A new hybrid signal amplification strategy for ultrasensitive electrochemical detection of DNA based on enzyme-assisted target recycling and DNA supersandwich assemblies

Portable sensor based on magnetic separation and enzyme-mediated immune nanomaterials for point-of-care testing of Listeria monocytogenes in food

Listeria monocytogenes (L. monocytogenes), a typical foodborne pathogen, poses a serious threat to public health safety. This stimulates to develop a point-of-care testing (POCT) method to achieve rapid, sensitive detection of L. monocytogenes. In this study, polyethylene glycol (PEG) mediated ampicillin functionalized magnetic beads (Amp-PEG-MBs) was prepared successfully and it achieved high efficiency (>90%) and rapid (5 min) capture for L. monocytogenes at room temperature. The innovative combination of antibody (Ab), glucose oxidase (GOD) and graphene oxide (GO) prepared Ab@GO@GOD for the specific recognition of L. monocytogenes. Finally, Amp-PEG-MBs and Ab@GO@GOD were successfully assembled into Amp-PEG-MBs@L. monocytogenes-Ab@GO@GOD sandwich structure which could catalyze the glucose, and the final detection results were recorded by a blood glucose meter (BGM). Magnetic separation (MS) combined with enzyme-catalyzed sensor (MS-Ab@GO@GOD-BGM) was successfully established to achieve the detection of L. monocytogenes in artificially contaminated juice within 66 min with the limit of detection was 10¹ CFU/mL. This sensor has potential for other pathogens detection by modifying specific antibodies.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Biosensors Coupled with Signal Amplification Technology for the Detection of Pathogenic Bacteria: A Review

Foodborne disease caused by foodborne pathogens is a very important issue in food safety. Therefore, the rapid screening and sensitive detection of foodborne pathogens is of great significance for ensuring food safety. At present, many research works have reported the application of biosensors and signal amplification technologies to achieve the rapid and sensitive detection of pathogenic bacteria. Thus, this review summarized the use of biosensors coupled with signal amplification technology for the detection of pathogenic bacteria, including (1) the development, concept, and principle of biosensors; (2) types of biosensors, such as electrochemical biosensors, optical biosensors, microfluidic biosensors, and so on; and (3) different kinds of signal amplification technologies applied in biosensors, such as enzyme catalysis, nucleic acid chain reaction, biotin-streptavidin, click chemistry, cascade reaction, nanomaterials, and so on. In addition, the challenges and future trends for pathogenic bacteria based on biosensor and signal amplification technology were also discussed and summarized.

Target-switchable DNA hydrogels coupled with a Bi2Sn2O7/Bi2S3 heterojunction based on in situ anion exchange for the "signal-on" photoelectrochemical detection of DNA

In this paper, a novel photoelectrochemical (PEC) "signal-on" biosensor based on a Bi2Sn2O7/Bi2S3 heterojunctioncoupled with target-switchable DNA hydrogels is reported for the ultrasensitive detection of P53 gene DNA. For the first time, sulfide ions are discovered to display an excellent PEC sensitization effect on Bi2Sn2O7 material by forming the Bi2Sn2O7/Bi2S3 heterojunction. The sensitization amplitude increased by 63 times, and the photocurrent polarity switched from cathodic to anodic. When the target DNA-induced-cycling amplification process produced a mass of product chains (PD), PD was introduced into the target-switchable DNA hydrogels to quantitatively release sulfide ions, which were further introduced to the Bi2Sn2O7-modified PEC platform and resulted in an enormous enhancement of the PEC signal due to the significant sensitization effect of sulfide ions on Bi2Sn2O7via an anion-exchange reaction. The corresponding PEC signal change of the Bi2Sn2O7/Bi2S3 platform was used for the detection of target DNA. This biosensing strategy opens up a novel sulfide ion-sensitized PEC platform and exhibits excellent analytical performance with a wide linear range (100 fM-10 nM), which has broad application prospects in bioanalysis and clinical diagnosis.

