Toehold Mediated One-Step Conformation-Switchable “Signal-On” Electrochemical DNA Sensing Enhanced with Homogeneous Enzymatic Amplification

Magnetic metal-organic frameworks as sensitive aptasensors for coronavirus spike protein

Electrochemical biosensors, known for their low cost, sensitivity, selectivity, and miniaturization capabilities, are ideal for point-of-care devices. The magnetic metal-organic framework (MMOF), synthesized using the in-situ growth method, consists of ferric salt, magnetic nanoparticles, histidine, and benzene tetracarboxylic acid. MMOF was sequentially modified with aptamer-biotin and streptavidin-horseradish peroxidase, serving as a detector for spike protein and a transducer converting electrochemical signals using H2O2-hydroquinone on a screen-printed electrode. MMOF facilitates easy washing and homogeneous deposition on the working electrode with a magnet, enhancing sensitivity and reducing noise. The physical and electrochemical properties of the modified MMOFs were thoroughly characterized using various analytical techniques. The aptasensors' performance achieved a detection limit of 6 pM for voltammetry and 5.12 pM for impedance spectroscopy in human serum samples. This cost-effective, portable MMOF platform is suitable for rapid point-of-care testing for SARS-CoV-2 spike proteins.

Enzyme-Assisted Amplification and Copper Nanocluster Fluorescence Signal-Based Method for miRNA-122 Detection

At present, a large number of studies have demonstrated that miRNAs can be used as biological indicators for the diagnosis and treatment of diseases such as tumours and cancer, so it is important to develop a new miRNA detection platform. In this work, miRNA-122 is used as the basis for targeting detection agents. We have designed an unlabelled DNA1 that undergoes partial hybridisation and has a 20 T base long strand. The fluorescent signal in this experiment is derived from copper nanoclusters (CuNCs) generated on the circular T-long strand of DNA1. At the same time, DNA1 is able to react with miRNA-122 and achieve hydrolysis of the part bound to miRNA-122 via the action of nucleic acid exonuclease III (Exo III), leaving a part of the DNA, called DNA3, while releasing miRNA-122 to participate in the next reaction, thus achieving circular amplification. DNA3 is able to react with DNA2, which is bound to streptavidin magnetic beads (SIBs) and separated from the reaction solution via the application of a magnetic field. Overall, this is a fluorescence signal reduction experiment, and the strength of the fluorescence signal from the copper nanoclusters can determine whether the target miRNA-122 is present or not. The degree of fluorescence reduction indicates how much DNA1, and thus the amount of target miRNA-122, has been hydrolysed. By evaluating the variations in the fluorescence signal under optimised conditions, we discovered that this method has good sensitivity, with a detection limit as low as 0.46 nM, better than many other previous works on fluorescence signal-based biosensors for miRNA detection. This technique offers high discrimination and selectivity and can serve as a persuasive reference for early diagnosis.

Electrochemical aptamer biosensor for DNA detection based on label-free aptamers

Electrochemical aptasensor has been broadly advanced for nucleic acid detection. However, it is a long-term goal to design an aptasensor with high specificity, flexibility, and simplicity. In this work, we develop a strategy of triblock DNA probe, which consists of two DNA probes at both ends and ployA fragments in the middle as probe-polyA-probe. PolyA fragment has high affinity to the surface of gold electrode, so it can be assembled on the electrode surface via polyA instead of traditional Au-S bonds. When the target DNA is simultaneously hybridized with the two capture probes, the hybridization stability can be improved due to the strong base stacking effect. [Ru(NH₃)₆]³⁺, as signal probe, can be electrostatically adsorbed on the negatively charged DNA skeleton. A wide linear range (10 pM-10 μM) is obtained with a detection limit of 2.9 pM. Our electrochemical aptasensor has good repeatability, stability, and specificity. More importantly, the electrochemical sensor can successfully detect DNA in human serum samples, which proves its practical value and extensive applicability in complex environment.

