Dual-probe electrochemical DNA biosensor based on the “Y” junction structure and restriction endonuclease assisted cyclic enzymatic amplification for detection of double-strand DNA of PML/RARα related fusion gene

Flexible genosensors based on polypyrrole and graphene quantum dots for PML/RARα fusion gene detection: A study of acute promyelocytic leukemia in children

Acute promyelocytic leukemia (APL) in children is associated with a favorable initial prognosis. However, minimal residual disease (MRD) follow-up remains poorly defined, and relapse cases are concerning due to their recurrent nature. Thus, we report two electrochemical flexible genosensors based on polypyrrole (PPy) and graphene quantum dots (GQDs) for label-free PML-RARα oncogene detection. Atomic force microscopy (AFM), scanning electron microscope (SEM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) were used to characterize the technological biosensor development. M7 and APLB oligonucleotide sequences were used as bioreceptors to detect oncogenic segments on chromosomes 15 and 17, respectively. AFM characterization revealed heterogeneous topographical surfaces with maximum height peaks for sensor layers when tested with positive patient samples. APLB/Genosensor exhibited a percentage change in anode peak current (ΔI) of 423 %. M7/Genosensor exhibited a ΔI of 61.44 % for more concentrated cDNA samples. The described behavior is associated with the biospecific recognition of the proposed biosensors. Limits of detection (LOD) of 0.214 pM and 0.677 pM were obtained for APLB/Genosensor and M7/Genosensor, respectively. The limits of quantification (LOQ) of 0.648 pM and 2.05 pM were estimated for APLB/Genosensor and M7/Genosensor, respectively. The genosensors showed reproducibility with a relative standard deviation of 7.12 % for APLB and 1.18 % for M7 and high repeatability (9.89 % for APLB and 1.51 % for M7). In addition, genetic tools could identify the PML-RARα oncogene in purified samples, plasmids, and clinical specimens from pediatric patients diagnosed with APL with high bioanalytical performance. Therefore, biosensors represent a valuable alternative for the clinical diagnosis of APL and monitoring of MRD with an impact on public health.

Combining hybrid nanoflowers with hybridization chain reaction for highly sensitive detection of SARS-CoV-2 nucleocapsid protein

BACKGROUND

COVID-19 (coronavirus disease 2019) pandemic has had enormous social and economic impacts so far. The nucleocapsid protein (N protein) is highly conserved and is a key antigenic marker for the diagnosis of early SARS-CoV-2 infection.

RESULTS

In this study, the N protein was first captured by an aptamer (Aptamer 58) coupled to magnetic beads (MBs), which in turn were bound to another DNA sequence containing the aptamer (Aptamer 48-Initiator). After adding 5'-biotinylated hairpin DNA Amplifier 1 and Amplifier 2 with cohesive ends for complementary hybridization, the Initiator in the Aptamer 48-Initiator began to trigger the hybridization chain reaction (HCR), generating multiple biotin-labeled DNA concatamers. When incubated with synthetic streptavidin-invertase-Ca3(PO4)2 hybrid nanoflower (SICa), DNA concatamers could specifically bind to SICa through biotin-streptavidin interaction with high affinity. After adding sucrose, invertase in SICa hydrolyzed sucrose to glucose, whose concentration could be directly read with a portable glucometer, and its concentration was positively correlated with the amount of captured N protein. The method is highly sensitive with a detection limit as low as 1 pg/mL.

SIGNIFICANCE

We believe this study provided a practical solution for the early detection of SARS-CoV-2 infection, and offered a new method for detecting other viruses through different target proteins.

