A cascade autocatalytic strand displacement amplification and hybridization chain reaction event for label-free and ultrasensitive electrochemical nucleic acid biosensing

Electrochemiluminescence Biosensor Based on a Duplex-Specific Nuclease and Dual-Output Toehold-Mediated Strand Displacement Cascade Amplification Strategy for Sensitive Detection of MicroRNA-499

The timely and accurate diagnosis of acute myocardial infarction (AMI) is of great significance to reduce mortality and morbidity associated with the condition. Herein, we developed an electrochemiluminescence (ECL) biosensor for the detection of the potential AMI biomarker microRNA-499 (miRNA-499), which was based on duplex-specific nuclease-assisted target recycling and dual-output toehold-mediated strand displacement (TMSD). First, miRNA-499 was converted into a large amount of single-stranded DNA through the DSN-assisted target recycling, which was further incubated with the DNA triple-stranded complex (S) to implement TMSD cycles. Thus, the Ru(bpy)32+-labeled signal strands were released and captured by the capture probe on the electrode surface, resulting in an intense ECL signal. Owing to the prominent cascade signal amplification, the constructed biosensor exhibited a good linear response to miRNA-499 within the range of 100 aM-100 pM with a detection limit of 69.99 aM. Furthermore, it demonstrated superior selectivity, stability, and reproducibility. In addition, the biosensor was successfully applied to detect miRNA-499 in real human serum samples, demonstrating its potential for nucleic acid detection in the early diagnosis of diseases.

One-step cascade amplification system based on entropy-driven catalysis and DNAzyme triggered DNA walker for label-free detection of acetamiprid

Herein, an electrochemical aptasensor for highly sensitive detection of acetamiprid (ACE) was constructed based on a one-step cascade amplification strategy. This innovative strategy integrated DNA walker containing DNAzyme sequence into entropy-driven catalysis (EDC) system. The trigger strand was released by aptamer-specific binding to ACE, initiating the EDC amplification circuit and delivering DNA walker strands. The dangling DNA walker continuously bound and cleaved hairpin substrate to form G-quadruplex fragments with the assistance of Mg2+. The G-quadruplex fragments folded and captured hemin to form multitudinous G-quadruplex/hemin complexes in the presence of K+, generating significantly enhanced current, enabling enzyme-free, label-free and highly sensitive detection of ACE, with a linear detection range of 100 fM to 50 nM and a detection limit of 68.36 fM (S/N = 3). The constructed aptasensor achieved the reliable detection of ACE in vegetable soil and cucumber samples, demonstrating its potential application prospects in environmental protection and food supervision.

Ratiometric electrochemical biosensor based on hybridization chain reaction signal amplification for sensitive microRNA-155 detection

In this work, a sensitive ratiometric electrochemical biosensor for microRNA-155 (miRNA-155) detection is reported based on a hybridization chain reaction amplifying the electrochemical signal. The biosensor was fabricated using Au NPs as a modified material to assemble capture DNA labeled with ferrocene (Fc) molecules, and a DNA probe labeled with methylene blue (MB) was employed for the signal probe. In the presence of target miRNA-155, it can be dual hybridized with capture and signal probe, especially with signal probe to continuously produce long concatemers containing lots of MB molecules. The electrochemical signal of Fc was used for the internal signal, and the signal from MB was used as an indicator signal. As the concentration of miRNA-155 was altered, the internal reference signal of Fc remained constant, and only the indicator signal changed in a sensitive way. The change in the ratio (IMB/IFc) between the indicator signal of MB and internal reference signal of Fc can be used to monitor the concentration of miRNA-155. Under optimal conditions, the prepared ratiometric biosensor could detect miRNA-155 within a wide linear range from 100 fM to 100 nM with low detection limit of 33 fM (at S/N = 3). Moreover, the biosensor was evaluated with human serum samples, and satisfactory recoveries were obtained, indicating that the ratiometric biosensor can be applied to clinical sample analysis.

Programmable DNA tweezers-SDA for ultra-sensitive signal amplification fluorescence sensing strategy

BACKGROUND

DNA tweezers, classified as DNA nanomachines, have gained prominence as multifunctional biosensors due to their advantages, including a straightforward structure, response mechanism, and high programmability. While the DNA tweezers demonstrate simultaneous, rapid, and stable responses to different targets, their detection sensitivity requires enhancement. Some small molecules, such as mycotoxins, often require more sensitive detection due to their extremely high toxicity. Therefore, more effective signal amplification strategies are needed to further enhance the sensitivity of DNA tweezers in biosensing.