Synthesis and characterization of Au-decorated graphene oxide nanocomposite for magneto-electrochemical detection of SARS-CoV-2 nucleocapsid gene

Fast and effective diagnosis is the first step in monitoring the current coronavirus 2 (CoV-2) pandemic. Herein, we establish a simple and sensitive electrochemical assay using magnetic nanocomposite and DNA sandwich probes to rapidly quantify the CoV-2 nucleocapsid (N) gene down to the 0.37 fM level. This assay uses a pair of specific DNA probes. The capture probe is covalently conjugated to Au-decorated magnetic reduced graphene oxide (AMrGO) nanocomposite for efficiently capturing target RNA. In contrast, the detection probe is linked to peroxidase for signal amplification. The probes target the COV-2 gene, allowing for specific magnetic separation, enzymatic signal amplification, and subsequent generation of voltammetric current with a total assay time of 45 min. The developed biosensor has high selectivity and can discriminate non-specific gene sequences. Synthetic COV-2 N-gene can be detected efficiently in serum and saliva, while 1-bp mismatch gene yielded a low response. The performance of the genosensor was good in an extensive linear range of 5 aM-50 pM. For synthetic N-gene, we achieved the detection limit of 0.37, 0.33, and 0.19 fM in human saliva, urine, and serum. This simple, selective, and sensitive genosensor could have various genetics-based biosensing and diagnostic applications.

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.

Homogeneous voltammetric sensing strategy for lead ions based on aptamer gated methylthionine chloride@UiO-66-NH2 framework as smart target-stimulated responsive nanomaterial

Herein an innovative electrochemical method is proposed for the determination of lead ions (Pb²⁺) based on a homogeneous voltammetric (HVC) sensing strategy using an aptamer gated methylthionine chloride@UiO-66-NH₂ framework as a smart target-stimulated responsive material. The proposed HVC sensor exhibits excellent sensing performance: ultralow detection limit (0.166 pM) and wide linearity (5.0 pM-500.0 nM), simultaneously, it avoids electrodeposition processes and it is simple to modify the electrode compared to previous electrochemical methods for Pb²⁺ detection. Thus our method shows great potential in the highly efficient detection of Pb²⁺ and other heavy metal ions by simply altering the related specific aptamer.

Three-Dimensional Surface-Enhanced Raman Scattering Platform with Hotspots Built by a Nano-mower for Rapid Detection of MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the greatest threats to human health due to its strong drug resistance, wide distribution range, and high infection rate. Rapid identification of MRSA strains is very important for accurate diagnosis and early treatment of MRSA infections. Here, we introduced an Exo III-assisted nanomotor mower to build 3D hotspots for rapid detection of MRSA by surface-enhanced Raman scattering (SERS). As the bacteria bound to the aptamer, two trigger chains were released from the double-stranded structure, and the nano-mowers were activated by opening a hairpin probe on gold nanoparticles (AuNPs). With the continued cleavage of Exo III and cyclic release of the trigger chain, multiple hairpin DNAs on the AuNPs were cleaved to increase the motor power. The resulting nano-mower continued slicing protective DNA from larger AuNPs, exposing the AuNPs. Without the protection of DNA, Mg²⁺ in the buffer induced spontaneous aggregation of the AuNPs, and a large number of hotspots were formed for SERS measurements. Under optimal conditions, MRSA can be detected within 40 min, and the concentration of MRSA showed a good linear relationship with the SERS intensity at 1342 cm^-1, with a limit of detection as low as 1 CFU/mL and a wide linear range (10⁰ to 10⁷ CFU/mL). This strategy creates a rapid bacterial detection method that performs well on actual samples utilizing portable Raman spectroscopy instruments, with potential applications in food detection, water detection, clinical treatment, and 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.

A label-free and ultrasensitive electrochemical biosensor for oral cancer overexpressed 1 gene via exonuclease III-assisted target recycling and dual enzyme-assisted signal amplification strategies

A label-free and ultrasensitive electrochemical biosensor for ORAOV1 gene via exonuclease III-assisted target recycling and dual enzyme-assisted signal amplification strategies. The detection limit of ORAOV1 gene was as low as 0.019 fM.