A Y-shape-structured electrochemiluminescence biosensor based on carbon quantum dots and locked nucleic acid probe for microRNA determination with single-base resolution

Since microRNAs (miRNAs) are predictors of tumorigenesis, accurate identification and quantification of miRNAs with highly similar sequences are expected to reflect tumor diagnosis and treatment. In this study, a highly selective and sensitive electrochemiluminescence (ECL) biosensor was constructed for miRNAs determination based on Y-shaped junction structure equipped with locked nucleic acids (LNA), graphene oxide-based nanocomposite to enrich luminophores, and conductive matrix. Specifically, two LNA-modified probes were designed for specific miRNA recognition, that is, a dual-amine functionalized hairpin capture probe and a signal probe. A Y-shaped DNA junction structure was generated on the electrode surface upon miRNA hybridizing across the two branches, so as to enhance the selectivity. Carbon quantum dots-polyethylene imine-graphene oxide (CQDs-PEI-GO) nanocomposites were developed to enrich luminophores CQDs, and thus enhancing the ECL intensity. For indirect signal amplification, an electrochemically activated poly(2-aminoterephthalic acid) (ATA) film decorated with gold nanoparticles was prepared on electrode as an effective matrix to accelerate the electron transfer. The fabricated ECL biosensor achieved sensitive determination of miRNA-222 with a limit-of-detection (LOD) as low as 1.95 fM (S/N = 3). Notably, Y-shaped junction structures equipped with LNA probes endowed ECL biosensor with salient single-base discrimination ability and anti-interference capacity. Overall, the proposed Y-shaped ECL biosensor has considerable promise for clinical biomarker determination.

An electrochemiluminescence resonance energy transfer biosensor based on CDs/PAMAM/rGO nanocomposites and Au@Ag2S nanoparticles for PML/RARα fusion gene detection

In recent years, electrochemiluminescence resonance energy transfer (ECL-RET) with low background signal and high specificity has attracted much attention among researchers. Herein, we established a novel ECL-RET biosensor for PML/RARα fusion gene detection. In this ECL-RET system, carbon dots (CDs) with low toxicity and prominent electrochemical activity were used as donor and Au@Ag2S core-shell nanoparticles (Au@Ag2S NPs) were employed as ECL acceptor. The Au@Ag2S NPs possessed a wide ultraviolet-visible (UV-vis) absorption spectrum between 500 nm and 700 nm, which completely overlapped with the ECL spectrum of CDs. Furthermore, the CDs-decorated poly-amidoamine/reduced graphene oxide (CDs/PAMAM/rGO) nanocomposites were prepared to improve the ECL signals and served as a substrate to stably load capture probe deoxyribonucleic acid (DNA). Based on the ECL-RET biosensing strategy, the Au@Ag2S NPs-labeled assistant probes and target DNA could pair with capture probes to form the sandwich-type DNA structure and the distance between donor and accepter was closed, leading to quenching of the ECL signal of CDs. The ECL-RET biosensor represented eminent analytical performance for PML/RARα fusion gene detection with a wide linear relationship from 5 fM to 500 pM and a low detection limit of 0.72 fM, which provided a novel technical means and theoretical basis for detection and diagnosis of acute promyelocytic leukemia.

Ultrasensitive amperometric determination of hand, foot and mouth disease based on gold nanoflower modified microelectrode

Given the widespread use of point-of-care testing for diagnosis of disease, micro-scale electrochemical deoxyribonucleic acid (DNA) biosensors have become a promising area of research owing to its fast mass transfer, high current density and rapid response. In this study, a gold nanoparticles modified gold microelectrode (AuNPs/Au-Me) was constructed to determine the hand, foot and mouth disease (HFMD)-related gene. The noble metal nanoparticles modification yielded ca. 7.4-fold increase in electroactive surface area of microelectrode, and the signal for HFMD-related gene was largely magnified. Under optimal conditions, the biosensor exhibited salient selectivity and sensitivity with a low detection limit of 0.3 fM (S/N = 3), which is sufficient for clinical diagnosis of HFMD. Additionally, the developed AuNPs/Au-Me was successfully applied to determining the polymerase chain reaction (PCR) amplified products of target gene. Thus, the electrochemical DNA biosensor possesses great potential in early-stage diagnosis and long-term monitoring of various disease.