RESULTS

We designed programmable DNA tweezers that detect small-molecule mycotoxins and miRNAs through simple sequence substitution. While the DNA tweezers demonstrate simultaneous, rapid, and stable responses to different targets, their detection sensitivity requires enhancement. We introduced the Strand Displacement Amplification (SDA) technique to address this limitation, proposing a strategy of novel programmable DNA tweezers-SDA ultrasensitive signal amplification fluorescence sensing. We specifically investigate the effectiveness of this approach concerning signal amplification for two critical mycotoxins: aflatoxin B1 (AFB1) and zearalenone (ZEN). Results indicate that the detection ranges of AFB1 and ZEN via this strategy were 1-10,000 pg mL -1 and 10-100,000 pg mL -1, respectively, with corresponding detection limits of 0.933 pg mL -1 and 1.07 pg mL -1. Compared with the DNA tweezers direct detection method for mycotoxins, the newly constructed programmable DNA tweezers-SDA fluorescence sensing strategy achieved a remarkable 104-fold increase in the detection sensitivity for AFB1 and ZEN.

SIGNIFICANCE

The constructed programmable DNA tweezers-SDA ultrasensitive signal-amplified fluorescence sensing strategy exhibits excellent detection performance for mycotoxins. The superb versatility of this strategy allows the developed method to be easily used for detecting other analytes by simply replacing the aptamer and cDNA, which has incredible potential in various fields such as food safety screening, clinical diagnostics, and environmental analysis.

A rapid and highly sensitive ctDNA detection platform based on locked nucleic acid-assisted catalytic hairpin assembly circuits

As a promising biomarker of liquid biopsy, circulating tumor DNA (ctDNA) plays a paramount role in the early diagnosis of noninvasive cancer. The isothermal catalytic hairpin assembly (CHA) strategy has great potential for in vitro detection of ctDNA in low abundance. However, a traditional CHA strategy for ctDNA detection at the earlier stages of cancer remains extremely challenging, as annoying signal leakage from the 'breathing' phenomenon and nuclease degradation occur. Herein, we report a locked nucleic acid (LNA)-incorporated CHA circuit for the rapid and sensitive detection of target ctDNA. The target ctDNA intelligently catalyzed LNA-modified hairpins H1 and H2via a range of toehold-mediated strand displacement processes, leading to the continuous generation of an H1-H2 hybrid for the amplified fluorescence signal. In comparison to conventional CHA circuits, the stronger binding affinity of LNA-DNA bases greatly inhibited the breathing effect, which endowed it with greater thermodynamic stability and resistance to nuclease degradation in the LNA-assisted CHA system, thus achieving a high signal gain. The developed CHA circuit demonstrated excellent performance during target ctDNA detection, with a linear range from 10 pM to 5 nM, and its target detection limit was reached at 3.3 pM. Moreover, this LNA-assisted CHA system was successfully applied to the analysis of target ctDNA in clinical serum samples of breast cancer patients. This updated CHA system provides a general and robust platform for the sensitive detection of biomarkers of interest, thus facilitating the accurate identification and diagnosis of cancers.

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.

Target Recognition- and HCR Amplification-Induced In Situ Electrochemical Signal Probe Synthesis Strategy for Trace ctDNA Analysis

An electrochemical-DNA (E-DNA) sensor was constructed by using DNA metallization to produce an electrochemical signal reporter in situ and hybridization chain reaction (HCR) as signal amplification strategy. The cyclic voltammetry (CV) technique was used to characterize the electrochemical solid-state Ag/AgCl process. Moreover, the enzyme cleavage technique was introduced to reduce background signals and further improve recognition accuracy. On the basis of these techniques, the as-prepared E-DNA sensor exhibited superior sensing performance for trace ctDNA analysis with a detection range of 0.5 fM to 10 pM and a detection limit of 7 aM. The proposed E-DNA sensor also displayed excellent selectivity, satisfied repeatability and stability, and had good recovery, all of which supports its potential applications for future clinical sample analysis.

Label-free fluorescent aptasensor for chloramphenicol based on hybridization chain reaction amplification and G-quadruplex/N-methyl mesoporphyrin IX complexation

The use of the broad-spectrum antibiotic chloramphenicol (CAP) in food is strictly regulated or banned in many countries. Herein, for the sensitive, rapid, and specific detection of CAP in milk, a label-free fluorescence strategy was established based on guanine (G)-quadruplex/N-methyl mesoporphyrin IX (NMM) complex formation and hybridization chain reaction (HCR) amplification. In this system, CAP can specifically bind to an aptamer (Apt) to release an Apt-C sequence from double-stranded DNA (Apt·Apt-C). Apt-C, can further hybridize with a functional hairpin DNA probe to release a primer sequence. The released primer sequence causes HCR and the formation of a nicked double-helix polymer, which contains G-quadruplex DNA. The recognition of G-quadruplex DNA by the NMM fluorochrome results in fluorescence enhancement. Consequently, CAP can be quantitatively detected by measuring the fluorescence intensity at 612 nm. The reliability of the aptasensor method was confirmed by comparison with an enzyme-linked immunosorbent assay. The proposed aptasensor was found to have a limit of detection of 0.8 pg mL-1 for CAP. Moreover, when the aptasensor was applied to the detection of CAP in milk samples, the average recoveries were 99.8-108.3% with relative standard deviations of 4.5-5.2%. Thus, this CAP detection method, which is rapid with high sensitivity and selectivity, has considerable potential for a wide range of food analysis applications.