A highly sensitive electrochemical aptasensor for vascular endothelial growth factor detection based on toehold-mediated strand displacement reaction

An electrochemical aptasensor with high sensitivity, specificity, and good intra-day reproducibility is reported to meet the detection needs of vascular endothelial growth factor (VEGF). The toehold-mediated strand displacement recycling amplification and VEGF aptamer are integrated in the biosensor. The probe A is hybridized with the VEGF aptamer to form the probe A-aptamer complex. When VEGF is introduced, the aptamer specifically binds with VEGF, and probe A can be liberated. Then, the free probe A captures the toehold region of the Hp1, leading the exposure of the toehold region on the other end of Hp1. Similarly, Hp2 and Hp3 are also immobilized on the surface of the electrode; thus, the methylene blue labelled on Hp2 and Hp3 causes the current response. With the signal transduction mechanism, the expression level of VEGF can be detected quantitatively. With a series of optimizations of sensor parameters, high sensitivity and specificity of the VEGF detection sensor can be achieved with a detection limit as low as 10 pg mL^-1. This significant performance has good intra-day reproducibility, and it can be applied to human biological samples such as serum, urine, and saliva to detect the VEGF content.

A novel electrochemical biosensor for lung cancer-related gene detection based on copper ferrite-enhanced photoinitiated chain-growth amplification

We reported an electrochemical biosensor via CuFe₂O₄-enhanced photoinitiated chain-growth polymerization for ultrasensitive detection of lung cancer-related gene. In this work, photoinitiated atom transfer radical polymerization (ATRP) was applied to amplify the electrochemical signal corresponding to lung cancer-related gene, and polymerization was triggered off under the illumination of blue light which was involved in copper-mediated reductive quenching cycle. At the same time, CuFe₂O₄-H₂O₂ system was also activated to enhance polymerization based on the photocatalysis of CuFe₂O₄, which was based on the reaction between •OH and methacrylic monomers to generate carbon-based radicals. Numerous ferrocene-based polymer was graft onto electrode surface through this amplification stages. The limit of detection was low to 1.98 aM (in 10 μL, ∼11.9 molecules) (R² = 0.998) with a wide linear range from 0.1 fM to 10 pM. This strategy made a good trade-off between cost-effectiveness and sensitivity, and it also presented a high selectivity and anti-interference. In addition, the operation was greatly simplified and detection time was also shortened, which endowed this electrochemical DNA biosensor great application potential.

Strategies for Biomolecular Analysis and Continuous Physiological Monitoring

Portable devices capable of rapid disease detection and health monitoring are crucial to decentralizing diagnostics from clinical laboratories to the patient point-of-need. Although technologies have been developed targeting this challenge, many require the use of reporter molecules or reagents that complicate the automation and autonomy of sensors. New work in the field has targeted reagentless approaches to enable breakthroughs that will allow personalized monitoring of a wide range of biomarkers on demand. This Perspective focuses on the ability of reagentless platforms to revolutionize the field of sensing by allowing rapid and real-time analysis in resource-poor settings. First, we will highlight advantages of reagentless sensing techniques, specifically electrochemical detection strategies. Advances in this field, including the development of wearable and in situ sensors capable of real-time monitoring of biomarkers such as nucleic acids, proteins, viral particles, bacteria, therapeutic agents, and metabolites, will be discussed. Reagentless platforms which allow for wash-free, calibration free-detection with increased dynamic range are highlighted as a key technological advance for autonomous sensing applications. Furthermore, we will highlight remaining challenges which must be overcome to enable widespread use of reagentless devices. Finally, future prospects and potential breakthroughs in precision medicine that will arise as a result of further development of reagentless sensing approaches are discussed.

Tumor-cell detection, labeling and phenotyping with an electron-doped bifunctional signal-amplifier

Cancer cell enumeration and phenotyping can predict the prognosis and the therapy efficacy in patients, yet it remains challenging to detect the rare tumor cells. Herein, we report an octopus-inspired, bifunctional aptamer signal amplifier-based cytosensor (OApt-cytosensor) for sensitive cell analysis. By assembling high-affinity antibodies on an electrode surface, the target cells could be specifically captured and thus been sandwiched by the cell surface marker-specific DNA aptamers. These on-cell aptamers function as electrochemical signal amplifiers by base-selective electronic doping with methylene blue. Such a sandwich configuration enables highly sensitive cell detection down to 10 cells/mL (equal to ~1-2 cells at a sampling volume of 150 μL), even in a large excess of nontarget blood cells. This approach also reveals the cell-surface markers and tracks the cellular epithelial-to-mesenchymal transition induced by signaling regulators. Furthermore, the electron-doped aptamer shows remarkable cell fluorescent labeling that guides the release of the captured cells from electrode surface via electrochemistry. These features make OApt-cytosensor a promising tool in revealing the heterogeneous cancer cells and anticancer drug screening at the single-cell level.

