Methylene blue covalently attached to single stranded DNA as electroactive label for potential bioassays

Synthesis, DNA binding of bis-naphthyl ferrocene derivatives and the application as new electroactive indicators for DNA biosensor

A series of bis-naphthyl ferrocene derivatives were synthesized and characterized. Based on the results obtained from UV-visible absorption titration and ethidium bromide (EB) displacement experiments, it was observed that the synthesized compounds exhibited a strong binding ability to dsDNA. In comparison to the viscosity curve of EB, the tested compounds demonstrated a bisintercalation binding mode when interacting with CT-DNA. Differential pulse voltammetry (DPV) was employed to assess the binding specificity of these indicators towards ssDNA and dsDNA. All tested indicators displayed more pronounced signal differences before and after hybridization between probe nucleic acids and target nucleic acids compared to Methylene Blue (MB). Among the evaluated compounds, compound 3j containing an ether chain showed superior performance as an indicator, making it suitable for constructing DNA-based biosensors. Under optimized conditions including probe ssDNA concentration and indicator concentration, this biosensor exhibited good sensitivity, reproducibility, stability, and selectivity. The limit of detection was calculated as 4.53 × 10-11 mol/L. Furthermore, when utilizing 3j as the indicator in serum samples, the biosensor achieved satisfactory recovery rates for detecting the BRCA1 gene.

An Electrochemical Aptasensor for the Detection of Freshwater Cyanobacteria

Aphanizomenon is a genus of cyanobacteria that is filamentous and nitrogen-fixing and inhabits aquatic environments. This genus is known as one of the major producers of cyanotoxins that can affect water quality after the bloom period. In this study, an electrochemical aptasensor is demonstrated using a specific aptamer to detect Aphanizomenon sp. ULC602 for the rapid and sensitive detection of this bacterium. The principal operation of the generated aptasensor is based on the conformational change in the aptamer attached to the electrode surface in the presence of the target bacterium, resulting in a decrease in the current peak, which is measured by square-wave voltammetry (SWV). This aptasensor has a limit of detection (LOD) of OD750~0.3, with an extension to OD750~1.2 and a sensitivity of 456.8 μA·OD750-1·cm-2 without interference from other cyanobacteria. This is the first aptasensor studied that provides rapid detection to monitor the spread of this bacterium quickly in a targeted manner.

Development of Sensitive Methods for the Detection of Minimum Concentrations of DNA on Martian Soil Simulants

Several methods used for the quantification of DNA are based on UV absorbance or the fluorescence of complexes with intercalator dyes. Most of these intercalators are used in gels to visualize DNA and its structural integrity. Due to many extraterrestrial samples, such as meteorites or comets, which are likely to contain very small amounts of biological material, and because the ability to detect this material is crucial for understanding the origin and evolution of life in the universe, the development of assays that can detect DNA at low limits and withstand the rigors of space exploration is a pressing need in the field of astrobiology. In this study, we present a comparison of optimized protocols used for the fast and accurate quantification of DNA using common intercalator dyes. The sensitivity of assays exceeded that generated by any commercial kit and allowed for the accurate quantification of minimum concentrations of DNA. The methods were successful when applied to the detection and measurement of DNA spiked on soil samples. Furthermore, the impact of UV radiation as a harsh condition on the surface of Mars was assessed by DNA degradation and this was also confirmed by gel electrophoresis. Overall, the methods described provide economical, simple-step, and efficient approaches for the detection of DNA and can be used in future planetary exploration missions as tests used for the extraction of nucleic acid biosignatures.

A Review of Detection Methods for Vancomycin-Resistant Enterococci (VRE) Genes: From Conventional Approaches to Potentially Electrochemical DNA Biosensors

Vancomycin-resistant Enterococci (VRE) genes are bacteria strains generated from Gram-positive bacteria and resistant to one of the glycopeptides antibiotics, commonly, vancomycin. VRE genes have been identified worldwide and exhibit considerable phenotypic and genotypic variations. There are six identified phenotypes of vancomycin-resistant genes: VanA, VanB, VanC, VanD, VanE, and VanG. The VanA and VanB strains are often found in the clinical laboratory because they are very resistant to vancomycin. VanA bacteria can pose significant issues for hospitalized patients due to their ability to spread to other Gram-positive infections, which changes their genetic material to increase their resistance to the antibiotics used during treatment. This review summarizes the established methods for detecting VRE strains utilizing traditional, immunoassay, and molecular approaches and then focuses on potential electrochemical DNA biosensors to be developed. However, from the literature search, no information was reported on developing electrochemical biosensors for detecting VRE genes; only the electrochemical detection of vancomycin-susceptible bacteria was reported. Thus, strategies to create robust, selective, and miniaturized electrochemical DNA biosensor platforms to detect VRE genes are also discussed.

