Exonuclease III-aided autocatalytic DNA biosensing platform for immobilization-free and ultrasensitive electrochemical detection of nucleic acid and protein

Highly sensitive biosensor for specific miRNA detection based on cascade signal amplification and magnetic electrochemiluminescence nanoparticles

Herein, magnetic electrochemiluminescence (ECL) nanoparticle Fe3O4@PtPd/Ru(bpy)32+ had been synthesized then been coupled with CRISPR/Cas13a system and Zn2+ dependent DNAzyme to design a novel ECL biosensor for specific detection of microRNA-145 (miRNA). The synthesized multifunctional magnetic nanoluminescent materials Fe3O4@PtPd/Ru(bpy)32+ not only load Ru(bpy)32+ to provide ECL signals, but also can quickly achieve separation and enrichment from complex matrices. In addition, ferrocene (Fc) was used as a quencher in the Ru(bpy)32+/tripropylamine (TPA) system. Fc was modified on DNA bound to Fe3O4@PtPd. Benefited from the highly specific recognition ability of CRISPR/Cas13a, the target miRNA induces CRISPR/Cas13a trans-cleavage to trigger the Zn2+-dependent DNAzyme cyclic cleavage to realize the dual signal amplification. DNA modified by Fc was split by target miRNA-induced cleaving, and then magnetic separation was performed to keep Fc away from the surface of the nanoparticles. Thus, the enhanced ECL signal was obtained to detect miRNA-145. Under optimized conditions, the prepared sensor showed a wide linear range (1 fM to 1 nM) and a low limit of detection (LOD) down to 0.41 fM. Furthermore, it shows excellent selectivity and good reproducibility. The proposed ECL platform has huge potential applications in the development of various sensitive sensors for detecting the other miRNA.

A dual-model immobilization-free photoelectrochemical/visual colorimetric bioanalysis based on microemulsion self-assemblies mediated multifunctional signal amplification strategy

Herein, a novel silver ion-loaded gold microemulsion assemblies (Au/Ag+ MAs) mediated multifunctional signal amplification strategy was proposed to construct a sensitive immobilization-free photoelectrochemical (PEC)/colorimetric biosensor for carcinoembryonic antigen (CEA) detection. Through the sandwiched reaction among CEA, the CEA aptamer (DNA1) loaded on the Au nanoparticles (NPs) functionalized iron oxide (Fe3O4) nanospheres and another CEA aptamer (DNA2) immobilized on Au/Ag+ MAs, a complex is formed and acquired by magnetic separation. Then, Au/Ag+ MAs of the complex are disassembled into Au NPs and Ag+ ions driven by an acetone response, and the obtained demulsification solution is transferred to the cadmium sulfide/cadmium telluride (CdS/CdTe) photoactive composites modified electrode. Based on the multiple inhibition functions (blocking effect of oleylamine; energy transfer effect of Au NPs; and electron snatching effect of Ag+), the photocurrent of the electrode decreases obviously, resulting in the ultrasensitive detection of CEA (a detection limit of 16 fg mL-1). Interestingly, the ion-exchange reactions between CdS/CdTe composites and Ag+ ions generate silver sulfide/silver telluride (Ag2S/Ag2Te) composites, and a color change of composites can be distinguished directly, leading to a quick visual detection of CEA. Compared with the traditional single-modal assay for CEA, such dual-modal PEC/colorimetric assay is a more accurate and reliable due to different mechanisms and independent signal conversion. This work will offer a new perspective for the applications of various self-assemblies in PEC bioanalysis.

Recent progress in optical and electrochemical aptasensor technologies for detection of aflatoxin B1

AFB1 (Aflatoxin B1) contamination is becoming a global concern issue due to its extraordinary occurrence, severe toxicity, as well as the great influence on the economic losses, food safety and environment. Therefore, it is desirable to develop novel analytical techniques for simple, rapid, accurate, and even point-of-care testing of AFB1. Fortunately, aptamer, considered as a new generation bioreceptor and even superior to classic antibody and enzyme, has been emerged remarkable application in food hazards detection. Correspondingly, aptasensors have been well-established toward AFB1 determination with outstanding performance. In this article, we first discuss and summarize the recent progress in optical and electrochemical aptasensors to monitor AFB1 over the past three years. In particular, the embedding of advanced nanomaterials for their improved analytical performance is highlighted. Furthermore, the critical analysis on various signal transduction strategies for aptasensors construction is discussed. Finally, we reveal the challenges and provide our opinion in future opportunities for aptasensor development.

Hybridization Chain Reaction-Based Electrochemical Biosensors by Integrating the Advantages of Homogeneous Reaction and Heterogeneous Detection

The conventional hybridization chain reaction (HCR)-based electrochemical biosensors usually require the immobilization of probes on the electrode surface. This will limit the applications of biosensors due to the shortcomings of complex immobilization processes and low HCR efficiency. In this work, we proposed astrategy for the design of HCR-based electrochemical biosensors by integrating the advantages of homogeneous reaction and heterogeneous detection. Specifically, the targets triggered the autonomous cross-opening and hybridization oftwobiotin-labeled hairpin probes to form long-nicked dsDNA polymers. The HCR products with many biotin tags were then captured by a streptavidin-covered electrode, thus allowing for the attachment of streptavidin-conjugated signal reporters through streptavidin-biotin interactions. By employing DNA and microRNA-21 as the model targets and glucose oxidase as the signal reporter, the analytical performances of the HCR-based electrochemical biosensors were investigated. The detection limits of this method were found to be 0.6 fM and 1 fM for DNA and microRNA-21, respectively. The proposed strategy exhibited good reliability for target analysis in serum and cellular lysates. The strategy can be used to develop various HCR-based biosensors for a wide range of applications because sequence-specific oligonucleotides exhibit high binding affinity to a series of targets. In light of the high stability and commercial availability of streptavidin-modified materials, the strategy can be used for the design of different biosensors by changing the signal reporter and/or the sequence of hairpin probes.