Toehold-Mediated Strand Displacement Reaction for Dual-Signal Electrochemical Assay of Apolipoprotein E Genotyping

Apolipoprotein E (apoE) polymorphic genes are one of the main genetic determinants of Alzheimer's disease (AD) risk. Relying on the toehold-mediated strand displacement reaction (SDR), the dual-signal electrochemical assay of apoE genotyping with potential applications in the early diagnosis of AD has been achieved. The displacement of the surface-confined methylene blue- and ferrocene-capped detection probe-modified gold nanoparticles (AuNPs) by the complementary sequences (Tc 1 and Tc 2, fragment of allele ε4 at codon 112 and that of allele ε3 or ε4 at codon 158, respectively), triggered by the highly specific SDR, results in decreased voltammetric signals. In contrast, partial strand displacement caused by the single mismatched sequences (Tsm 1 and Tsm 2, fragment of allele ε2 or ε3 at codon 112 and that of allele ε2 at codon 158, respectively) produces larger voltammetric signals. The proposed method serves as a versatile platform for the discrimination of six apoE genotypes, including three homozygotes (ε2/2, ε3/3, and ε4/4) and three heterozygotes (ε2/3, ε2/4, and ε3/4), and for the quantification of apoE ε3/3 from genomic DNA extracts of AD patients.

Nanostructuring Synergetic Base-Stacking Effect: An Enhanced Versatile Sandwich Sensor Enables Ultrasensitive Detection of MicroRNAs in Blood

MicroRNA (MiRNA)-based noninvasive diagnostics are hampered by the challenge in the quantification of circulating miRNAs using a general strategy. Here, we present a base-stacking effect-mediated ultrasensitive electrochemical miRNA sensor (BSee-miR) with a universal sandwich configuration. In the BSee-miR, a short DNA probe (10 nucleotides) self-assembled on a gold electrode surface could effectively capture the target miRNA synergizing with another sequence based on coaxial sandwich base-stacking, which rivals the fully complementary strength. Importantly, such a sandwich structure is flexible to incorporate signal amplification strategies (e.g., biotin-avidin) that are usually difficult to achieve in short sequence detection. Using this design, the BSee-miR achieves a broad dynamic range with a detection limit down to 7.5 fM. Furthermore, we found a high-curvature nanostructuring synergetic base-stacking effect that could improve the sensitivity of the BSee-miR by two orders of magnitude (79.3 aM). Our BSee-miR also has a single-base resolution to discriminate the highly homologous miRNAs. More importantly, this approach is universal and has been used to probe target miRNAs varying in sequences and secondary structures. Our ultrasensitive sensor could detect miRNA in cell lysates and human blood and distinguish cancer patients from normal individuals, promising a versatile tool to measure clinically relevant miRNAs for tumor diagnostics.

Dual-output toehold-mediated strand displacement amplification for sensitive homogeneous electrochemical detection of specie-specific DNA sequences for species identification

The determination of specie-specific DNA sequences is a key factor for identification of animal species and detection of meat adulteration. Herein, a simple homogeneous electrochemical biosensor was developed for sensitive detection of specie-specific DNA sequences from meat products based on high efficient and specific dual-output toehold-mediated strand displacement (TMSD). After incubation with target DNA, large amount of methylene blue (electrochemical signal molecule) labeled probes (MB-P) were released from preformed DNA duplex structures by the process of dual-output TMSD amplification. The free MB-P could be further digested by Exonuclease I, and the enzymatic products contain little negative charge could diffuse to the surface of indium tin oxide electrode, generating significantly electrochemical signal. As a result, the designed biosensor showed a broad dynamic range from 0.01 pM to 100 pM, with a low detection limit of 8.2 fM, and ideal selectivity and reproducibility. Meanwhile, the approach exhibited acceptable accuracy for the detection of specie-specific DNA sequences, and possessed the potential application for the identification of animal species from meat products.