Electrochemical Biosensors in the Diagnosis of Acute and Chronic Leukemias

Until now, morphological assessment with an optical or electronic microscope, fluorescence in situ hybridization, DNA sequencing, flow cytometry, polymerase chain reactions, and immunohistochemistry have been employed for leukemia identification. Nevertheless, despite their numerous different vantages, it is difficult to recognize leukemic cells correctly. Recently, the electrochemical evaluation with a nano-sensing interface seems an attractive alternative. Electrochemical biosensors measure the modification in the electrical characteristics of the nano-sensing interface, which is modified by the contact between a biological recognition element and the analyte objective. The implementation of nanosensors is founded not on single nanomaterials but rather on compilating these components efficiently. Biosensors able to identify the molecules of deoxyribonucleic acid are defined as DNA biosensors. Our review aimed to evaluate the literature on the possible use of electrochemical biosensors for identifying hematological neoplasms such as acute promyelocytic leukemia, acute lymphoblastic leukemia, and chronic myeloid leukemia. In particular, we focus our attention on using DNA electrochemical biosensors to evaluate leukemias.

Utilizing Electrochemical-Based Sensing Approaches for the Detection of SARS-CoV-2 in Clinical Samples: A Review

The development of precise and efficient diagnostic tools enables early treatment and proper isolation of infected individuals, hence limiting the spread of coronavirus disease 2019 (COVID-19). The standard diagnostic tests used by healthcare workers to diagnose severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection have some limitations, including longer detection time, the need for qualified individuals, and the use of sophisticated bench-top equipment, which limit their use for rapid SARS-CoV-2 assessment. Advances in sensor technology have renewed the interest in electrochemical biosensors miniaturization, which provide improved diagnostic qualities such as rapid response, simplicity of operation, portability, and readiness for on-site screening of infection. This review gives a condensed overview of the current electrochemical sensing platform strategies for SARS-CoV-2 detection in clinical samples. The fundamentals of fabricating electrochemical biosensors, such as the chosen electrode materials, electrochemical transducing techniques, and sensitive biorecognition molecules, are thoroughly discussed in this paper. Furthermore, we summarised electrochemical biosensors detection strategies and their analytical performance on diverse clinical samples, including saliva, blood, and nasopharyngeal swab. Finally, we address the employment of miniaturized electrochemical biosensors integrated with microfluidic technology in viral electrochemical biosensors, emphasizing its potential for on-site diagnostics applications.

Molecularly imprinted polymers-based DNA biosensors

In multiple biological processes, molecular recognition performs an integral role in detecting bio analytes. Molecular imprinted polymers (MIPs) are tailored sensing materials that can biomimic the biologic ligands and can detect specific target molecules selectively and sensitively. The formulation of molecularly imprinted polymers is followed by the formulation of a control termed as non-imprinted polymer (NIP), which, in the absence of a template, is commonly formulated to evaluate whether distinctive imprints have been produced for the template. Given the difficulties confronting bioanalytical researchers, it is inevitable that this strategy would come out as a central route of multidisciplinary studies to create extremely promising stable artificial receptors as a replacement or accelerate biological matrices. The ease of synthesis, low cost, capability to 'tailor' recognition element for analyte molecules, and stability under harsh environments make MIPs promising candidates as a recognition tool for biosensing. Compared to biological systems, molecular imprinting techniques have several advantages, including high recognition ability, long-term durability, low cost, and robustness, allowing molecularly imprinted polymers to be employed in drug delivery, biosensor technology, and nanotechnology. Molecular imprinted polymer-based sensors still have certain shortcomings in determining biomacromolecules (nucleic acid, protein, lipids, and carbohydrates), considering the vast volume of the latest literature on biomicromolecules. These potential materials are still required to address a few weaknesses until gaining their position in recognition of biomacromolecules. This review aims to highlight the current progress in molecularly imprinted polymers (MIPs)-based sensors for the determination of deoxyribonucleic acid (DNA) or nucleobases.

pDNA conjugated with citrate capped silver nanoparticles towards ultrasensitive bio-assay of haemophilus influenza in human biofluids: A novel optical biosensor

A sensitive and specific approach was developed for the determination of Haemophilus influenza using DNA based bio-assay. In this study, citrate capped silver nanoparticle was synthesized and employed for bioconjugation with pDNA toward target sequences detection. In this study, synthesized probe (SH-5'-AAT TTT CCA ACT TTT TCA CCT GCA T-3') of Haemophilus influenza was detected with great sensitivity and selectivity after hybridization with cDNA (5'-ATG CAG GTG AAA AAG TTG GAA AAT T-3'). Regarding to the obtained results, the low limit of quantification (LLOQ) of DNA sample was 1 ZM using 15 μL of probe and 200 μL of Cit/AgNPs. According to ultra-sensitivity of the fabricated optical DNA-based bio-assay, it has potential for bacterial determination both in clinical and environmental specimens. To evaluate the selectivity of developed DNA based biosensor, three mismatch sequences were applied. Finally, the designed genosensor is a significant diagnostic strategy for detection of Haemophilus influenza with great selectivity.