Longer amplicons provide better sensitivity for electrochemical sensing of viral nucleic acid in water samples using PCB electrodes

The importance of monitoring environmental samples has gained a lot of prominence since the onset of COVID-19 pandemic, and several surveillance efforts are underway using gold standard, albeit expensive qPCR-based techniques. Electrochemical DNA biosensors could offer a potential cost-effective solution suitable for monitoring of environmental water samples in lower middle income countries. In this work, we demonstrate electrochemical detection of amplicons as long as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${503}\,\hbox {bp}$$\end{document}503bp obtained from Phi6 bacteriophage (a popular surrogate for SARS-CoV-2) isolated from spiked lake water samples, using ENIG finish PCB electrodes with no surface modification. The electrochemical sensor response is thoroughly characterised for two DNA fragments of different lengths (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${117}\,\hbox {bp}$$\end{document}117bp and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${503}\,\hbox {bp}$$\end{document}503bp), and the impact of salt in PCR master mix on methylene blue (MB)-DNA interactions is studied. Our findings establish that length of the DNA fragment significantly determines electrochemical sensitivity, and the ability to detect long amplicons without gel purification of PCR products demonstrated in this work bodes well for realisation of fully-automated solutions for in situ measurement of viral load in water samples.

Rapid electrochemical detection of COVID-19 genomic sequence with dual-function graphene nanocolloids based biosensor

Discovered in December 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (aka SARS-CoV-2 or 2019-nCoV) has attracted worldwide attention and concerns due to its high transmissibility and the severe health consequences experienced upon its infection, particularly by elderly people. Over 329 million people have been infected till date and over 5.5 million people could not survive the respiratory illness known as COVID-19 syndrome. Rapid and low-cost detection methods are of utmost importance to monitor the diffusion of the virus and to aid in the global fight against the pandemic.

We propose here the use of graphene oxide nanocolloids (GONC) as an electroactive nanocarbon material that can act simultaneously as a transducing platform as well as the electroactive label for the detection of 2019-nCoV genomic sequences. The ability of GONC to provide an intrinsic electrochemical signal arising from the reduction of the electrochemically reducible oxygen functionalities present on its surface, allows GONC to be used as a simple and sensitive biosensing platform. Different intrinsic electroactivity of the material was obtained at each step of the genosensing process, starting from the immobilization of a short-stranded DNA probe and followed by the incubation with different concentrations of the target 2019-nCoV DNA strand. Monitoring such variations enabled the quantification of the target analyte over a wide dynamic range between 10⁻¹⁰ and 10⁻⁵ M.

All in all, this proof-of-concept system serves as a stepping stone for the development of a rapid, sensitive and selective analytical tool for the detection of 2019-nCoV as well as other similar viral vectors. The use of cost-effective electrochemical detection methods coupled with the vast availability and suitability of carbon-based nanomaterials make this sensing system a valid candidate for low-cost and point-of-care analysis.

Application of silver solid amalgam electrodes in electrochemical detection of DNA damage

In this study, a mercury meniscus-modified silver solid amalgam electrode was used for the first time for the detection of UV-induced DNA damage. The integrity of the double-stranded DNA (dsDNA) layer was detected indirectly using the evaluation of the methylene blue reduction within its accumulation into dsDNA after the UV irradiation of the biosensor surface with two different wavelengths (254 nm and 365 nm), monitored by differential pulse voltammetry. Moreover, a simple electrochemical characterization of the biosensor surface was performed using cyclic voltammetry of the redox indicator hexaammineruthenium chloride (RuHex) present in the solution. Electrochemical impedance spectroscopy (EIS) was used in both cases for the verification of results. Individual electrochemical signals depend on the time of biosensor exposure to UV irradiation as well as on the selected wavelengths and are different for both used types of dsDNA (salmon sperm and calf thymus). The highest degradation degree up to 60% was observed using sensitive EIS of methylene blue after 10 min irradiation of the biosensor at 254 nm. The use of RuHex seems to be less sensitive for the detection of dsDNA structural changes, when the degradation degree up to 40% was observed, using EIS at the same conditions.

