparin interferes with detection.

Amperometric Biosensing of miRNA-21 in Serum and Cancer Cells at Nanostructured Platforms Using Anti-DNA-RNA Hybrid Antibodies

This paper describes a disposable amperometric biosensor for simple and sensitive determination of miRNA-21. The bioplatform consists of gold nanoparticles-nanostructured electrode surfaces on which a direct hybridization assay involving the immobilization of a specific thiolated DNA capture probe and recognition of the formed DNA-miRNA-21 heteroduplex by a specific antibody is implemented. The antibody is further recognized through its Fc region by a commercial bacterial protein containing 40 units of horseradish peroxidase (HRP) (ProtA-polyHRP40). The amperometric detection of the hybridization process using the H₂O₂/hydroquinone system allows quantification of the target miRNA in the 0.096-25 pM linear range with a detection limit of 29 fM (0.29 amol in 10 μL of sample). The bioplatform offers excellent selectivity against noncomplementary sequences and very acceptable against sequences with an unpaired base (only 30% of the response obtained for the target miRNA). In addition, the bioplatform was shown to be useful for the determination of the endogenous content of the target oncomiR directly in blood serum from breast cancer patients and in breast cancer cells using only 10 ng of total extracted RNA.