An accurate and ultrasensitive ratiometric electrochemical aptasensor for determination of Ochratoxin A based on catalytic hairpin assembly

Ochratoxin A (OTA) pollution in agricultural products has raised the pressing to develop sensitive, accurate and convenient detection methods. Herein, an accurate and ultrasensitive ratiometric electrochemical aptasensor was proposed based on catalytic hairpin assembly (CHA) for OTA detection. In this strategy, the target recognition and CHA reaction were both accomplished in the same system, which avoided tedious multi-steps operation and extra reagents, providing the advantage of convenience with only a one-step reaction and without enzyme. The labeled Fc and MB were used as the signal-switching molecules, avoiding various interferences and greatly improving the reproducibility (RSD: 3.197%). This aptasensor achieved trace-level detection for OTA with LOD of 81 fg/mL in the linear range of lower concentration (100 fg/mL-50 ng/mL). Moreover, this strategy was successfully applied to OTA detection in cereals with comparable results of HPLC-MS. This aptasensor provided a viable platform for accurate, ultrasensitive, and one-step detection of OTA in food.

Simulation-Guided Rational Design of DNA Probe for Accurate Discrimination of Single-Nucleotide Variants Based on "Hill-Type" Cooperativity

The accurate discrimination of single-nucleotide variants is of great interest for disease diagnosis and clinical treatments. In this work, a unique DNA probe with "Hill-type" cooperativity was first developed based on toehold-mediated strand displacement processes. Under simulation, this probe owns great thermodynamics advantage for specificity due to two mismatch bubbles formed in the presence of single-nucleotide variants. Besides, the strategies of ΔG' = 0 and more competitive strands are also beneficial to discriminate single-nucleotide variants. The feasibility of this probe was successfully demonstrated in consistent with simulation results. Due to "Hill-type" cooperativity, the probe allows a steeper dynamic range compared with previous probes. With simulation-guided rational design, the resulting probe can accurately discriminate single-nucleotide variants including nucleotide insertions, mutation, and deletions, which are arbitrarily distributed in target sequence. Two specificity parameters were calculated to quantitatively evaluate its good discrimination ability. Hence, "Hill-type" cooperativity can serve as a novel strategy in DNA probe's design for accurate discrimination of single-nucleotide variants.

Homogeneous Electrochemical Immunoassay Using an Aggregation-Collision Strategy for Alpha-Fetoprotein Detection

Homogeneous immunoassays represent an attractive alternative to traditional heterogeneous assays due to their simplicity and high efficiency. Homogeneous electrochemical assays, however, are not commonly accessed due to the requirement of electrode immobilization of the recognition elements. Herein, we demonstrate a new homogeneous electrochemical immunoassay based on the aggregation-collision strategy for the quantification of tumor protein biomarker alpha-fetoprotein (AFP). The detection principle relies on the aggregation of AgNPs induced by the molecular biorecognition between AFP and AgNPs-anti-AFP probes, which leads to an increased AgNP size and decreased AgNP concentration, allowing an accurate self-validated dual-mode immunoassay by performing nanoimpact electrochemistry (NIE) of the oxidation of AgNPs. The intrinsic one-by-one analytical capability of NIE as well as the participation of all of the atoms of the AgNPs in signal transduction greatly elevates the detection sensitivity. Accordingly, the current sensor enables a limit of detection (LOD) of 5 pg/mL for AFP analysis with high specificity and efficiency. More importantly, reliable detection of AFP in diluted human sera of hepatocellular carcinoma (HCC) patients is successfully achieved, indicating that the NIE-based homogeneous immunoassay shows great potential in HCC liquid biopsy.

Surface-tethered electrochemical biosensor for telomerase detection by integration of homogeneous extension and hybridization reactions

The general electrochemical biosensors for telomerase detection require the immobilization of primers on the electrode surface for telomeric extension and hybridization reactions. However, immobilization of primers may suffer from the challenges of hindrance effect and configuration freedom, thus reducing the extension and hybridization efficiency. Herein, we developed a sensitive electrochemical biosensor for telomerase detection by integration of homogeneous extension and hybridization reactions and surface-tethered detection. In the presence of telomerase, the biotinylated primer (bio-primer) was efficiently elongated with telomeric repeats of (TTAGGG)_n at the 3' end in solution. Then, the extension product (bio-DNA) was hybridized with the signal probe DNA modified on the surface of ferrocene (Fc)-capped gold nanoparticle (AuNP). The bio-DNA/DNA/Fc-AuNP hybrids were then tethered by streptavidin-modified electrodes through the specific avidin-biotin interactions, thus producing strong electrochemical signals from the oxidation of Fc tags. The biosensor was successfully used to determine telomerase in HeLa cells and monitor the inhibition efficiency of inhibitor. A wide linear range for the detection of telomerase extracted from HeLa cells was attained. This method has great potential in clinical diagnosis and anti-cancer drug development, and should be beneficial for the fabrication of novel biosensors by integration of homogeneous catalysis and hybridization reactions.