Singlet oxygen-based photoelectrochemical detection of DNA

The current work, designed for the photoelectrochemical detection of DNA, evaluates light-responsive DNA probes carrying molecular photosensitizers generating singlet oxygen (¹O₂). We take advantage of their chromophore's ability to produce ¹O₂ upon photoexcitation and subsequent photocurrent response. Type I, fluorescent and type II photosensitizers were studied using diode lasers at 406 nm blue, 532 nm green and 659 nm red lasers in the presensce and absence of a redox reporter, hydroquinone (HQ). Only type II photosensitizers (producing ¹O₂) resulted in a noticeable photocurrent in 1-4 nA range upon illumination, in particular, dissolved DNA probes labeled with chlorin e6 and erythrosine were found to give a well-detectable photocurrent response in the presence of HQ. Whereas, Type I photosensitizers and fluorescent chromophores generate negligible photocurrents (<0.15 nA). The analytical performance of the sensing system was evaluated using a magnetic beads-based DNA assay on disposable electrode platforms, with a focus to enhance the sensitivity and robustness of the technique in detecting complementary DNA targets. Amplified photocurrent responses in the range of 70-100 nA were obtained and detection limits of 17 pM and 10 pM were achieved using magnetic beads-captured chlorin e6 and erythrosine labeled DNA probes respectively. The presented novel photoelectrochemical detection can further be optimized and employed in applications for which enzymatic amplification such as polymerase chain reaction (PCR) is not applicable owing to their limitations and as an effective alternative to colorimetric detection when rapid detection of specific nucleic acid targets is required.

Development of a rapid and sensitive quantum dot nanobead-based double-antigen sandwich lateral flow immunoassay and its clinical performance for the detection of SARS-CoV-2 total antibodies

Owing to the over-increasing demands in resisting and managing the coronavirus disease 2019 (COVID-19) pandemic, development of rapid, highly sensitive, accurate, and versatile tools for monitoring total antibody concentrations at the population level has been evolved as an urgent challenge on measuring the fatality rate, tracking the changes in incidence and prevalence, comprehending medical sequelae after recovery, as well as characterizing seroprevalence and vaccine coverage. To this end, herein we prepared highly luminescent quantum dot nanobeads (QBs) by embedding numerous quantum dots into polymer matrix, and then applied it as a signal-amplification label in lateral flow immunoassay (LFIA). After covalently linkage with the expressed recombinant SARS-CoV-2 spike protein (RSSP), the synthesized QBs were used to determine the total antibody levels in sera by virtue of a double-antigen sandwich immunoassay. Under the developed condition, the QB-LFIA can allow the rapid detection of SARS-CoV-2 total antibodies within 15 min with about one order of magnitude improvement in analytical sensitivity compared to conventional gold nanoparticle-based LFIA. In addition, the developed QB-LFIA performed well in clinical study in dynamic monitoring of serum antibody levels in the whole course of SARS-CoV-2 infection. In conclusion, we successfully developed a promising fluorescent immunological sensing tool for characterizing the host immune response to SARS-CoV-2 infection and confirming the acquired immunity to COVID-19 by evaluating the SRAS-CoV-2 total antibody level in the crowd.

Emerging materials for the electrochemical detection of COVID-19

The SARS-CoV-2 virus is still causing a dramatic loss of human lives worldwide, constituting an unprecedented challenge for the society, public health and economy, to overcome. The up-to-date diagnostic tests, PCR, antibody ELISA and Rapid Antigen, require special equipment, hours of analysis and special staff. For this reason, many research groups have focused recently on the design and development of electrochemical biosensors for the SARS-CoV-2 detection, indicating that they can play a significant role in controlling COVID disease. In this review we thoroughly discuss the transducer electrode nanomaterials investigated in order to improve the sensitivity, specificity and response time of the as-developed SARS-CoV-2 electrochemical biosensors. Particularly, we mainly focus on the results appeard on Au-based and carbon or graphene-based electrodes, which are the main material groups recently investigated worldwidely. Additionally, the adopted electrochemical detection techniques are also discussed, highlighting their pros and cos. The nanomaterial-based electrochemical biosensors could enable a fast, accurate and without special cost, virus detection. However, further research is required in terms of new nanomaterials and synthesis strategies in order the SARS-CoV-2 electrochemical biosensors to be commercialized.