Recent Advances in Signal Amplification to Improve Electrochemical Biosensing for Infectious Diseases

The field of infectious disease diagnostics is burdened by inequality in access to healthcare resources. In particular, “point-of-care” (POC) diagnostics that can be utilized in non-laboratory, sub-optimal environments are appealing for disease control with limited resources. Electrochemical biosensors, which combine biorecognition elements with electrochemical readout to enable sensitive and specific sensing using inexpensive, simple equipment, are a major area of research for the development of POC diagnostics. To improve the limit of detection (LOD) and selectivity, signal amplification strategies have been applied towards these sensors. In this perspective, we review recent advances in electrochemical biosensor signal amplification strategies for infectious disease diagnostics, specifically biosensors for nucleic acids and pathogenic microbes. We classify these strategies into target-based amplification and signal-based amplification. Target-based amplification strategies improve the LOD by increasing the number of detectable analytes, while signal-based amplification strategies increase the detectable signal by modifying the transducer system and keep the number of targets static. Finally, we argue that signal amplification strategies should be designed with application location and disease target in mind, and that the resources required to produce and operate the sensor should reflect its proposed application, especially when the platform is designed to be utilized in low-resource settings. We anticipate that, based on current technologies to diagnose infectious diseases, incorporating signal-based amplification strategies will enable electrochemical POC devices to be deployed for illnesses in a wide variety of settings.

Isothermal nucleic acid amplification technology for rapid detection of virus

While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.

In Situ Assembly of Nanomaterials and Molecules for the Signal Enhancement of Electrochemical Biosensors

The physiochemical properties of nanomaterials have a close relationship with their status in solution. As a result of its better simplicity than that of pre-assembled aggregates, the in situ assembly of nanomaterials has been integrated into the design of electrochemical biosensors for the signal output and amplification. In this review, we highlight the significant progress in the in situ assembly of nanomaterials as the nanolabels for enhancing the performances of electrochemical biosensors. The works are discussed based on the difference in the interactions for the assembly of nanomaterials, including DNA hybridization, metal ion-ligand coordination, metal-thiol and boronate ester interactions, aptamer-target binding, electrostatic attraction, and streptavidin (SA)-biotin conjugate. We further expand the range of the assembly units from nanomaterials to small organic molecules and biomolecules, which endow the signal-amplified strategies with more potential applications.

Rapid heavy metal sensing platform: A case of triple signal amplification strategy for the sensitive detection of serum copper

Heavy metals are considered as hazardous substances to human because of their toxicity, persistence and bioaccumulation, and the level in serum is an important factor to evaluate the caused health risk, which depends on efficient and sensitive analytical methods. Here, a triple signal-amplified electrochemical sensing platform based on metal-dependent DNAzymes was fabricated for sensitive determination of heavy metals in serum (copper as a model target). Under the optimized conditions, the proposed method showed good sensitivity (limit of detection, 0.33 fM for Cu²⁺) with excellent selectivity and stability, which is ascribed to: (i) tetrahedral DNA nanostructures (TDNs) that was used as a promising scaffold to adjust the selective transformation between heterogeneous and homogeneous reactions, preventing the nonspecific binding of electrodes surface and DNA probes; (ii) the magnetic beads (MBs) used which led to signal amplification and decreased background owing to its excellent properties of extracting equivalent targets from the complex samples; (iii) two signal amplification strategy of catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR). In addition, the proposed sensing platform displayed satisfactory accuracy through the validation with inductively coupled plasma-mass spectrometry (ICP-MS) and a spike-recovery analysis (recoveries, 87.92-111.61%; RSD, 4.89-8.85%), indicating the great potential for rapid and sensitive detection of Cu²⁺ or other metal ions.

Multifunctional electrochemical biosensor with "tetrahedral tripods" assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA

Nucleic acids are genetic materials in the human body that play important roles in storing, copying, and transmitting genetic information. Abnormal nucleic acid sequences, base mutations, and genetic changes often lead to cancer and other diseases. Meanwhile, methylated DNA is one of the main epigenetic modifications, which is considered to be an excellent biomarker in the early detection, prognosis, and treatment of cancers. Therefore, a multifunctional electrochemical biosensor was constructed with sturdy tetrahedral tripods, which assisted multiple tandem hairpins through base complementary pairing and effective ultra-sensitive detection of targets (DNA, microRNA, and methylated DNA). In the experiments, experimental conditions were optimized, and different DNA concentrations in serum were detected to verify the sensitivity of the biosensor and the feasibility of this protocol. In addition, microRNA and DNA methylation were detected through different designs of tetrahedral tripods (TTs) that capture probes to prove the superiority of this scheme. A sturdy pyramid structure of TTs extremely enhanced the capture efficiency of targets. The targets triggered the one-step isothermal multi-tandem amplification reaction by incubating multiple hairpin assemblies. To our knowledge, a combination of two parts, which greatly reduced background interference and decreased non-specific substance interference, has appeared for the first time in this paper. Moreover, the load area of electrochemical substances was significantly increased than that in previous studies. This greatly increased the detection range and detection limit of targets. The electrochemical signal responses were generated in freely diffusing hexaammineruthenium(iii) chloride (RuHex). RuHex could adhere to the DNA phosphate backbone by a powerful electrostatic attraction, causing increased current responses.

