Electrochemical DNA sensor-based strategy for sensitive detection of DNA demethylation and DNA demethylase activity

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

Photoelectrochemical biosensor for DNA demethylase detection based on enzymatically induced double-stranded DNA digestion by endonuclease-exonuclease system and Bi4O5Br2-Au/CdS photoactive material

A novel photoelectrochemical (PEC) biosensor for the detection of DNA demethylase MBD2 was developed based on Bi₄O₅Br₂-Au/CdS photosensitive material. Bi₄O₅Br₂ was firstly modified with gold nanoparticles (AuNPs), following with the modification onto the ITO electrode with CdS to realize the strong photocurrent response as a result of AuNPs had good conductibility and the matched energy between CdS and Bi₄O₅Br₂. In the presence of MBD2, double-stranded DNA (dsDNA) on the electrode surface was demethylated, which triggered the digestion activity of endonuclease HpaII to cleave dsDNA and induced the further cleavage of the dsDNA fragment by exonuclease III (Exo III), causing the release of biotin labeled dsDNA and inhibiting the immobilization of streptavidin (SA) onto the electrode surface. As a results, the photocurrent was increased greatly. However, in the absence of MBD2, HpaII digestion activity was inhibited by DNA methylation modification, which further caused the failure in the release of biotin, leading to the successful immobilization of SA onto the electrode to realize a low photocurrent. The sensor had a detection of 0.3-200 ng/mL and a detection limit was 0.09 ng/mL (3σ). The applicability of this PEC strategy was assessed by studying the effect of environmental pollutants on MBD2 activity.

Assay for TET1 activity and its inhibitors screening with signal amplification by both nanoparticles and Ru(III) redox recycling

Ten-eleven translocation protein 1 (TET1) is one member of TET proteins family which plays a key role in dynamic DNA methylation-demethylation process. Herein, a novel biosensor was constructed for TET1 detection and its inhibitors screening utilizing restriction digestion of endonuclease enzyme MspI. Half-methylated oligonucleotide (5mC DNA) was used as target and Ru(NH₃)₆³⁺ as electrochemical signal probe. After the treatment by TET1 and T4 β-glucosyltransferase (T4 β-GT), target oligonucleotide would not be recognized and digested. If there was no TET1, the target would be digested and the response of biosensor decreased greatly. The current difference of biosensor with and without the incubation with TET1 was therefore dependent on the concentration of TET1. To increase sensitivity of the biosensor, nanostructured film at electrode surface and nanoparticles modified oligonucleotides were employed as signal amplification elements for Ru(NH₃)₆³⁺ recycling. Finally, this biosensor showed high performance with a wide linear range of TET1 concentration from 3.5-21 ng/μL and a low detection limit of 0.33 ng/μL, which is superior to other existing methods. The inhibition effects of Bobcat339 on TET1 was successfully proved by our biosensor with an IC₅₀ of 38 μM. Not only that, but the feasibility of the biosensor for inhibitors screening was evaluated and further confirmed by other compounds including two anticancer drugs and three active ingredients of traditional Chinese medicine.

A robust host-guest interaction controlled probe immobilization strategy for the ultrasensitive detection of HBV DNA using hollow HP5-Au/CoS nanobox as biosensing platform

The combination of supramolecular chemistry and nanotechnology has potentially applied in the construction of biosensors, and thus improves the analytical performance and robustness of electron devices. Herein, a new sandwich-type DNA sensor was constructed for ultrasensitive determination of hepatitis B virus (HBV) DNA, a recognized marker for chronic hepatitis B. The water-soluble pillar[5]arene stabilized Pd NPs combined with reduced graphene oxide nanosheet (WP5-Pd/RGO) was synthesized and employed as supporting material for the modification of electrode surface. The probe DNA was immobilized onto the electrode surface through a new strategy based on the host-guest interaction between WP5 and methylene blue labeled DNA (MB-DNA). Moreover, MOF-derived cobalt sulfide nanobox was prepared to anchor the hydroxylatopillar[5]arene stabilized Au NPs (HP5-Au/CoS), which had superior electrocatalytic performance towards H₂O₂ reduction to achieve signal amplification. Under the optimized conditions, the proposed sensor displayed a linear relationship between amperometric currents and the logarithm of tDNA solution from 1 × 10^-15 mol/L to 1 × 10^-9 mol/L, and a low detection limit of 0.32 fmol/L. What's more, the DNA sensor had remarkable behaviors of stability, reproducibility, specificity, and accuracy, which provided a potential and promising prospect for clinical diagnosis and analysis.