Sensitive detection of streptomycin in milk using a hybrid signal enhancement strategy of MOF-based bio-bar code and target recycling

A MOF-based bio-bar code material was synthesized and firstly applied to develop an electrochemical streptomycin (STR) aptasensor. By using MOF-based bio-bar code and enzyme-assisted target recycling for dual-signal amplification, highly sensitive detection of STR was achieved. The sensing surface was simply fabricated by immobilizing a mixed monolayer of thiolated cDNA/aptamer duplexes (dsDNA) and 6-mercapto-1-hexanol (MCH) on the gold nanoparticle modified screen printed carbon electrode (Au/SPCE). The presence of target STR caused highly efficient removal of the aptamers from dsDNA assisted by Exo I enzyme. Then MOF-based bio-bar codes were backfilled to achieve the adsorption of electroactive Ru(NH₃)₆³⁺ (RuHex) on electrode surface. The electrochemical signal of the surface-confined RuHex was used for quantitation. The analytical performance for STR was satisfactory with a wide linear range of 0.005-150 ng mL^-1, a low detection limit of 2.6 pg mL^-1 and a good selectivity towards other three antibiotics. Moreover, the application of this aptasensor for determination of STR in real milk samples was also realized. With these merits, this dual-signal amplification assay might provide one of the effective ways for food safety monitoring.

Label-Free Detection of E. coli O157:H7 DNA Using Light-Addressable Potentiometric Sensors with Highly Oriented ZnO Nanorod Arrays

The detection of bacterial deoxyribonucleic acid (DNA) is of great significance in the quality control of food and water. In this study, a light-addressable potentiometric sensor (LAPS) deposited with highly oriented ZnO nanorod arrays (NRAs) was used for the label-free detection of single-stranded bacterial DNA (ssDNA). A functional, sensitive surface for the detection of Escherichia coli (E. coli) O157:H7 DNA was prepared by the covalent immobilization of the specific probe single-stranded DNA (ssDNA) on the LAPS surface. The functional surface was exposed to solutions containing the target E. coli ssDNA molecules, which allowed for the hybridization of the target ssDNA with the probe ssDNA. The surface charge changes induced by the hybridization of the probe ssDNA with the target E. coli ssDNA were monitored using LAPS measurements in a label-free manner. The results indicate that distinct signal changes can be registered and recorded to detect the target E. coli ssDNA. The lower detection limit of the target ssDNA corresponded to 1.0 × 102 colony forming units (CFUs)/mL of E. coli O157:H7 cells. All the results demonstrate that this DNA biosensor, based on the electrostatic detection of ssDNA, provides a novel approach for the sensitive and effective detection of bacterial DNA, which has promising prospects and potential applications in the quality control of food and water.

Dual-Signal Readout of DNA Methylation Status Based on the Assembly of a Supersandwich Electrochemical Biosensor without Enzymatic Reaction

A highly sensitive and selective biosensing system was designed to analyze DNA methylation using a dual-signal readout technique in combination with the signal amplification of supersandwich DNA structure. Through the ingenious design of target-triggered cascade of hybridization chain reaction, one target DNA could initiate the formation of supersandwich structure with multiple signal probes. As a result, one-to-multiple amplification effect was achieved, which conferred high sensitivity to target molecular recognition. Based on probe 1 labeled with ferrocene and probe 2 modified with methylene blue, the target DNA was clearly recognized by two electrochemical signals at independent potentials, which was helpful for the acquisition of more accurate detection results. Taking advantage of bisulfite conversion, the methylation status of cytosine (C) was changed to nucleic acid sequence status, which facilitated the hybridization-based detection without enzymatic reaction. Consequently, the methylated DNA was detected at the femtomolar level with satisfactory analytical parameters. The proposed system was effectively used to assess methylated DNA in human blood serum samples, illuminating the possibility of the sensing platform for applications in disease diagnosis and biochemistry research.

Bioapplications of DNA nanotechnology at the solid-liquid interface

DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.