Schematic illustration of the fabricated electrochemical biosensor. TTs assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA.

Application of tetrahedral -deoxyribonucleic acid electrochemistry platform coupling aptazymes and hybridized hairpin reactions for the measurement of extracellular adenosine triphosphate in plants

Extracellular ATP (eATP) is an important biological signal transduction molecule. Although a variety of detection methods have been extensively used in ATP sensing and analysis, accurate detection of eATP remains difficult due to its extremely low concentration and spatiotemporal distribution. Here, an eATP measurement strategy based on tetrahedral DNA (T-DNA)-modified electrode sensing platform and hybridization chain reaction (HCR) combined with G-quadruplex/Hemin (G4/Hemin) DNAzyme dual signal amplification is proposed. In this strategy, ATP aptamer and RNA-cleaving DNAzyme were combined to form a split aptazyme. In the presence of ATP, this aptazyme hydrolyzes the cleaving substrate strand with high selectivity, releasing cleaved ssDNA, which are captured by the T-DNA assembled on the electrode surface, triggering an HCR on the electrode surface to form numerous linker sequences of the HCR dsDNA product. When G-quadruplex@AuNPs (G4) spherical nucleic acid enzymes (SNAzymes) with other linkers are used as nanocatalyst tags, they are captured by HCR dsDNA through sticky linkers present on the electrode surface. An amplified electrochemical redox current signal is generated through SNAzyme-mediated catalysis of H₂O₂, enabling easy detection of picomole amounts of ATP. Using this strategy, eATP levels released by tobacco suspension cells were accurately measured and the distribution and concentration of eATP released on the surface of an Arabidopsis leaf was determined.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

An fluorescence resonance energy transfer sensing platform based on signal amplification strategy of hybridization chain reaction and triplex DNA for the detection of Chloramphenicol in milk

The use of chloramphenicol (CAP) in food had been strictly regulated or banned in many countries. Herein, an enzyme-free fluorescence resonance energy transfer (FRET) strategy was established for sensitive, rapid and specific detection of CAP in milk, which was based on triplex DNA and hybridization chain reaction amplification. CAP can specifically bind to the aptamer and release the trigger sequence, causing HCR to efficiently prime and forming triplex DNA, hence the FRET pairs (FAM and TAMRA) were close enough to cause fluorescent decreases. Consequently, CAP can be quantitatively detected by measuring the fluorescence reduction at 520 nm, and the reliability of the method was confirmed by enzyme-linked immunosorbent assay. The limit of CAP detection for 1.2 pg·mL-1, and the average recoveries of milk samples were 97.5%-106%, and the relative standard deviation were 3.9%-5.3%. Thus, this method has a wide range of potential applications in CAP detection.

Novel electrochemical biosensor based on Exo III-assisted digestion of dsDNA polymer from hybridization chain reaction in homogeneous solution for CYFRA 21-1 DNA assay

A novel electrochemical biosensing strategy was proposed to detect cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA based on Exo III-assisted digestion of dsDNA polymer (EADDP) from hybridization chain reaction (HCR). Primarily, the presence of target can drive a catalytic hairpin assembly (CHA) reaction, which was aimed to achieve target recognition and circulation. Then the HCR can be triggered for further signal amplification and generate long dsDNA polymer with signal tags. Subsequently, the introduction of Exo III can digest the long dsDNA polymer to produce large amounts of double signal fragments (DSFs). The above experiments were all carried out in homogeneous solution. Finally, the released DSF can be captured onto the electrode directly by capture probe (CP) and a highly amplified electrochemical signal can be detected. The EADDP in homogeneous solution circumvented complex solid-liquid interface reaction and tedious operation steps on electrode. Besides, one target can be converted into abundant DSFs, which greatly improved the sensitivity. This biosensor exhibited a low detection limit (0.0348 fM) and wide linear range (5 fM ∼ 50 nM) for CYFRA 21-1 DNA biosensing with reliable specificity and stability.

Complete antigen-bridged DNA strand displacement amplification immuno-PCR assay for ultrasensitive detection of salbutamol

Monitoring of low-level analytes are typical examples for analytical challenges. Salbutamol (SAL), a phenol-β2-agonist, has a very low residual content in the environment. Here, we present an ultrasensitive complete antigen-bridged PCR assay for detecting salbutamol (SAL). These DNA probes modified SAL complete antigens target recognition SAL antibodies and agglutinate synthetic DNA conjugates, thus enabling ligation of DNA probes to form a full-length DNA amplicon that contained a recognition site for cleavage endonuclease and subsequent quantification by qPCR. Moreover, SAL antibodies were modified with magnetic beads which were used to reduce the background noise and sample matrix effect, and the DNA signals were isothermally amplified by strand displacement amplification technology. Some key parameters which influence assay performance were optimized: the length of the bridge oligonucleotide, the concentration of immunomagnetic beads, SAL probes, and initiation chain, etc. Under the optimum conditions, the signal amplification of proposed Immuno-PCR assay for the detection of SAL was exponential, resulting in high potential sensitivity(~1 fg/mL) and a broad detection dynamic range (> 10⁵ fold). Using this proposed method, we detected SAL in spiked tap water and urine samples with acceptable recoveries ranging from 88.1 to 103.3%. Theoretically, the method developed here has broad applicability and practical utility in immunoassays of a wide variety of analytes.