Ultrasensitive Electrochemical Biosensor Developed by Probe Lengthening for Detection of Genomic DNA in Human Serum

As an alternative to most of the reported nucleic acid amplification-based electrochemical DNA biosensors used for detection of trace levels of genomic DNA, we herein present a novel detection concept. The proposed system involves the conversion of two short double-stranded DNAs (dsDNAs), labeled with a thiol-tag or biotin-tag, into a single integrated dsDNA containing thiol and biotin at both terminals in the presence of target DNA through ligase chain reaction (LCR) and followed by the immobilization of these integrated dsDNAs on a bovine serum albumin (BSA)-modified gold electrode surface. Owing to rapid depletion of the two short dsDNAs via LCR, the integrated dsDNAs were generated in an exponential manner so that this sensoring approach offered a limit of detection of 25 yoctomoles (15 copies in 50 μL sample volumes), a high discrimination of single-base mismatch and a wide linear concentration range (across 6 orders of magnitude) for target DNA. Significantly, the proposed sensor, which has simplicity in operation and ease of miniaturization, detected the target of interest in total nucleic acid extracts derived from clinical serum samples with excellent results, thereby demonstrating its considerable diagnostic potential in fields ranging from virus detection to the diagnosis of genetic diseases.

2'-Fluoro ribonucleic acid modified DNA dual-probe sensing strategy for enzyme-amplified electrochemical detection of double-strand DNA of PML/RARα related fusion gene

In the study, a novel sensing strategy based on dual-probe mode, which involved two groups of 2'-fluoro ribonucleic acid (2'-F RNA) modified probes, was designed for the detection of synthetic target double-strand DNA (dsDNA) of PML/RARα fusion genes in APL. And each pair of probes contained a thiolated capture probe (C1 or C2) immobilized on one of electrode surfaces in the dual-channel electrochemical biosensor and a biotinylated reporter probe (R1 or R2). The two groups of 2'-F RNA modified probes were separately complementary with the corresponding strand (Sa or Sb) from target dsDNA in order to prevent renaturation of target dsDNA. Through flanking target dsDNA, two "sandwitch" complexes (C1/Sa/R1 and C2/Sb/R2) were separately shaped by capture probes (C1 and C2) and free reporter probes (R1 and R2) in hybridization solution on the surfaces of different electrodes after the thermal denaturation. The biotin-modified enzyme which produced the measurable electrochemical current signal was localized to the surface by affinity binding between biotin with streptavidin. Under the optimal condition, the biosensor was able to detect 84 fM target dsDNA and showed a good specificity in PBS hybridization solution. Otherwise, the investigations of the specificity and sensitivity of the biosensor were carried out further in the mixed hybridization solution containing different kinds of mismatch sequences as interference background. It can be seen that under a certain interference background, the method still exhibited excellent selectivity and specificity for the discrimination between the fully-complementary and the mismatch sequences. The results of our research laid a good basis of further detection research in practical samples.

A simple surface plasmon resonance biosensor for detection of PML/RARα based on heterogeneous fusion gene-triggered nonlinear hybridization chain reaction

In this work, a simple and enzyme-free surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of two major PML/RARα (promyelocytic leukemia, retinoic acid receptor alpha) subtypes based on the heterogeneous fusion gene-triggered nonlinear hybridization chain reaction (HCR). On the gold chip surface, the cascade self-assembly process is triggered after the introduction of PML/RARα. The different fragments of PML/RARα can specifically hybridize with capture probes (Cp) immobilized on the chip and the hybridization DNA₁ (H₁). Then, the nonlinear HCR is initiated by the complex of Cp-PML/RARα-H₁ with the introduction of two hybridization DNA chains (H₂ and H₃). As a result, a dendritic nanostructure is achieved on the surface of chip, leading to a significant SPR amplification signal owing to its high molecular weight. The developed method shows good specificity and high sensitivity with detection limit of 0.72 pM for "L" subtype and 0.65 pM for "S" subtype. Moreover, this method has been successfully applied for efficient identification of clinical positive and negative PCR samples of the PML/RARα subtype. Thus, this developed biosensing strategy presents a potential platform for analysis of fusion gene and early diagnosis of clinical disease.