Fluorescence biosensing of the leukemia gene by combining Target-Programmed controllable signal inspiring engineering

Clinical diagnosis urgently requires ultrasensitive, accurate and rapid monitoring of low-abundance biomarkers. A biosensing strategy capable of detecting target genes at the femtomolar scale was designed in this work. In the biosensing strategy, the target can induce the specially designed hairpin probe H1 to self-fold and form a 3' blunt-ended structure. When there are the hybrid double-stranded P1-T1, ligase, polymerase and nickase, the target gene was recycled, and at the same time the system produces a lot of T1 and T2. T1 and T2 can simultaneously trigger HCR, causing the modified fluorophore FAM on the DNA strand to move away from the quencher group BHQ. The amplified fluorescent signal can be captured by a fluorescence instrument. It is exciting for us that three signal amplifications are involved to achieve femtomolar detection of target genes, namely target recycling, dual-triggered HCR of T1 and T2, and HCR. In addition, it still has good detection ability in actual samples simulated by serum. We expect that the sensing strategy proposed in this paper offers great potential for biomarker detection of leukemia for early clinical diagnosis.

A self-powered and reagent-less electrochemical aptasensor based on a DNA walker and tetraferrocene for the detection of aflatoxin B1

We constructed a self-powered and reagent-less electrochemical aptamer sensor for sensitive detection of aflatoxin B1 (AFB1). Here, the metal ion Mn²⁺ required for the DNAzyme to drive a DNA walker is wrapped in UIO-66(Zr)-(COOH)₂ and AFB1 triggers the DNAzyme walking strands to automatically and continuously cut the tetraferrocene-labeled substrate strands, which results in a significant decrease in the electrochemical signal. Under the optimal conditions, the concentration dependence of AFB1 is linear in the concentration range of 0.1 pg mL^-1 to 0.195 μg mL^-1, and the limit of detection is as low as 4.8 fg mL^-1. The sensor displayed good performance even for samples with a complex matrix, such as a peanut sample. The recoveries of AFB1 obtained ranged from 95.5 to 106.8%. The developed sensing platform is reagent-less, self-powered, and highly sensitive. It holds great potential for detection of AFB1 in environmental and food samples.

Proximity hybridization induced DNA assembly for label-free surface-enhanced Raman spectroscopic detection of carcinoembryonic antigen

In our research, label-free and surface-enhanced Raman dyes-free Raman spectroscopy which was used to detect carcinoembryonic antigen (CEA) according to poly adenine (Poly A)-regulated self-assembly methods was developed and studied. CEA induced partial hybridization of Ab-H2 and Ab-H1, and Ab-H1-CEA-Ab-H2 (a sandwich proximity CEA-DNA complex) was formed, which unfolded molecular beacon 1 (MB1) and modified the substrate. Subsequently, MB2-AuNPs were hybridized with MB1, and Ab-H1-CEA-Ab-H2 was released via toehold regulated displacements of DNA strands. Therefore, hybridization processes of MB2 and MB1 were induced and promoted by CEA-DNA complexes which worked as catalysts. The misplaced target then induced a next round of strand exchange, and the signals for determination of CEA were amplified by AuNPs absorbed on the substrate. It was indicated that the spectral characteristics of adenine at 736 cm^-1 were consistent with the SERS spectrum of DNA. Adenine acted as an internal marker for label-free SERS detection of CEA. Moreover, satisfactory stability and reproducibility were found. Meanwhile, the antibody could specifically recognize the corresponding antigen. Since adenine was dominant in SERS spectra, which was also proximal to Au surface, the sensitivity of the novel method was high without modifications. The analytical performance of this method in determining serum CEA was satisfactory.

Heterogeneous sensing of post-translational modification enzymes by integrating the advantage of homogeneous analysis

Heterogeneous analysis has great application prospects in the detection of post-translational modification (PTM) enzymes with the advantages of signal enhancement, less sample demand, and high sensitivity and selectivity. Nevertheless, once the substrate was fixed on a solid interface, the steric hindrance might limit the approaching of catalytic center to the substrate, thus reducing the efficiency of PTM. Herein, we suggested that the avidin-modified interface could be used to develop heterogeneous sensing platforms with biotin-labeled substrates as the probes, in which the enzymatic PTM was performed in solution and the heterogeneous assay was conducted on a solid surface. The sensing strategy integrates the advantages but overcomes the defects of both homogeneous and heterogeneous assays. Protein kinase A (PKA) and histone acetyltransferase (HAT) were determined as the examples by using sequence-specific peptide substrates. The signal changes were monitored by HRP-based colorimetric assay and antibody-amplified surface plasmon resonance (SPR). The methods were used for analysis of cell lysates and evaluation of inhibition efficiency with satisfactory results. The strategy can be used for the detection of a variety of biological enzymes and provide a new idea for the design of various heterogeneous biosensors. Thus, this work should be of great significance to the popularization and practical application of biosensors.

Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection

The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.

Electrochemical detection of kinase by converting homogeneous analysis into heterogeneous assay through avidin-biotin interaction

In the classical heterogeneous electrochemical assay, phosphorylation of peptide substrate is usually performed on the solid-liquid surface. However, immobilization of probe on the solid surface may limit the interaction between the reaction site of probe and the active center of kinase due to the steric hindrance effect. In this work, we proposed a heterogeneous electrochemical method for kinase detection, in which the probe is immobilization-free during the phosphorylation reaction. A biotinylated peptide was used as the kinase substrate. After phosphorylation, the biotinylated phosphopeptide was captured by the neutravidin (NA)-modified electrode through the avidin-biotin interaction. The phosphate groups on the electrode surface were then recognized by the conjugates preformed between biotinylated Phos-tag™ (Bio-tag-Phos) and ferrocene (Fc)-capped NA-modified gold nanoparticle (Fc-AuNP-NA). The method integrates the advantages of homogeneous reaction and heterogeneous detection with high simplicity, sensitivity and specificity. The strategy can be applied to design other heterogeneous biosensors without the immobilization of probe during the enzyme catalyzed reaction.