The Recent Development of Hybridization Chain Reaction Strategies in Biosensors

With the continuous development of biosensors, researchers have focused increasing attention on various signal amplification strategies to pursue superior performance for more applications. In comparison with other signal amplification strategies, hybridization chain reaction (HCR) as a powerful signal amplification technique shows its certain charm owing to nonenzymatic and isothermal features. Recently, on the basis of conventional HCR, this technique has been developed and improved rapidly, and a variety of HCR-based biosensors with excellent performance have been reported. Herein, we present a systematic and critical review on the research progress of HCR in biosensors in the last five years, including the newly developed HCR strategies such as multibranched HCR, migration HCR, localized HCR, in situ HCR, netlike HCR, and so on, as well as the combination strategies of HCR with isothermal signal amplification techniques, nanomaterials, and functional DNA molecules. By illustrating some representative works, we also summarize the advantage and challenge of HCR in biosensors, and offer a deep discussion of the latest progress and future development trends of HCR in biosensors.

Target Induced-DNA strand displacement reaction using gold nanoparticle labeling for hepatitis E virus detection

DNA strand displacement is an attractive, enzyme-free target hybridization strategy for nano-biosensing. The target DNA induces a strand displacement reaction by replacing the pre-hybridized strand that is labeled with gold nanoparticles (AuNPs). Thus, the amount of displaced-AuNP-labeled strand is proportional to the amount of target DNA in the sample. The use of a magnetogenosensing technique to isolate the target DNA allows for a simple, one-pot detection approach, which minimizes possible carry-over contamination and pipetting errors. We sought a proof-of-concept for this technology in its ability to detect DNA-equivalent of hepatitis E virus (HEV), which causes acute viral hepatitis for which rapid and simple diagnostic methods remain limited. Signal detection was done via visual observation, spectrophotometry, and electrochemistry. The sensor demonstrated good sensitivity with detection limits of 10 pM (visual), 10 pM (spectrophotometry) and 1 fM (electrochemical). This sensor also exhibited high specificity for real target amplicons and could discriminate between perfect and mismatched sequences. Lyophilized biosensor reagents stored at 4 °C, 25 °C, and outdoor ambient temperature, were stable for up to 90, 50, and 40 days, respectively. The integration of magnetic separation and target DNA-induced strand displacement reaction in a dry reagent form makes the sensing platform easy-to-use and suitable for field settings.

Cellulose-based Biosensor for Bio-molecules Detection in Medical Diagnosis: A Mini-Review

Background::

Biosensors are widely applied for the detection of bio-molecules in blood glucose , cholesterol, and gene. Cellulose as the most dominating natural polymer has attracted more and more interest, especially in the field of medicine such as advanced medical diagnosis. Cellulose could endow biosensors with improved biocompatibility, biodegradability and nontoxicity, which could help in medical diagnosis. This mini-review summarizes the current development of cellulose-based biosensors as well as their applications in medical diagnosis in recent years.

Methods:

After reviewing recent years’ publications we can say that, there are several kinds of cellulose used in biosensors including different cellulose derivatives, bacterial cellulose and nanocellulose. Different types of cellulose-based biosensors, such as membrane, nano-cellulose and others were briefly described in addition to the detection principle. Cellulose-based biosensors were summarized as in the previous papers. The description of various methods used for preparing cellulose-based biosensors was also provided.

Results:

Cellulose and its derivatives with their unique chemical structure proved to be versatile materials providing a good platform for achieving immobilizing bioactive molecules in biosensors. These cellulose-based biosensors possess various desirable properties such as accuracy, sensitivity, convenience, low cost and fast response. Among them, cellulose paper-based biosensors have the advantages of low cost and easy operation. Nano-cellulose has unique properties such as a large aspect ratio, good dispersing ability and high absorption capacity.

Conclusion:

Cellulose displays a promising application in biosensors which could be used to detect different bio-molecules such as glucose, lactate, urea, gene, cell, amino acid, cholesterol, protein and hydroquinone. In future, the attention will be focused on designing miniaturized, multifunctional, intelligent and integrated biosensors. Creation of low cost and environmentally friendly biosensors is also very important.