Electrochemical micropipette-tip for low-cost environmental applications: Determination of anionic surfactants through their interaction with methylene blue

Miniaturization is one of the main requirements in the design of portable devices that allow in-field analysis. This is especially interesting in environmental monitoring, where the time of the sample-to-result process could be decreased considerably by approaching the analytical platforms to the sampling point. We employed traditional mass-produced and low-cost elements (micropipette tips and pins) in an out-of-box application to generate an innovative and cost-effective platform for analytical purposes. We have designed simple and easy-to-use electrochemical cells inside polypropylene micropipette tips with three stainless-steel pins acting as the working, reference and counter electrodes of a potentiostatic system. The pin acting as working electrode was previously coated with carbon ink, meanwhile the rest were used unmodified. In this way, electrochemical in-the-tip measurements were done directly using low volumes (μL) of sample. The devices showed good reproducibility, with a relative standard deviation of 7% (n = 5) for five different tip-based complete electrochemical cells. As a proof-of-concept, its utility has been probed by the determination of an anionic surfactant (sodium dodecyl sulphate, SDS) in water through its interaction with methylene blue (MB). Two different alternatives were presented based on the: 1) increase in the current intensity of the cathodic peak of MB due to the presence of SDS; 2) electrochemical determination of the MB remaining in the aqueous phase after extraction of the pair SDS-MB to an organic medium.

Ultrasensitive Materials for Electrochemical Biosensor Labels

Since the fabrication of the first electrochemical biosensor by Leland C. Clark in 1956, various labeled and label-free sensors have been reported for the detection of biomolecules. Labels such as nanoparticles, enzymes, Quantum dots, redox-active molecules, low dimensional carbon materials, etc. have been employed for the detection of biomolecules. Because of the absence of cross-reaction and highly selective detection, labeled biosensors are advantageous and preferred over label-free biosensors. The biosensors with labels depend mainly on optical, magnetic, electrical, and mechanical principles. Labels combined with electrochemical techniques resulted in the selective and sensitive determination of biomolecules. The present review focuses on categorizing the advancement and advantages of different labeling methods applied simultaneously with the electrochemical techniques in the past few decades.

The potential of electrochemistry for the detection of coronavirus-induced infections

Human coronaviruses (HCoV) are no stranger to the global environment. The etiology of previous outbreaks with reported symptoms of respiratory tract infections was attributed to different coronavirus strains, with the latest global pandemic in 2019 also belonging to the coronavirus family. Timely detection, effective therapeutics and future prevention are stake key holders in the management of coronavirus-induced infections. Apart from the gold standard clinical diagnostics, electrochemical techniques have also demonstrated their great potentials in the detection of different viruses and their correlated antibodies and antigens, showing high sensitivities and selectivities, and faster times for the analysis. This article aims to critically review the multifaceted electrochemical approaches, not only in the development of point-of-care portable devices but also as alternative detection strategies that can be coupled with traditional methods for the detection of various strains of coronaviruses.

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Electrochemical biosensing detection methods for coronavirus-induced infections.

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Potential rapid and cost-effective point-of-care diagnostics for mass testing.

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Electrochemistry helps to overcome limitations faced by gold standard diagnostics.

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Experimental schemes, strengths, and drawbacks of various electrochemical strategies.

Folding-Based Electrochemical Aptasensor for the Determination of β-Lactoglobulin on Poly-L-Lysine Modified Graphite Electrodes

Nowadays, food allergy is a very important health issue, causing adverse reactions of the immune system when exposed to different allergens present in food. Because of this, the development of point-of-use devices using miniaturized, user-friendly, and low-cost instrumentation has become of outstanding importance. According to this, electrochemical aptasensors have been demonstrated as useful tools to quantify a broad variety of targets. In this work, we develop a simple methodology for the determination of β-lactoglobulin (β-LG) in food samples using a folding-based electrochemical aptasensor built on poly-L-lysine modified graphite screen-printed electrodes (GSPEs) and an anti-β-lactoglobulin aptamer tagged with methylene blue (MB). This aptamer changes its conformation when the sample contains β-LG, and due to this, the spacing between MB and the electrode surface (and therefore the electron transfer efficiency) also changes. The response of this biosensor was linear for concentrations of β-LG within the range 0.1-10 ng·mL-1, with a limit of detection of 0.09 ng·mL-1. The biosensor was satisfactorily employed for the determination of spiked β-LG in real food samples.