Zero background and triple-signal amplified fluorescence aptasensor for antibiotics detection in foods

It's important to eliminate matrix interference for accurate detecting antibiotic residues in complex food samples. In this study, we designed a zero-backgrounded fluorescence aptasensor to achieve on-site detection of antibiotic residues, with chloramphenicol (CAP) as representative analyte. Moreover, a three stir-bars assisted target recycling system (TSBTR) was designed to achieve triple signal amplification and increase the sensitivity. The bars included one magnetic stir-bar modified with two kinds of long DNA chains, and two gold stir-bars modified with Y shape-duplex DNA probes respectively. In the presence of CAP, the target could recurrently react with the probes on the bars and replace a large amount of long DNA chains into supernatant. After then, the bars were taken out and SYBR green dye was added to the solution. The dye can specifically intercalate into the duplex structures of DNA chains to emit fluorescence while not emitting a signal in its free state. Under the optimized experimental conditions, a wide linear response range of 5 orders of magnitude from 0.001 ng mL^-1 to 10 ng mL^-1 was achieved with a detection limit of 0.033 pg mL^-1 CAP. The assay was successfully employed to detect CAP in food samples (milk & fish) with consistent results with ELISA's. High selectivity and sensitivity were attributed to the zero background signal and triple signal-amplification strategy. Moreover, the detection time can be shortened to 40 min due to that three signal amplified process can occur simultaneously. The fluorescent aptasensor was also label- and enzyme-free. All these ensure the platform to be rapid, cost-effective, easily-used, and is especially appropriate for detection antibiotics in food safety.

Ultrasensitive Photoelectrochemical Assay with PTB7-Th/CdTe Quantum Dots Sensitized Structure as Signal Tag and Benzo-4-chlorohexadienone Precipitate as Efficient Quencher

Herein, an ultrasensitive photoelectrochemical (PEC) assay was developed for the monitoring of microRNA-141 (miRNA-141) based on poly{4,8-bis[5-(2-ethylhexyl)thiophen-2-yl]benzo[1,2- b:4,5- b']dithiophene-2,6-diyl- alt-3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4- b]thiophene-4,6-diyl}/CdTe quantum dots ( PTB7-Th/CdTe QDs) sensitized structure as signal tag and the benzo-4-chlorohexadienone (4-CD) precipitate as efficient quencher. PTB7-Th and CdTe QDs were successively modified on the electrode surface to form a novel sensitized structure with eminent photovoltaic performances and surpassing film-forming ability. The PTB7-Th/CdTe QDs sensitized structure served as signal tag for achieving a strong initial PEC signal. Besides, a tiny amount of target (miRNA-141) could be transformed into numerous DNA products via enzyme-assisted target cycling procedure, which further triggered the formation of a DNA supersandwich structure on the electrode surface for loading abundant manganese porphyrin (MnPP). Thereafter, MnPP as mimetic enzyme could catalyze 4-chloro-1-naphthol (4-CN) to generate 4-CD precipitate on the sensing interface in the presence of H₂O₂, which could efficiently block electron transfer, leading to a significantly quenched PEC signal for determination of miRNA-141. The designed PEC biosensor performed a wide detection range from 0.1 fM to 1 nM with a low detection limit of 33 aM for miRNA-141, which paved a new avenue for highly accurate and ultrasensitive monitoring of multifarious analytes in bioanalysis and clinical diagnosis.

Ultrasensitive electrochemical detection of nucleic acid by coupling an autonomous cascade target replication and enzyme/gold nanoparticle-based post-amplification

Owing to the intrinsic importance of nucleic acid as bio-targets, the development of isothermal and ultrasensitive electrochemical DNA biosensor is very essential for biological studies and medical diagnostics. Herein, the autonomous cascade DNA replication strategy was effectively married with the enzyme/gold nanoparticle-based post-amplification strategy to promote the detection performance toward target DNA. A hairpin DNA probe (HP) is designed that consists of an overhang at 3'-end as the recognition unit for target DNA, a recognition site for nicking endonuclease, and an alkane spacer to terminate polymerization reaction. The autonomous DNA replication-scission-displacement reaction operated by the nicking endonuclease/KF polymerase induced the autocatalytic opening of HP, which was then specifically bound by the enzyme/gold nanoparticles for further dual-signal amplification toward target-related sensing events. A low detection limit of 0.065 fM with an excellent selectivity toward target DNA could be achieved. The proposed biosensor could be also easily regenerated for target detection. The developed biosensor creates an opportunity for the effective coupling of the target replication with post-amplification strategies and thus opens a promising avenue for the detection of nucleic acid with low abundance in bioanalysis and clinical biomedicine.