A sensitive fluorometric sensor for Ag+ based on the hybridization chain reaction coupled with a glucose oxidase dual-signal amplification strategy

In this work, an efficient and sensitive fluorometric sensor was developed to detect silver ions (Ag⁺). It is based on the cytosine–Ag⁺–cytosine (C–Ag⁺–C) structure via a dual-signal amplification strategy using glucose oxidase (GOx) and the hybridization chain reaction (HCR). A silver-coated glass slide (SCGS) acts as an ideal material for separation. Cytosine rich (C-rich) capture DNA (C-DNA) assembled themselves on the SCGS via Ag–S bonds and hybridized with signal DNA (S-DNA) to trigger the HCR. With specific base-pairing, the S-DNA and HCR products bind on the SCGS. Then, the GOx–biotin–streptavidin (SA) complexes bind to the HCR products through SA–biotin interactions. Owing to the formation of a particular C–Ag⁺–C structure between two neighboring C-rich C-DNA on the SCGS, the C-DNA/S-DNA/HP1-GOx/HP2-GOx complex gradually moved away from the SCGS as the concentration of Ag⁺ increased and the combined GOx fell into the buffer. H₂O₂ could be generated during the oxidation of glucose, catalyzed by GOx in the buffer. Afterward, H₂O₂ could oxidize the substrate (3-(p-hydroxyphenyl)-propanoic acid) when Horseradish peroxidase was present, giving rise to blue fluorescence. The proposed strategy reached a limit of detection (LOD) of 1.8 pmol L⁻¹ with a linear detection range of 5 to 1000 pmol L⁻¹ for Ag⁺. Moreover, this assay has been commendably used for the detection of Ag⁺ in actual samples with fairly good results.

An assay for Ag⁺ based on a C–Ag⁺–C structure by utilizing a HCR/GOx dual-signal amplification strategy and SCGS as an ideal separation material.

Construction of an ultrasensitive electrochemical sensing platform for microRNA-21 based on interface impedance spectroscopy

A hybridization chain reaction (HCR) amplification-based electrochemical impedimetric biosensor is fabricated for the quick, sensitive, and specific detection of miRNA-21 (miR-21) via monitoring of electrode interfacial property changes in real-time. Two sequences of H1 and H2 are adopted to trigger HCR amplification. A large amount of linear DNA concatemer are formed which could change the interfacial properties of the electrode. Interfacial charge transfer resistance difference (R_ct) is probed via electrochemical impedance spectroscopy (EIS) and Randles equivalent circuit. After amplifying via HCR, oligonucleotides with negatively charged repelling [Fe(CN)₆]^3-/4- ions can form a spatial blockage. HCR amplification strategy markedly enhanced the electrochemical signal with a limit of detection (LOD) down to 4.63 fM (S/N = 3). This strategy exhibited excellent selectivity for three different miRNAs: miR-199a, miR-141, and miR-155. Moreover, results show that the proposed method can be applied to miR-21 detection in the total RNA extracted from five cells. This work presents an enzyme-free and label-free EIS nucleic acid sensor for sensitively and selectively detecting miR-21, offering a promising approach in early diseases diagnosis.

Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks

DNA-based circuits and computational tools offer great potential for advanced biomedical and technological applications. However, leakage, which is the production of an output in the absence of an input, widely exists in DNA network. As a new approach to leakage reduction, this study utilizes availability to reduce leakage in an entropy-driven autocatalytic DNA reaction networks. Here, we report the performance improvements resulting from direct tailoring of fuel strand availability through two novel approaches: (1) the addition of interfering domains to fuel strands, and (2) the introduction of separate small interfering strands. The best performing fuel designs resulted in increased performance ratios of up to 22%. Employing small interfering strands (5-12 nucleotides (nt)) improved the performance ratios by up to 21%. Furthermore, the stability of the network using either leakage reduction method matched well with computed availability and experimental results showing Spearman correlation coefficients of -0.84 for modified fuel strands and -0.92 for small interfering strands.

An enzyme-free electrochemical sandwich DNA assay based on the use of hybridization chain reaction and gold nanoparticles: application to the determination of the DNA of Helicobacter pylori

An ultrasensitive enzyme-free electrochemical sandwich DNA biosensor is described for the detection of ssDNA oligonucleotides. A DNA sequence derived from the genom of Helicobacter pylori was selected as a model target DNA. The DNA assay was realized through catching target DNA on capture DNA immobilized gold electrode; then labeling the target DNA with reporter DNA (rpDNA) and initiator DNA (iDNA) co-modified gold nanoparticles (AuNPs). The high density of iDNAs serves as one of the amplification strategies. The iDNA triggers hybridization chain reaction (HCR) between two hairpins. This leads to the formation of a long dsDNA concatamer strand and represents one amplification strategy. The electrochemical probe [Ru(NH₃)₅L]²⁺, where L stands for 3-(2-phenanthren-9-ylvinyl)pyridine, intercalated into dsDNA chain. Multiple probe molecules intercalate into one dsDNA chain, serving as one amplification strategy. The electrode was subjected to differential pulse voltammetry for signal acquisition, and the oxidation peak current at -0.28 V was recorded. On each AuNP, 240 iDNA and 25 rpDNA molecules were immobilized. Successful execution of HCR at the DNA-modified AuNPs was confirmed by gel electrophoresis and hydrodynamic diameter measurements. Introduction of HCR significantly enhances the DNA detection signal intensity. The assay has two linear ranges of different slopes, one from 0.01 fM to 0.5 fM; and one from 1 fM to 100 fM. The detection limit is as low as 0.68 aM. Single mismatch DNA can be differentiated from the fully complementary DNA. Conceivably, this highly sensitive and selective assay provides a general method for detection of various kinds of DNA. Graphical abstractSchematic representation of the detection and the amplification principles of the electrochemical sandwich DNA assay. Purple curl: Captured DNA; Green curl: Reporter DNA; Orange curl: HCR initiator DNA; Yellow solid-circle: Gold nanoparticle; H1 and H2: Two hairpin DNA; [Ru(NH₃)₅L]²⁺: Signal probe.