Construction of electrochemical aptasensor of carcinoembryonic antigen based on toehold-aided DNA recycling signal amplification

Carcinoembryonic antigen (CEA), serves as a broad-spectrum tumor marker, and plays an important role in reflecting the existence, therapeutic evaluation, development, monitoring and prognosis of many types of cancer. An electrochemical aptasensor was designed for CEA detection based on toehold-aided DNA recycling. A partially hybridized Probe-4 (i.e. P2/P3/P4) was self-assembled on the surface of a gold electrode serving as the sensing platform. For CEA detection, CEA can bind with aptamer and free probe-1 (P1) can hybridize with P4, triggering toehold-aided DNA recycling. This enables the hybridization of more probe-5 (P5) (labeled with methylene blue (MB)) with P4, causing more methylene blue (MB) to be brought close to the electrode surface. An amplified current signal was thus generated due to more MB in the electrode surface. The proposed design showed good linearity between current response and log CEA concentration ranging from 0.1 to 50 ng·mL^-1, with a detection limit of 20 pg mL^-1. This aptasensor also showed high specificity for CEA detection, and was successfully used in spiked biological samples.

Fluorometric determination of ssDNA based on functionalized magnetic microparticles and DNA supersandwich self-assemblies

A method is described for the determination of DNA via nucleic acid amplification by using nucleic acid concatemers that result from DNA supersandwich self-assemblies (SSAs). The method employs two auxiliary probes to form self-assembled biotin SSAs. These exhibit strong fluorescence if labeled with intercalator SYBR Green I. In the presence of the target (as exemplified for a 30-mer), streptavidin is released from the surface of the functionalized magnetic microparticles (FMMPs) by competitive hybridization on the surface. However, the SSA products do not conjugate to the FMMPs. This leads to a large amount of SYBR Green I intercalated into the concatemers and eventually results in amplified fluorescence in the supernate. The SSA products can be prepared beforehand, and amplification therefore can be completed within 50 min. The method is more efficient than any other conventional amplification. The detection limit for the 30-mer is 26.4 fM which is better by a factor of 10 compared to other amplification methods. Conceivably, the method can be further extended to the determination of a wide variety of targets simply by replacing the sequences of the probes. Finally, this rapid and highly sensitive method was employed for detection of Ebola virus gene (≈30-mer) and ATP in spiked serum with satisfactory results. Graphical abstract A high sensitivity and efficiency bioassay is described based on functionalized magnetic microparticles and DNA supersandwich self-assemblies.

Synergy of Peptide-Nucleic Acid and Spherical Nucleic Acid Enabled Quantitative and Specific Detection of Tumor Exosomal MicroRNA

Exosomal microRNAs are essential in intercellular communications and disease progression, yet it remains challenging to quantify the expression level due to their small size and low abundance in blood. Here, we report a "sandwich" electrochemical exosomal microRNA sensor (SEEmiR) to detect target microRNA with high sensitivity and specificity. In SEEmiR, neutrally charged peptide nucleic acid (PNA) enables kinetically favorable hybridization with the microRNA target relative to negatively charged DNA, particularly in a short sequence (10 nt). More importantly, this property allows PNA to cooperate with a spherical nucleic acid (SNA) nanoprobe that heavily loads with oligonucleotide-adsorbed electroactive tags to enhance detection sensitivity and specificity. Such a PNA-microRNA-SNA sandwich construct is able to minimize the background noise via PNA, thereby maximizing the SNA-mediated signal amplification in electrostatic adsorption-based SEEmiR. The synergy between PNA and SNA makes the SEEmiR sensor able to achieve a broad dynamic range (from 100 aM to 1 nM) with a detection limit down to 49 aM (2 orders of magnitude lower than that without SNA) and capable of distinguishing a single-base mismatch. This ultrasensitive sensor provides label-free and enzyme-independent microRNA detection in cell lysates, unpurified tumor exosomal lysates, cancer patients' blood, and accurately differentiates the patients with breast cancer from the healthy ones, suggesting its potential as a promising tool in cancer diagnostics.