Sensitive detection of multiple pathogens using a single DNA probe

A simple but promising electrochemical DNA nanosensor was designed, constructed and applied to differentiate a few food-borne pathogens. The DNA probe was initially designed to have a complementary region in Vibrio parahaemolyticus (VP) genome and to make different hybridization patterns with other selected pathogens. The sensor was based on a screen printed carbon electrode (SPCE) modified with polylactide-stabilized gold nanoparticles (PLA-AuNPs) and methylene blue (MB) was employed as the redox indicator binding better to single-stranded DNA. The immobilization and hybridization events were assessed using differential pulse voltammetry (DPV). The fabricated biosensor was able to specifically distinguish complementary, non-complementary and mismatched oligonucleotides. DNA was measured in the range of 2.0×10(-9)-2.0×10(-13)M with a detection limit of 5.3×10(-12)M. The relative standard deviation for 6 replications of DPV measurement of 0.2µM complementary DNA was 4.88%. The fabricated DNA biosensor was considered stable and portable as indicated by a recovery of more than 80% after a storage period of 6 months at 4-45°C. Cross-reactivity studies against various food-borne pathogens showed a reliably sensitive detection of VP.

Methylene blue phosphoramidite for DNA labelling

We report the first synthesis of a methylene blue (MB) phosphoramidite derivative suitable for DNA solid-phase synthesis. The electrochemical and optical properties of the resulting MB modified oligonucleotides were confirmed. This new molecule is an important breakthrough in the design of new probes labelled with MB.

Enzymatic amplification-free nucleic acid hybridisation sensing on nanostructured thick-film electrodes by using covalently attached methylene blue

Amplification-free (referring to enzymatic amplification step) detection methodologies are increasing in biosensor development due to the need of faster and simpler protocols. However, for maintaining sensitivity without this step, highly detectable molecules or very sensitive detection techniques are required. The nanostructuration of transducer surfaces with carbon nanotubes (CNTs), gold nanoparticles (AuNPs) or both in nanohybrid configurations has been employed in this work for DNA hybridisation sensing purposes. Methylene blue (MB), covalently attached to single stranded DNA, (ssDNA) was incubated with a complementary sequence immobilized on nanostructured screen-printed electrodes (AuSPEs). Although CNTs can increase notoriously the signal of the marker, adsorptive properties should also be considered when bioassays are performed because non-specific adsorption (NSA) phenomena are magnified. In this work, strategies for decreasing NSA were thoroughly evaluated for the detection of Mycoplasma pneumoniae (MP) on CNTs-nanostructured screen-printed electrodes. Among them, the employ of UV-radiation or long incubation times (72h) allowed obtaining higher signals for the complementary strand with respect to the non-complementary one. The use of CNTs/AuNPs nanohybrids, together with the use of streptavidin-biotin (ST-B) interaction allows the higher differentiation (with a 3.5 ratio) in the genosensing of M. pneumoniae.

Highly sensitive electrochemical detection of DNA hybridisation by coupling the chemical reduction of a redox label to the electrode reaction of a solution phase mediator

We have described a highly sensitive method for detecting DNA hybridisation using a redox-labeled stem loop probe. The redox labels were poly(styrene-co-acrylic) (PSA) spheres of 454 nm diameter, modified by methylene blue (MB) deposited alternatively with poly(sodium 4-styrene sulphonate) (PSS) in a layer-by-layer process. Each PSA sphere carried approx. 3.7 × 10(5) molecules of MB, as determined optically. DIG-tagged stem loop probes were immobilised on screen printed electrodes bearing anti-DIG antibodies. Binding with the target enabled straightening of the stem loop, which made attachment to the MB-coated PSA spheres possible. For measuring the current from the direct reduction of MB by differential pulse voltammetry, a 30 mer DNA target common to 70 strains of Escherichia coli was calibrated across the range 1.0 fM to 100 pM (gradient = 3.2 × 10(-8) A (log fM)(-1), r(2) = 0.95, n = 60), with an LOD of ∼58 fM. By using Fe(CN)6(3-/4-) as a solution phase mediator for the MB reduction, we were able to lower the LOD to ∼39 aM (gradient = 5.95 × 10(-8) A (log aM)(-1), r(2) = 0.96, n = 30), which corresponds to the detection of 0.76 ag (∼50 molecules) in the 2 μL analyte sample. We hypothesise that the lowering of the LOD was due to the fact that not all the MB labels were able to contact the electrode surface.