Using dual exonucleases to finely distinguish structural adjustment of aptamers for small-molecule detection

The binding of small molecules to their DNA aptamers can modulate their susceptibility to digestion by exonucleases, however, absolute differentiation between digestion and inhibition has never been reported. Here, we show that the digestion of aptamers by T7 exonuclease can be completely inhibited upon binding of small-molecule targets and exploit this finding for the first time to achieve sensitive, label-free small-molecule detection. We use a quinine-binding aptamer to show that target binding entirely halts T7 exonuclease digestion, leaving behind an intact double-stranded product that retains strong target affinity. On the contrary, digestion of nontarget-bound aptamer produces a single-stranded product incapable of target binding. Exonuclease I efficiently eliminates these single-stranded products but is unable to digest the target-bound double-stranded product. The remaining products can be fluorescently quantified with SYBR Gold to determine target concentrations, giving a limit of detection of 100 nM with the linear range from 0 to 8 μM. We demonstrate the first example of a dual-exonuclease-mediated approach capable of producing a concentration-dependent response in terms of aptamer digestion modules, therefore improving performance of the current aptamer-based assay for small-molecule detection.

Dual exonucleases to finely distinguish structural adjustment of aptamers to produce absolute differentiation between digestion and inhibition.

Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins

Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. The present targets can specifically compel the MH-template to transform into an "activate" conformation that primes a target-recyclable EXPAR. The method is simple and sensitive, can accurately and facilely detect long-chain single-stranded nucleic acids or proteins without the need of exogenous primer probes, and has a high amplification efficiency theoretically more than 2ⁿ. For a proof-of-concept demonstration, the SPEXPAR method was used to sensitively detect the characteristic sequence of the typical swine fever virus (CSFV) RNA and thrombin, as nucleic acid and protein models, with limits of detection down to 43 aM and 39 fM, respectively, and even the CSFV RNA in attenuated vaccine samples and thrombin in diluted serum samples. The SPEXPAR method may serve as a powerful technique for the biological research of single-stranded nucleic acids and proteins.

Ultrasensitive colorimetric strategy for Hg2+ detection based on T-Hg2+-T configuration and target recycling amplification

A novelty aptasensor for ultrasensitive detection of Hg²⁺ is developed, exploiting the combination of plasmonic properties of gold nanoparticles (AuNPs) and exonuclease III (Exo III)-assisted target recycling for signal amplification. In the presence of Hg²⁺, a DNA duplex can be formed due to the strong coordination of Hg²⁺ and T bases of single-stranded DNA (ssDNA) probe. Exo III digests the DNA duplex from the 3' to 5' direction, resulting in the releasing of Hg²⁺. Then, the released Hg²⁺ binds with another ssDNA probe through T-Hg²⁺-T coordination. After Exo III-assisted Hg²⁺ cycles, numerous ssDNA probes are exhausted, which promotes poly(diallyldimethylammonium chloride) (PDDA)-induced AuNP aggregation, leading to an obvious color change and aggregation-induced plasmon red shift of AuNPs (from 520 to 610 nm). Therefore, this biosensor is ultrasensitive, which is applicable to the detection of trace level of Hg²⁺ with a linear range from 5 pM to 0.6 nM and an ultralow detection limit of 0.2 pM. Furthermore, it enables visual detection of Hg²⁺ as low as 50 pM by the naked eye. More importantly, the assay can be applied to the reliable determination of spiked Hg²⁺ in sea water samples with good recovery.

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.

Surface plasmon resonance biosensor for the detection of miRNAs by combining the advantages of homogeneous reaction and heterogeneous detection

The hybridization and enzymolysis reactions for nucleic acid detection were carried out on the chip surface in the traditional surface plasmon resonance (SPR) biosensors. Herein, we proposed an innovative method for microRNA (miRNA) detection in which the hybridization-enzymolysis recycling reactions were performed in solution. Duplex-specific nuclease (DSN) and streptavidin-modified gold nanoparticles (SA-AuNPs) were employed for enhancing the assay sensitivity. In the absence of miRNA, the biotinylated DNA probe (bio-DNA-bio, biotin tags at both the 3' and 5' termini of DNA) was attached to the SA-modified chip through the SA-biotin binding, allowing the capture of SA-AuNPs with the same interaction. As a result, a larger SPR signal was attained. However, in the presence of miRNA, bio-DNA-bio hybridized with miRNA was digested by DSN. In this process, the miRNA strand remained intact and participated in the next hybridization-enzymolysis recycling process. Thus, one miRNA could promote the hydrolysis of many bio-DNA-bio probes and allow the generation of numerous bio-DNA fragments. Meanwhile, the produced bio-DNA competed with the undigested bio-DNA-bio to bind SA on the chip surface. The digestion of bio-DNA-bio and the competitive binding between bio-DNA-bio and bio-DNA led to the attachment of fewer SA-AuNPs and then smaller SPR signals. The change in SPR signal at the concentration as low as 1 fM miRNA has been readily determined. The strategy possessed the advantageous properties of simple operation, fast response, high sensitivity and excellent specificity, serving as a viable means for the fabrication of novel sensing platforms.