Fluorescence recognition of double-stranded DNA based on the quenching of gold nanoparticles to a fluorophore labeled DNA probe

This work described an ultrasensitive fluorescent sensor for sequence-specific recognition of dsDNA based on the quenching of gold nanoparticles (AuNPs) to a fluorophore labeled DNA probe.

Lable-free quadruple signal amplification strategy for sensitive electrochemical p53 gene biosensing

A versatile label-free quadruple signal amplification biosensing platform for p53 gene (target DNA) detection was proposed. The chitosan-graphene (CS-GR) modified electrode with excellent electron transfer ability could provide a large specific surface for high levels of AuNPs-DNA attachment. The large amount of AuNPs could immobilize more capture probes and enhance the electrochemical signal with the excellent electrocatalytic activity. Furthermore, with the assist of N.BstNB I (the nicking endonuclease), target DNA could be reused and more G-quadruplex-hemin DNAzyme could be formed, allowing significant signal amplification in the presence of H2O2. Such strategy can enhance the oxidation-reduction reaction of adsorbed methylene blue (MB) and efficiently improve the sensitivity of the proposed biosensor. The morphologies of materials and the stepwise biosensor were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and cyclic voltammetry (CV). Differential pulse voltammetry (DPV) signals of MB provided quantitative measures of the concentrations of target DNA, with a linear calibration range of 1.0 × 10(-15)-1.0 × 10(-9)M and a detection limit of 3.0 × 10(-16)M. Moreover, the resulting biosensor also exhibited good specificity, acceptable reproducibility and stability, indicating that the present strategy was promising for broad potential application in clinic assay.

Enzyme-assisted target recycling (EATR) for nucleic acid detection

Fast, reliable and sensitive methods for nucleic acid detection are of growing practical interest with respect to molecular diagnostics of cancer, infectious and genetic diseases. Currently, PCR-based and other target amplification strategies are most extensively used in practice. At the same time, such assays have limitations that can be overcome by alternative approaches. There is a recent explosion in the design of methods that amplify the signal produced by a nucleic acid target, without changing its copy number. This review aims at systematization and critical analysis of the enzyme-assisted target recycling (EATR) signal amplification technique. The approach uses nucleases to recognize and cleave the probe-target complex. Cleavage reactions produce a detectable signal. The advantages of such techniques are potentially low sensitivity to contamination and lack of the requirement of a thermal cycler. Nucleases used for EATR include sequence-dependent restriction or nicking endonucleases or sequence independent exonuclease III, lambda exonuclease, RNase H, RNase HII, AP endonuclease, duplex-specific nuclease, DNase I, or T7 exonuclease. EATR-based assays are potentially useful for point-of-care diagnostics, single nucleotide polymorphisms genotyping and microRNA analysis. Specificity, limit of detection and the potential impact of EATR strategies on molecular diagnostics are discussed.

Ultrasensitive electrochemical biosensing for DNA using quantum dots combined with restriction endonuclease

A sensitive platform using endonuclease and AuNPs as well as environmental Bi film for the detection of DNA has been developed.