A dandelion-like liposomes-encoded magnetic bead probe-based toehold-mediated DNA circuit for the amplification detection of MiRNA

The development of facile and sensitive miRNA quantitative detection methods is a central challenge for the early diagnosis of miRNA-related diseases. Herein, we propose a strategy for a liposome-encoded magnetic bead-based DNA toehold-mediated DNA circuit for the simple and sensitive detection of miRNA based on a toehold-mediated circular strand displacement reaction (TCSDR) coupled with a personal glucometer (PGM ). In this strategy, a glucoamylase-encapsulated liposomes (GELs)-encoded magnetic bead (GELs-MB) probe is designed to integrate target binding, magnetic separation, and signal response. Upon sensing the target miRNA-21, a GELs-MB probe-based toehold-mediated circular strand displacement reaction (TCSDR) was initiated with the help of fuel-DNA, constructing a DNA circuit system, and realizing target recycling amplification and the disassembly of the liposomes. The disassembled liposomes were finally removed via magnetic separation, and the encapsulated glucoamylase was liberated to catalyze amylose hydrolysis with multiple turnovers to glucose for a PGM readout. Benefiting from target recycling amplification initiated by the toehold-mediated DNA circuit and the liposome multiple-label amplification, a small quantity of target miRNA-21 can be transformed into a large glucose signal. The strategy realized the quantification of miRNA-21 down to a level of 0.7 fM without enzymatic amplification or precise instrumentation. Moreover, the high-density GELs-MB probe allows the sensitive detection of miRNA-21 to be accomplished within 1.5 h. Furthermore, this strategy exhibits the advantages of specificity and simplicity, since a toehold-mediated strand displacement reaction, magnetic separation and portable PGM were used. Importantly, this strategy has been demonstrated to allow the high-confidence quantification of miRNA. Therefore, with the advantages of low cost, ease of use, portability, and sensitivity, the reported method holds great potential for the early diagnosis of miRNA-related diseases.

Photothermal Soft Nanoballs Developed by Loading Plasmonic Cu2- xSe Nanocrystals into Liposomes for Photothermal Immunoassay of Aflatoxin B1

Photothermal effects (PTEs) have been greatly concerned with the fast development of new photothermal nanomaterials. Herein we propose a photothermal immunoassay (PTIA) by taking mycotoxins (AFB1) as an example based on the PTEs of plasmonic Cu2- xSe nanocrystals (NCs). By loading plasmonic Cu2- xSe NCs into liposomes to form photothermal soft nanoballs (ptSNBs), on which aptamer of AFB1 previously assembled, a sandwich structure of AFB1 could be formed with the aptamer on ptSNBs and capture antibody. The heat released from the ptSNBs under NIR irradiation, owing to the plasmonic photothermal light-to-heat conversion through photon-electron-phonon coupling, makes the temperature of substrate solution increased, and the increased temperature has a linear relationship with the AFB1 content. Owing to the large amounts of plasmonic Cu2- xSe NCs in the ptSNBs, the PTEs get amplified, making AFB1 higher than 1 ng/mL detectable in food even if with a rough homemade immunothermometer. The proposal of PTIA opens a new field of immunoassay including developing photothermal nanostructures, new thermometers, PTIA theory, and so on.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

Colorimetric and visual mercury(II) assay based on target-induced cyclic enzymatic amplification, thymine-Hg(II)-thymine interaction, and aggregation of gold nanoparticles

A colorimetric biosensor and visual test is described for the determination of mercury(II). It relies on the specific thymine-Hg(II)-thymine (T-Hg²⁺-T) interaction which induces a cyclic amplification process (caused by the enzyme exonuclease III) and the aggregation of gold nanoparticles. These results in a color change from red to violet. Under optimized conditions, this colorimetric assay (best performed at 524 nm) has a detection limit as low as 0.9 nM with a detection range over 4 orders of magnitude (from 1 nM to 10 μM). Graphical abstract Schematic of a colorimetric method for determination of mercury ions (Hg²⁺) based on the thymine-Hg²⁺-thymine interaction-triggered cyclic enzymatic amplification and aggregation of gold nanoparticles with the aid of exonuclease III (Exo III).