Electrochemical determination of caspase-3 using signal amplification by HeLa cells modified with silver nanoparticles

An electrochemical sensor capable of quantitative determination of caspase-3 activities was developed. A thiolated peptide whose sequence contained a caspase-3 cleaved site and a cell penetration sequence was preimmobilized onto an electrode. The quantification of caspase-3 was accomplished after cell penetration and the subsequent adsorption of silver nanoparticles (AgNPs). The oxidation current of AgNPs was found to be inversely proportional to the concentration of caspase-3 between 0.02 and 0.2 U/mL. A detection limit of 0.02 U/mL for caspase-3 was achieved due to the large number of positively charged AgNPs adsorbed onto the negatively charged cells. The proof of concept was demonstrated by monitoring the cleavage of surface-confined peptide substrates by caspase-3 in cell lysates. The current sensor could be extended to detect cells by replacing the surface-confined peptide with aptamers that recognize cells. Thus, the use of a cell as a matrix for AgNPs shows excellent potential for constructing electrochemical sensors and provides a useful alternative for sensor development in the future. Cells modified with silver nanoparticles were utilized as the electrochemical readout of an electrochemical assay.

Homogeneous electrochemical biosensor for microRNA based on enzyme-driven cascaded signal amplification strategy

Infectious diseases are a long-standing and severe global public health problem. The rapid diagnosis of infectious diseases is an urgent need to solve this problem. MicroRNA (miRNA) plays an important role in the intervention of some infectious diseases and is expected to become a potential biomarker for the diagnosis and prognosis of infectious diseases. It is of great significance to develop rapid and sensitive methods for detecting miRNA for effective control of infectious diseases. In this study, a simple and highly sensitive homogeneous electrochemical method for microRNAs using enzyme-driven cascaded signal amplification has been developed. In the presence of target miRNA, the reaction system produced plenty of MB-labeled single-nucleotide fragments (MB-MF) containing a few negative charges, which can diffuse to the negative surface of the ITO electrode easily, so an obvious electrochemical signal enhancement was obtained. Without the target, MB-HP contains a relatively large amount of negative charges due to the phosphates on the DNA chain, which cannot be digested by the enzyme and cannot diffuse freely to the negatively charged ITO electrode, so only a small signal was detected. The enhanced electrochemical response has a linear relationship with the logarithm of miRNA concentration in the range of 10 fM to 10 nM and the limit of detection as low as 3.0 fM. Furthermore, the proposed strategy showed the capability of discriminating single-base mismatch and performed eligibly in the analysis of miRNA in cell lysates, exhibiting great potential for disease diagnosis and biomedical research. Graphical abstract.

Highly sensitive host-guest mode homogenous electrochemical thrombin signal amplification aptasensor based on tetraferrocene label

The development of sensitive and convenient detection methods to monitor thrombin without the use of enzymes or complex nanomaterials is highly desirable for the diagnosis of cardiovascular diseases. In this article, tetraferrocene was first synthesized and then a sensitive and homogeneous electrochemical aptasensor was developed for thrombin detection based on host-guest recognition between tetraferrocene and β-cyclodextrin (β-CD). In the absence of thrombin, the double stem-loop of thrombin aptamer (TBA) prevented tetraferrocenes labeled at both ends from entering the cavity of β-CD deposited on gold electrode surface. After binding with thrombin, the stem-loop structure of TBA opened and transformed into special G-quarter structure, forcing tetraferrocene into the cavity of β-CD. As a result, thrombin allowed eight ferrocene molecules to reach the gold electrode surface, greatly amplifying the response signal. The obtained aptasensors showed dynamic detection range from 4 pM to 12.5 nM with detection limit around 1.2 pM. Overall, the results indicate that the proposed aptasensors are promising for future rapid clinical detection of thrombin and development of signal amplification strategies for detection of various proteins.

A sensitive homogenous aptasensor based on tetraferrocene labeling for thrombin detection

In this work, a novel homogeneous electrochemical aptasensor based on electrically assisted bond and tetraferrocene signal amplification was constructed for thrombin detection. Importantly, modification of the electrode is not necessary for this sensor, requiring only the construction of a simple and efficient probe. In addition, a brand new signal marker-tetraferrocene, containing four ferrocene molecules, was employed as a label to the terminal position of the probe. Compared with a single ferrocene moiety, tetraferrocene possesses a larger amplification signal for rapid detection of thrombin. In the detection of thrombin, the selected aptamer probe with a stem-loop structure was labeled with tetraferrocene at the 3' terminal and thiol at the 5' terminal, respectively. Confinement of the thiol to the stem-loop structure of the probe, the ability of thiol to reach the surface of electrode lossed even with the aid of the applied potential. However, upon treatment with the target protein of thrombin the stem-loop structure opened, promoting rapid attachment of the thiol group to the electrode interface generating Au-S self-assembly with the action of potential-assistance. The electrochemical signal of tetraferrocene could be measured by differential pulse voltammetry (DPV), which was subsequently used for target quantitative detection. This strategy displayed a detection limit as low as 0.126 pM, and an inherently high specificity for the detection of a single mismatch. Moreover, it exhibited advanced specificity against common interfering proteins.