Label-free probes using DNA-templated silver nanoclusters as versatile reporters

DNA-templated silver nanoclusters (DNA-AgNCs) have demonstrated pervasive applications in analytical chemistry recently. As a way of signal output in DNA-based detection methods, DNA-AgNCs have prominent advantages: first, the recognition and synthesizing sequences are naturally integrated in one DNA probe without any chemical modification or connection; second, the emissive wavelength of DNA-AgNCs can be adjusted in a wide range by employing different sequences; third, DNA-AgNCs can be utilized for producing not only fluorescence, also electrochemiluminescence and electrochemical signals. Besides, they also show potential applications for cell imaging, and are considered to be one of the most ideal nanomaterials for in-vivo imaging due to their ultra-small particle size. In this review, a brief and comprehensive introduction of DNA-AgNCs is firstly given, then label-free probes using DNA-AgNCs are classified and summarized, lastly concluding perspectives are provided on the defects and application potentials.

Review of Electrochemical DNA Biosensors for Detecting Food Borne Pathogens

The vital importance of rapid and accurate detection of food borne pathogens has driven the development of biosensor to prevent food borne illness outbreaks. Electrochemical DNA biosensors offer such merits as rapid response, high sensitivity, low cost, and ease of use. This review covers the following three aspects: food borne pathogens and conventional detection methods, the design and fabrication of electrochemical DNA biosensors and several techniques for improving sensitivity of biosensors. We highlight the main bioreceptors and immobilizing methods on sensing interface, electrochemical techniques, electrochemical indicators, nanotechnology, and nucleic acid-based amplification. Finally, in view of the existing shortcomings of electrochemical DNA biosensors in the field of food borne pathogen detection, we also predict and prospect future research focuses from the following five aspects: specific bioreceptors (improving specificity), nanomaterials (enhancing sensitivity), microfluidic chip technology (realizing automate operation), paper-based biosensors (reducing detection cost), and smartphones or other mobile devices (simplifying signal reading devices).

Mesoporous Silica Containers and Programmed Catalytic Hairpin Assembly/Hybridization Chain Reaction Based Electrochemical Sensing Platform for MicroRNA Ultrasensitive Detection with Low Background

In this work, based on mesoporous silica containers (MSNs) with the programmed enzyme-free DNA assembly amplification of catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR), an ultrasensitive electrochemical sensing platform with low background is developed for the detection of microRNA (miRNA). Herein, the electrochemical reporter methylene blue (MB) was sealed in the pores of MSNs by the double-stranded DNA (dsDNA) gate of hairpin DNA H1 and anchor DNA. In the absence of target, neither the CHA nor the HCR process happened, which enabled a low background. After target was added, DNA H1 was displaced from the MSNs surface and participated in the CHA process with the assistance of hairpin DNA H2, which accelerated the release of MB from the MSNs pore. Meanwhile, the CHA products H1-H2 were hybridized with the capture probes (SH-CP) on the electrode surface, which further initiated the HCR process. The released MB from the MSNs will effectively intercalate into long dsDNA polymers of HCR products, resulting in a significant electrochemical response. Taking miRNA-21 as the model target, the proposed sensing platform achieves a satisfactory detection limit down to 0.037 fM, which is lower than that of electrochemical assay with amplification methods. In addition, the strategy shows good selectivity against other miRNAs and is capable in practical analytes. Benefitting from the features of being label-free and enzyme-free and having low background, high sensitivity, and selectivity, this strategy shows great potential in bioanalysis and clinical diagnostics.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

Sensitive fluorescent detection of Listeria monocytogenes by combining a universal asymmetric polymerase chain reaction with rolling circle amplification