Versatile biosensing platform for DNA detection based on a DNAzyme and restriction-endonuclease-assisted recycling

On the basis of a DNAzyme and a restriction-endonuclease-assisted target recycling strategy using Pd-Au alloy nanocrystals to immobilize probe DNA on an electrode and catalyze the reduction of H2O2 which amplified signal and promoted the detection sensitivity, a versatile biosensing platform for DNA detection was proposed. Using p53 and oral cancer genes as models, hemin/G-quadruplex simultaneously acted as a reduced nicotinamide adenine dinucleotide (NADH) oxidase and a horseradish peroxidase (HRP)-mimicking DNAzyme, and a versatile DNA biosensor was designed for the first time based on the good electrocatalytic activity of Pd-Au alloy nanocrystals. Hemin/G-quadruplex catalyzed the reduction of H2O2, which was generated from NADH in the presence of O2, to produce an electrochemical signal when thionine functioned as the electron mediator. Moreover, the nicking endonuclease N.BstNB I caused the target DNA to cycle for multiple rounds and further amplified the electrochemical response. This versatile DNA biosensor exhibited linear ranges for the detection of p53 and oral cancer genes from 0.1 fmol L(-1) to 0.1 nmol L(-1) and 0.1 fmol L(-1) to 1 nmol L(-1), respectively. The detection limits, established as 3σ, were estimated to be 0.03 and 0.06 fmol L(-1) for the p53 and oral cancer genes, respectively. The as-prepared biosensor could discriminate mismatched sequences, indicating a satisfactory selectivity and validating the feasibility of the proposed strategy. More importantly, simply by changing the helper DNA, this versatile DNA biosensor could detect different target DNA species, which could create a new avenue for the potential diagnosis of cancer.

Fabricating a reversible and regenerable electrochemical biosensor for quantitative detection of antibody by using "triplex-stem" DNA molecular switch

A reversible and regenerable electrochemical biosensor is fabricated for quantitative detection of antibody based on "triplex-stem" molecular switches. A hairpin-shaped oligonucleotide (hairpin DNA) labeled with ferrocene (Fc) at the 3'-end is fixed on the gold electrode serving as a signal transduction probe. Its hairpin structure leads Fc close to the surface of gold electrode and produces a strong current signal (on-state). A single-strand oligonucleotide modified with two digoxin molecules on the two arm segments (capture DNA) interact with hairpin DNA with the help of Ag(+) ions. The "triplex-stem" DNA forms, which separates Fc from the electrode and reduces the electrochemical signal (off-state). Binding of digoxin antibody to digoxin releases capture DNA from the hairpin DNA, creating an effective "off-on" current signal switch. The stability of the "triplex-stem" structure of hairpin/capture DNA is critical to the signal switch and the sensitivity of the method, which can be adjusted conveniently and efficiently by changing Ag(+) concentrations. Based on the "off-on" current signal switch, this biosensor is used to detect digoxin antibody sensitively in blood serum. The linear range is 1.0-500 pg with a correlation coefficient of 0.996, and the detection limit is 0.4 pg. Also, this biosensor shows excellent reversibility and reproducibility, which are significant requirements for practical biosensor applications.

Emerging technologies for hybridization based single nucleotide polymorphism detection

Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.

Electrochemiluminescence recovery-based aptasensor for sensitive Ochratoxin A detection via exonuclease-catalyzed target recycling amplification

Based on the recovery of the quantum dot (QD) electrochemiluminescence (ECL) and exonuclease-catalyzed target recycling amplification, the development of a highly sensitive aptasensor for Ochratoxin A (OTA) detection is described. The duplex DNA probes containing the biotin-modified aptamer are immobilized on a CdTe QD composite film-coated electrode. The presence of the OTA target leads to effective removal of the biotin-aptamers from the electrode surface via exonuclease-catalyzed recycling and reuse of OTA, which prevents the attachment of streptavidin-alkaline phosphatase (STV-ALP) through biotin-STV interaction. The electron transfer (ET) from the excited state CdTe QD ([CdTe](⁎)) to the electro-oxidized species of the enzymatic product of ALP during the potential scan is thus inhibited and the QD ECL emission is restored for quantitative OTA detection. Due to the exonuclease-catalyzed target recycling amplification, the inhibition effect of ET is significantly enhanced to achieve sensitive detection of OTA down to 0.64 pg mL(-1). The proposed method is selective for OTA and can be used to monitor OTA in real red wine samples. Our developed ECL recovery-based aptasensor thus offers great potential for the development of new ECL sensing platforms for various target analytes.