Ultrasensitive colorimetric aptasensor for Hg2+ detection using Exo-III assisted target recycling amplification and unmodified AuNPs as indicators

Facile and ultrasensitive detection of Hg²⁺ in water environment remains challenging. Exonuclease III (Exo-III)-assisted target recycling is one of the most popular amplification strategies. Although the magnesium (II) ions are widely acting as cofactors of Exo-III, we recognized that Mg²⁺ cofactors would strongly disturb the charge distribution on citrate-stablized gold nanoparticles (in the general sense, unmodified AuNPs) surface, thus generate false positive colorimetric signals. To address this issue, we first put forward the view that the cobalt (II) ions can function as the Exo-III cofactor and successfully construct a novel label-free colorimetric aptasensor for facile and ultrasensitive detection of Hg²⁺ using Hg²⁺-triggered Exo-III-assisted signal amplification and unmodified AuNPs as indicators. A hairpin-looped DNA probe was rationally designed with thymine-rich recognition termini and specifically recognized trace Hg²⁺ by a stable T-Hg²⁺-T structure. A blue-to-red color change of AuNPs with the addition of Hg²⁺ provided the quantitative detection of Hg²⁺ with a limit of detection of 0.2 nM and a linear working range from 0.5 nM to 5.0 nM. The whole testing time for one assay was approximately 40 min. Real water samples, even containing Hg²⁺ at 1 nM, could be determined by the aptasensor with recovery rates from 97% to 103%.

Immobilization-free photoelectrochemical aptasensor for environmental pollutants: Design, fabrication and mechanism

Atrazine (ATZ) is one of the most widely used and highly toxic triazine herbicides in the world. Photoelectrochemical (PEC) method is an attractive and sensitive alternate for ATZ. However, for conventional PEC sensors, recognition elements usually need to immobilize on electrode surface, where a complex procedure is unavoidable and the reproducibility of sensors fabrication is usually poor. Therefore, we herein proposed a new and feasible strategy for developing a signal-on immobilization-free PEC aptasensor to ATZ. Aptamer for ATZ is combined with graphene to obtain APT-GN complex, serving as the recognition element in solution. TiO₂ nanotubes (NTs) electrode deposited with Au nanoparticles (NPs) is used as the substrate electrode. After further self-assembled with 1-Mercaptooctane (MCT), the photo-generated carriers transfer between the resultant electrode and the electrolyte will be blocked, leading to a signal-off of the photocurrent. But when sensing ATZ, aptamers on APT-GN will be grasped by ATZ, leaving free graphene to assemble onto MCT/Au NPs/TiO₂ NTs, which will largely "turn on" the photocurrent response of the substrate electrode due to the efficient carrier transport efficiency of graphene. Meanwhile, simultaneous addition of deoxyribonuclease I (DNase I) can bring about further cycling amplification of the signal enhancement. The as-designed PEC aptasensor exhibits a linear range from 50.0 fM to 0.3 nM with detection limit of 12.0 fM for ATZ. Since the reaction of recognition elements and targets ATZ occurs in homogeneous solution rather than on the photoelectrode surface, this PEC aptasensor exhibits advantages of high stability, anti-interference ability, reproducibility, and wide pH and ion strength feasibility range. A promising immobilization-free aptasensing platform has thus been provided not only for ATZ but also for other kinds of environmental pollutants.

Photoelectrochemical biosensor of HIV-1 based on cascaded photoactive materials and triple-helix molecular switch

In this work, an ultrasensitive photoelectrochemical (PEC) biosensor was proposed to detect nucleic acids on the basis of cascaded photoactive materials and triple-helix molecular switch. DNA sequence of human immunodeficiency virus type 1 (HIV-1) was chosen as the target DNA (T-DNA). Cascaded photoactive structure was formed via different sizes of CdTe quantum dots (QDs) sensitized ZnO nanorods (ZnO NRs), which was employed as a cascaded photoactive interface to amplify the photocurrent signal. A hairpin structure DNA (H-DNA) as capture probe was conjugated onto the photoactive interface through amide bond, and then a single-stranded DNA modified with gold nanoparticles labeled alkaline phosphatase (ALP-Au NPs-DNA) at each end was introduced to hybridize with the H-DNA to form a triple-helix conformation. The T-DNA detection was based on the photocurrent response change resulted from conformation change of the triple-helix molecule after hybridization with T-DNA. In the absence of T-DNA, the triple-helix molecule was in a closed state and the ALP of ALP-Au NPs-DNA could specifically catalyze the ascorbic acid 2-phosphate (AAP) to generate ascorbic acid (AA) as electron donors, which resulted in a significant photocurrent response due to the rapid electron transfer process. However, in the presence of T-DNA, the T-DNA hybridized with the ALP-Au NPs-DNA molecule, which caused triple-helix molecule in an opened state and compelled ALP-Au NPs-DNA away from the electrode surface, resulting in the absence of ALP which could catalyze AAP to generate AA. Subsequently, the photocurrent response significantly decreased. The proposed PEC biosensor not only had a wide detection range of 1fM-1nM and low detection limit (0.65 fM), but also showed excellent reproducibility, specificity and stability, which had great application prospect and opened up a new research method in the early clinical diagnosis and cancer research.

Duplexed aptamers: history, design, theory, and application to biosensing

Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.

Electrochemical DNA Biosensing via Electrochemically Controlled Reversible Addition-Fragmentation Chain Transfer Polymerization