Ultrasensitive electroluminescence biosensor for a breast cancer marker microRNA based on target cyclic regeneration and multi-labeled magnetized nanoparticles

An electrochemiluminescent (ECL) biosensor is described for the determination of the breast cancer biomarker microRNA. The method is based on the amplification via target cyclic regeneration through a system of hairpin DNA probes, primers, and Klenow fragment of DNA polymerases combined with CdTe quantum dots (QDs) and gold nanoparticles. The assay is performed by exploiting the luminescence properties of CdTe-QDs and K₂S₂O₈ as a co-reactive agent to increase the ECL signal. It was successfully applied to ECL-based detection of a 20-mer microRNA. The sensor has a linear response in the 0.1 fM to 0.2 pM microRNA concentration range and a detection limit as low as 33 aM. The assay has been applied to the determination of microRNA spiked in serum samples, and recoveries ranged from 94.4 to 100.5%. Graphical abstract A novel electroluminescence biosensor based on the amplification of target cyclic regeneration is described. It is achieved by using a system of hairpin DNA probes, primers, and Klenow fragment of DNA polymerases combined with CdTe QDs and Au NPs, and was successfully applied to microRNA detection.

Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection

Nucleic acid probes are very useful tools in biological and medical science. However, the essential sensing mechanism of nucleic acid probes was prone to the interference of surrounding sequences. Especially when the target sequences formed secondary structures such as hairpin or quadruplex, the nucleic acid probes were hindered from hybridizing with target strands, greatly disabled the function of probes. Herein, we have established an Open strand based strategy for eliminating the influence of secondary structures on the performance of nucleic acid probes. The strategy was general toward different lengths, secondary structures and sequences of the targeting strand, and we found that the improvement was higher when the secondary structure of the targeting strand was more complicated. Experiments on synthetic single stranded DNA and real clinical genomic DNA samples were conducted for low abundance mutation detection, and the limit of detection for TERT-C228T and BRCA2 rs80359065 mutations could be 0.02% and 0.05% respectively, demonstrating the clinical practicability of our proposed strategy in low abundance mutation detection.

Evaluation of carbon nanotube based copper nanoparticle composite for the efficient detection of agroviruses

We report a biosensor that combines the construction of a three-dimensional nanocomposite with electrochemical methods for the detection of viruses in plants. This is the first report, where carbon nanotubes are used as a conductive frame to anchor highly electrolytic agglomerates of copper nanoparticles to detect agroviruses. Morphological analysis of nanocomposite revealed the presence of carbon nanotubes having a diameter of 50-100nm with copper nanoparticles of 20-100nm, attached in the form of bunches. This material was applied to assess the infection caused by geminiviruses which are a major threat to the cotton plants in Asian and African countries. The hybridization events were studied by monitoring differential pulse voltammetry signals using methylene blue as a redox indicator. In the presence of target DNA, sensor signals decreased from 7×10^-4 to 1×10^-4Ampere. The probe exhibited 97.14% selectivity and the detection limit was found to be 0.01ngμL^-1. The developed biosensor is stable for at least four weeks, losing only 4.3% of the initial signal value. This sensor was able to detect the presence of viruses in sap extracted from cotton leaves, thus providing a promising platform to detect a range of other crops-infecting viruses.

Investigating the potential of multiwalled carbon nanotubes based zinc nanocomposite as a recognition interface towards plant pathogen detection

The emergence of nanotechnology has opened new horizons for constructing efficient recognition interfaces. This is the first report where the potential of a multiwalled carbon nanotube based zinc nanocomposite (MWCNTs-Zn NPs) investigated for the detection of an agricultural pathogen i.e. Chili leaf curl betasatellite (ChLCB). Atomic force microscope analyses revealed the presence of multiwalled carbon nanotubes (MWCNTs) having a diameter of 50-100nm with zinc nanoparticles (Zn-NPs) of 25-500nm. In this system, these bunches of Zn-NPs anchored along the whole lengths of MWCNTs were used for the immobilization of probe DNA strands. The electrochemical performance of DNA biosensor was assessed in the absence and presence of the complementary DNA during cyclic and differential pulse voltammetry scans. Target binding events occurring on the interface surface patterned with single-stranded DNA was quantitatively translated into electrochemical signals due to hybridization process. In the presence of complementary target DNA, as the result of duplex formation, there was a decrease in the peak current from 1.89×10^-04 to 5.84×10^-05A. The specificity of this electrochemical DNA biosensor was found to be three times as compared to non-complementary DNA. This material structuring technique can be extended to design interfaces for the recognition of the other plant viruses and biomolecules.

Current trends in electrochemical sensing and biosensing of DNA methylation

DNA methylation plays an important role in physiological and pathological processes. Several genetic diseases and most malignancies tend to be associated with aberrant DNA methylation. Among other analytical methods, electrochemical approaches have been successfully employed for characterisation of DNA methylation patterns that are essential for the diagnosis and treatment of particular diseases. This article discusses current trends in the electrochemical sensing and biosensing of DNA methylation. Particularly, it provides an overview of applied electrode materials, electrode modifications and biorecognition elements applications with an emphasis on strategies that form the core DNA methylation detection approaches. The three main strategies as (i) bisulfite treatment, (ii) cleavage by restriction endonucleases, and (iii) immuno/affinity reaction were described in greater detail. Additionally, the availability of the reviewed platforms for early cancer diagnosis and the approval of methylation inhibitors for anticancer therapy were discussed.