Prevention and control of emergent infectious disease with high specific antigen sensor

This study aims to evaluate the application of a new type of high specificity antigen sensor in detecting the viruses in sudden infectious diseases. Influenza A (H1N1) virus immunosensor was used for the respective determination of the six kinds of antigens of H1N1, H3N2 viral protein, HA protein of H7N9, influenza B virus, adenovirus, and EV71 virus of same dilution degree on the Screen Printed Carbon Electrode (SPCE), so as to test the specificity of the detection method. In addition, various batches of chick embryo allantoic saliva dilution simulation samples were also detected on their recovery (accuracy), repeatability (precision), and stability. The results were as follows: the linear equation was y = 121.33x + 168; the slope of the linear equation was 121.33 nA/HA unit, representing the sensitivity; correlation coefficient was R²=0.9921 > 0.90. Using Statistical Analysis System (SAS) software, we found that: the W values of seven sets of data after Shapiro-Wilk detection were 0.853, 0.991, 0.901, 0.906, 0.825, 0.974, and 0.992, respectively; P values were 0.247, 0.831, 0.386, 0.405, 0.174, 0.691, and 0.821, respectively, all of which were greater than 0.05, suggesting that normality was met. The results of homogeneity test for variance were as follows: F = 2.44, P = 0.0775 > 0.05, suggesting that homogeneity of variance was met. The parametric test results were as follows: F = 19114.0, P < 0.0001, suggesting that there were obvious differences between testing data of the seven groups. The determination recovery rate of electrochemical immunosensor was 80-110%. Relative Standard Deviation (RSD) values of repeatability (precision) test of H1N1 influenza virus electrochemical immunosensor were 7.74%, 3.54%, and 2.01%, all of which were smaller than 10%. The signal response of H1N1 electrochemical immune biological sensor could still maintain more than 85% of the original signal within 30 days of storage. In conclusion, H1N1 electrochemical immune biosensor has good specificity and the test results are not affected by other viruses of the same type. Besides, it has good accuracy which can realize the accurate determination of A (H1N1) influenza virus in actual detection. Thus, the requirement of precision measurement of A (H1N1) flu virus detection can be met. Therefore, H1N1 electrochemical immune biosensors can be used in actual detection with good stability.

Ce-based metal-organic frameworks and DNAzyme-assisted recycling as dual signal amplifiers for sensitive electrochemical detection of lipopolysaccharide

In this work, a sensitive electrochemical aptasensor was designed for lipopolysaccharide (LPS) detection based on Ce-based metal-organic frameworks (Ce-MOFs) and Zn(2+) dependent DNAzyme-assisted recycling as dual signal amplifiers. Herein, Ce-MOFs were decorated with gold nanoparticles (AuNPs) to obtain AuNPs/Ce-MOFs, and the resultant AuNPs/Ce-MOFs not only acted as nanocarriers to capture -SH terminated hairpin probes 2 (HP2) for acquiring HP2/AuNPs/Ce-MOFs signal probes, but also as catalysts to catalyze the oxidation of ascorbic acid (AA). In the presence of target LPS, report DNA was released from the prepared duplex DNA and then hybridized with hairpin probes 1 (HP1, which were immobilized on the electrode). With the help of Zn(2+), report DNA could act as Zn(2+) dependent DNAzyme to cleave HP1 circularly. Then a large amount of capture probes were produced on the electrode to combine with HP2/AuNPs/Ce-MOFs signal probes. When the detection solution contained electrochemical substrate of AA, AuNPs/Ce-MOFs could oxide AA to obtain enhanced signal. Under the optimized conditions, this proposed aptasensor for LPS exhibited a low detection limit of 3.3 fg/mL with a wide linear range from 10fg/mL to 100ng/mL.