Sensitive and selective sensing of biological molecules is fundamental to disease diagnosis and infectious disease surveillance. Herein, an ultrasensitive and highly selective electrochemical DNA biosensor is described by exploiting the electrochemically controlled reversible addition-fragmentation chain-transfer (eRAFT) polymerization as a signal amplification strategy and the peptide nucleic acid (PNA) probes as the recognition elements. Specifically, the PNA probes with a thiol at their 5'-terminals are anchored to a gold electrode surface (via gold-sulfur self-assembly) for sequence-specific recognition of target DNA (tDNA) fragments, of which the phosphate sites serve as the anchorages for the targeted labeling (via the well-established phosphate-Zr⁴⁺-carboxylate chemistry) of the carboxyl-group-containing chain-transfer agents (CTAs) for the succedent eRAFT polymerization, wherein the initiating radicals are generated through electrochemical reduction of aryl diazonium salts under a potentiostatic condition. In the presence of ferrocenylmethyl methacrylate (FcCH═CH₂) as the monomer, the grafting of polymer chains from the CTA-anchored sites as a result of the eRAFT polymerization brings numerous electroactive Fc tags to the electrode surface, outputting a high electrochemical sensing signal even in the presence of trace amounts of tDNA fragments. Under the optimized conditions, the linear range of the described electrochemical DNA biosensor spans from 10 aM to 10 pM ( R² = 0.998), with an attomolar detection limit (4.1 aM) being achieved. Moreover, the described electrochemical DNA biosensor is highly selective and applicable to the sensing of tDNA fragments in complex serum samples. Given its high efficiency, easy operation, and low cost, this biosensor shows great promise in real applications.

Application of hairpin DNA-based biosensors with various signal amplification strategies in clinical diagnosis

Biosensors have been commonly used in biomedical diagnostic tools in recent years, because of a wide range of application, such as point-of-care monitoring of treatment and disease progression, drug discovery, commonly use food control, environmental monitoring and biomedical research. Additionally, development of DNA biosensors has been increased enormously over the past few years as confirmed by the large number of scientific publications in this field. A wide range of techniques can be used for the development of DNA biosensors, such as DNA nano-machines and various signal amplification strategies. This article selectively reviews the recent advances in DNA base biosensors with various signal amplification strategies for detection of cancer DNA and microRNA, infectious microorganisms, and toxic metal ions.

Exonuclease III-assisted multiple cycle amplification for the sensitive detection of DNA with zero background signal

Detection of low-abundant DNA is essential for disease diagnosis and treatment. DNA polymerase-based amplification is frequently used due to its excellent sensitivity, but it suffers from time-consuming and labour-intensive procedures, complex template/primer design, and inherent nonspecific amplification. Alternatively, Exonuclease III (Exo III)-assisted target recycling provides a new approach for DNA assay because of its simplicity and general applicability, but it suffers from high background signal due to the nonspecific Exo III digestion and poor sensitivity due to single cycle signal amplification. Herein, we demonstrate the development of Exo III-assisted multiple cycle amplification (exonuclease chain reaction) for the sensitive detection of DNA with zero background signal. The binding of single-stranded DNA binding protein (SSB) to the hairpin probes can protect them from nonspecific digestion by Exo III, resulting in near zero background signal. The presence of the target DNA initiates the Exo III-triggered multiple cycle amplification, enabling the achievement of high sensitivity with a detection limit of 3 fM and excellent selectivity with single base mismatch discrimination capability, holding great potential in disease diagnosis and biomedical research.

An ultrasensitive electrochemical immunoassay based on a proximity hybridization-triggered three-layer cascade signal amplification strategy

An ultrasensitive electrochemical immunoassay based on a proximity hybridization-triggered three-layer cascade signal amplification strategy.

Recognition-Enhanced Metastably Shielded Aptamer for Digital Quantification of Small Molecules

Aptamers are recognized as competitive affinity reagents; their application, however, often suffers from their relatively low target binding affinity, especially for small molecules. We herein introduce the concept of a recognition-enhanced metastably shielded aptamer probe (RMSApt) and explore its performance for digital quantification of low-affinity small molecules. The RMSApt design employs the idea of constructing an allosteric aptamer probe conferring a minor energy gap in the recognition switch process to facilitate target binding and probe response, in turn significantly improving the recognition efficiency for low-affinity targets. The probe design strategy boosts the application of aptamers for precisely quantifying targets with a dissociation constant K_d ranging from 10^-4 to 10^-9 M, which would cover most of the small-molecule species that exist binding aptamers. Thus, RMSApt would facilitate the translation of aptamers for medical diagnosis, food safety, and environmental screening.

Electrochemical detection of tobramycin based on enzymes-assisted dual signal amplification by using a novel truncated aptamer with high affinity

An aptamer with the length of only 15 nucleotides specific for tobramycin was obtained through rationally designed truncation from a previously reported long sequence. The structural and binding properties of the aptamer were characterized. The dissociation constant (K_d) was determined to be 42.12 nM, indicating high affinity of the aptamer for tobramycin. Then an electrochemical sensor based on this aptamer was developed, which employed an enzymes-assisted dual signal amplification cycle through target recycling and strand-displacement DNA polymerization. A hairpin probe containing the aptamer sequence was designed and used to start the production cycle of a short ssDNA fragment in the presence of tobramycin, with the help of phi29 DNA polymerase and nicking endonuclease Nt.AlwI. The ssDNA fragment was captured by a signal transduction probe modified on gold electrode to form a triple-helix structure. With the help of [Ru(NH₃)₆]³⁺, a significant electrochemical signal was observed in differential pulse voltammetry (DPV). Under the optimal conditions, the current in DPV is linearly related with the concentration of tobramycin in the range of 10-200 nM, and the detection limit is 5.13 nM. The electrochemical sensor showed high specificity for tobramycin when it was challenged by other antibiotics. In addition, the constructed sensor was used to detect tobramycin in milk and water samples, and showed satisfactory performance. Therefore, the screened aptamer as well as the developed sensor has great application prospects in the fields of food safety control, medical test and environment monitoring.