A new, facile, low-cost, and highly sensitive method for detection of Listeria monocytogenes involving a combination of asymmetric polymerase chain reaction (aPCR) and rolling circle amplification (RCA) had been developed. The aPCR-RCA processes were not new but components of the processes made the assay useful. Twenty-one thymine (21-T) tagged forward primer generated universal twenty-one adenine (21-A) aPCR amplicons after aPCR amplification. A poly-T sequence dumbbell-like RCA template was produced through the blunt-end ligation activity of T4 DNA ligase. After the mixture of aPCR amplicons and dumbbell-like RCA template, the RCA reaction would initiate when the addition of phi29 DNA polymerase, then a large number of G-quadruplex sequences were produced which allowed the intercalation of Thioflavin T (3,6-dimethyl-2-(4-dimethylaminophenyl) benzo-thiazolium cation, THT) for easy fluorescence detection. Under the optimal conditions, the assay showed a limit of detection (LOD) of 4.8 × 10¹ CFU/mL in pure culture and 4.0 × 10² CFU/g in spiked lettuce homogenates. By changing the aPCR primer, the aPCR-RCA method developed in this study had a potential to detect other bacteria without the design an RCA template for each bacterium.

Visual/CVG-AFS/ICP-MS multi-mode and label-free detection of target nucleic acids based on a selective cation exchange reaction and enzyme-free strand displacement amplification

Visual/CVG-AFS/ICP-MS three-mode detection of DNA based on the selective cation exchange reaction and enzyme-free strand displacement amplification.

Liquid biopsy of circulating tumor DNA and biosensor applications

Circulating tumor DNA (ctDNA) as a class of liquid biopsy is a type of gene fragment that contains tumor-specific gene changes in body fluids such as human peripheral blood. More and more evidences show that ctDNA is an excellent tumor biomarker for diagnosis, prognosis, tumor heterogeneity and so on. ctDNA is a tumor code in the blood. Liquid biopsy of ctDNA is firstly summarized. Compared with the traditional detection technologies of ctDNA, the biosensor is an excellent choice for the detection of ctDNA because of its portability, sensitivity, specificity and ease of use. This review mainly evaluates various biosensors applied to the detection of ctDNA. We discuss the most commonly used bioreceptors to specifically identify and bind ctDNA, including complementary DNA (cDNA), peptide nucleic acid (PNA) and anti-5 MethylCytosines, and the biotransducers which convert biological signals to analysable signs. The review also discusses signal amplification strategies in biosensors to detect ctDNA.

A facile DNA strand displacement reaction sensing strategy of electrochemical biosensor based on N-carboxymethyl chitosan/molybdenum carbide nanocomposite for microRNA-21 detection

Herein, we report a facile enzyme-free microRNA (miRNA) target-triggered strand displacement reaction (SDR) amplification strategy with ferrocene (Fc) as a signal molecule to fabricate a two-dimensional electroactive molybdenum carbide (Mo₂C)-based biosensor. In the presence of miRNA-21, SDR was initiated and many hairpin DNA1 (HDNA1) and hairpin DNA2 (HDNA2) duplexes, which could be captured by probe DNA leading the Fc-modified HDNA2 close to the electrode surface, were produced continuously. MiRNA-21 could be detected by monitoring the redox signal of Fc. The prepared N-carboxymethyl chitosan/Mo₂C nanocomposite featured excellent conductivity, great dispersion, and multiple functional groups (amine groups). When the nanocomposite was introduced to a miRNA biosensor electrode interface to ensure its strong connection to the DNA probe, the developed miRNA-21 biosensor demonstrated a reliable linear range of 1.0 fM to 1.0 nM with a detection limit of 0.34 fM and showed good selectivity, reproducibility, and stability. The biosensor was employed to detect miRNA-21 in human serum samples, and it showed great potential in the early clinical diagnosis of various genetic diseases.

Ultrasensitive and label-free electrochemical aptasensor of kanamycin coupling with hybridization chain reaction and strand-displacement amplification

This work reports the proof-of-concept of an ultrasensitive label-free electrochemical aptasensor for Kanamycin (Kana) detection coupling strand-displacement amplification (SDA) with hybridization chain reaction (HCR). In the presence of target Kana, the analyte triggers conformational change of hairpin HP1 (HP1) and two-staged SDA to produce short single-stranded DNA (S1) with the aid of KF polymerase and nicking endonuclease. Meanwhile, the as-produced S1 hybridizes with the immobilized hairpin HP2 (HP2) on the electrode to open the hairpin, thereby resulting in the formation of DNA duplex. Thereafter, DNA duplex is selectively digested by Exo III accompanying S1 recycling. The residual single-stranded probe (S2) on the electrode opens another two hairpins in sequence and propagates a chain reaction of hybridization events between two alternating hairpins (H1 and H2) to form a long nicked double-helix. Upon addition of redox-active methylene blue (MB), numerous indicators are intercalated into the grooves of double-helix DNA polymers, each of which produces an electrochemical signal within the applied potentials. Under optimum conditions, the SDA/HCR-based electrochemical aptasensor exhibits a high sensitivity for detection of Kana down to 36 fM with a linear range from 0.05 to 200 pM. Additionally, the as-prepared aptasensor is successfully employed to determinate the Kana in animal derived food (milk). With the advantages of high sensitivity, label-free strategy and excellent selectivity, the developed aptasensor possesses great potential application value in food-safety analysis field.