A dual-channel homogeneous aptasensor combining colorimetric with electrochemical strategy for thrombin

In this protocol, a dual-channel homogeneous aptasenor was proposed for protein molecule determination, employing thrombin as target analyte. The colorimetric and electrochemical transducers were combined in a single analytical system for signal readout. In this dual-channel sensing strategy, the G-quadruplex sequence was released and incorporated with hemin to form DNAzyme for naked-eye colorimetric detection. Meanwhile, the hydroxyapatite nanoparticle as signal probe was combined with magnetic nanoparticles to construct sandwich-type structure for generating the electrochemical current when thrombin was present in solution. By introducing two kinds of reporter probes and transducers, this dual-channel sensor produced two different kinds of signal to improve the analytical accuracy and diversity. The results revealed that the dual-channel sensor achieved the quantatitive determination of thrombin with low limit of detection (0.40 fM) and wide range (0.1 fM to 1 nM), which offer a promise for rapid and accurate detection of biomolecule.

Homogeneous electrochemical aptasensor for mucin 1 detection based on exonuclease I-assisted target recycling amplification strategy

A sensitive and homogeneous electrochemical aptasensor was fabricated for the detection of mucin 1 (MUC1) by combining a well-designed DNA bulge-loop (L-DNA) structure with high-efficient exonuclease I (Exo I)-assisted target recycling amplification strategy. The L-DNA probe was constructed via the hybridization of the MUC1 aptamer and methylene blue (MB) labeled complementary DNA (cDNA) (cDNA-MB) and hence could not diffuse freely to the negatively charged ITO electrode surface due to the strong electrostatic repulsion, so small electrochemical signal was detected. The addition of MUC1 caused the dissociation of L-DNA structure due to the specificity between aptamer and MUC1. Then Exo I was implemented to digest the released cDNA-MB into mononucleotides and then produced short MB-labeled mononucleotides fragments (MB-MFs). As the MB-MFs contained few negative charges, it diffused easily to the negatively charged ITO electrode surface and resulted in the enhanced electrochemical signal. Meanwhile, the MUC1-aptamer complex was also specifically digested by Exo I, resulting in the liberation of MUC1 and hence realized the target recycling and then caused the amplification of the electrochemical signal. The enhanced electrochemical signal has a good linear relationship with logarithm of MUC1 concentration in the range of 1.0 pg mL^-1-50 ng mL^-1 with a limit of detection of 0.40 pg mL^-1 (S/N = 3). Additionally, the fabricated aptasensor has been successfully applied to detect MUC1 in serum samples with satisfactory results and thereby it exhibits great potential in the practical application of clinical diagnosis.

Homogeneous and label-free electrochemiluminescence aptasensor based on the difference of electrostatic interaction and exonuclease-assisted target recycling amplification

The difference of electrostatic interaction between free Ru(phen)₃²⁺ and Ru(phen)₃²⁺ embedded in double strand DNA (dsDNA) to the negatively charged indium tin oxide (ITO) electrode has been applied to develop a homogeneous and label-free electrochemiluminescence (ECL) aptasensor for the first time. Ochratoxin A (OTA) has been chosen as the model target. The OTA aptamer is first hybridized with its complementary single strand DNA (ssDNA) to form dsDNA and then interacted with Ru(phen)₃²⁺ via the grooves binding mode to form dsDNA-Ru(phen)₃²⁺ complex, which remains negatively charged feature as well as low diffusion capacity to the negatively charged ITO electrode surface owing to the electrostatic repulsion. Meanwhile, the intercalated Ru(phen)₃²⁺ in the grooves of dsDNA works as an ECL signal reporter instead of the labor-intensive labeling steps and can generate much more ECL signal than that from the labeling probe. In the presence of target, the aptamer prefers to form an aptamer-target complex in lieu of dsDNA, which induces the releasing of Ru(phen)₃²⁺ from the dsDNA-Ru(phen)₃²⁺ complex into the solution. With the assistance of RecJ_f exonuclease (a ssDNA specific exonuclease), the released ssDNA and the aptamer in the target-complex were digested into mononucleotides. In the meantime, the target can be also liberated from OTA-aptamer complex and induce target cycling and large amount of free Ru(phen)₃²⁺ present in the solution. Since Ru(phen)₃²⁺ contains positive charges, which can diffuses easily to the ITO electrode surface because of electrostatic attraction, causing an obviously enhanced ECL signal detected. Under the optimal conditions, the enhanced ECL of the system has a linear relationship with the OTA concentration in the range of 0.01-1.0 ng/mL with a detection limit of 2 pg/mL. This innovative system not only expands the immobilization-free sensors in the electrochemiluminescent fields, but also can be developed for the detection of different targets easily with the same strategy by changing the aptamer used.

Homogeneous electrochemical aptasensor based on a dual amplification strategy for sensitive detection of profenofos residues

A homogeneous type of electrochemical aptasensor was designed based upon the principle of target-induced and tool enzyme-assisted signal amplification, which was employed for the detection of profenofos residues.

Kinetically-enhanced DNA detection via multiple-pass exonuclease III-aided target recycling

One of the promising approaches to address the challenge of detecting dilute nucleic acid analytes is exonuclease III-aided target recycling. In this strategy, the target DNA self-assembles with the reactant DNA probes and displays itself as a reactant and product at the same time. This provides an autonomous mechanism to release and reuse the analyte from each round of reactions for repetitive cycles, which amplifies the signal without amplifying the analyte itself. However, for very low amounts of the analyte, it takes a considerably long time before a detectable signal is generated. Thus, in this paper, we report a kinetically-enhanced target recycling strategy by designing two more target recycling sub-reactions that are triggered by the byproducts of the first reaction involving the target analyte. In this manner, concentrations of up to 0.5 pM of target DNA can be detected in 15 minutes.

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.