Rapid Detection of the Bursaphelenchus Xylophilus by Denaturation Bubble-mediated Strand Exchange Amplification

Bursaphelenchus xylophilus (B. xylophilus) is one of the most important causal agents of infectious diseases in forest pathology. Obviously, the rapid detection of B. xylophilus is an urgent need for its prevention and cure. We have developed a detection method of B. xylophilus by strand exchange amplification (SEA). This method could detect 10⁵ copies of genomic DNA of B. xylophilus, and it was sufficiently sensitive to detect a single nematode as short as 40 min. Moreover, because the amplification result could be visualized by the naked eyes, the only equipment required throughout the process was a simple isothermal block. Therefore, our method would be a potential for developing on-site detection of B. xylophilus to prevent and control its spread.

Ultrasensitive electrochemical detection of Hg2+ based on an Hg2+-triggered exonuclease III-assisted target recycling strategy

In the present work, a simple, rapid, isothermal, and ultrasensitive homogeneous electrochemical biosensing platform for target Hg2+ detection was developed on the basis of an exonuclease III (Exo III)-aided target recycling amplification strategy. In the assay, a label-free hairpin probe (HP1) was ingeniously designed, containing a protruding DNA fragment at the 3'-termini as the recognition unit for target Hg2+. Also, the DNA fragment in the loop region and 5'-termini (Helper) could be used when a secondary target analog is introduced, but it is caged in the stem region of HP1 when without such a target. The produced secondary target Helper opened the methylene blue (MB)-labeled hairpin probe (HP2) and triggered the Exo III cleavage process, accompanied with the secondary target recycling. This accordingly resulted in the autonomous reduction of the electroactive material MB on the electrode, inducing a distinct decrease in the electrochemical signal. The current developed homogeneous strategy provides a means for the ultrasensitive electrochemical detection of Hg2+ down to the 227 pM level, with high selectivity. It could be further used as a general autocatalytic and homogeneous strategy toward the detection of a wide spectrum of analytes and may be associated with more analytical techniques.

Enzyme-free homogeneous electrochemical biosensor for DNA assay using toehold-triggered strand displacement reaction coupled with host-guest recognition of Fe3O4@SiO2@β-CD nanocomposites

Taking advantages of the toehold-triggered strand displacement reaction (TSDR) and host-guest interaction of β-cyclodextrin (β-CD), a facile enzyme-free and homogeneous electrochemical sensing strategy was designed for the sensitive assay of target DNA using Fe₃O₄@SiO₂@β-CD nanocomposites and ferrocene-labeled hairpin DNA (H-1) as the capture and electrochemical probes, respectively. Upon addition of target molecule, the initiated TSDR process induced the conformational change of H-1, and subsequently stimulated the dynamic assembly of assist probes (A-1 and A-2) to generate H-1:A-1:A-2 duplex along with the release of target sequence. The released target could drive the next TSDR recycling and finally result in the formation of numerous DNA duplex. After the molecular recognition of Fe₃O₄@SiO₂@β-CD nanocomposites, a large number of duplex were easily separated from the supernatant solution under an external magnetic field, which led to a decreased H-1 concentration in residual solution, concomitant with a remarkable reduction of peak current. Under the optimized conditions, wide linear range (1-5000 pM), low detection limit (0.3 pM), desirable reproducibility, good selectivity, and satisfactory practical analysis were obtained by the combination of the superior recognition capability of β-CD, TSDR-induced signal amplification, and homogeneous electroanalytical method. The proposed detection strategy could offer a universal approach for the monitoring of various biological analytes via the rational design of probe sequences.

Ultrasensitive amperometric aptasensor for the epithelial cell adhesion molecule by using target-driven toehold-mediated DNA recycling amplification

An amperometric aptasensor is reported for the electrochemical determination of the epithelial cell adhesion molecule (EpCAM). It is based on a combination of EpCAM-driven toehold-mediated DNA recycling amplification, the specific recognition of EpCAM aptamer, and its binding to EpCAM. Hairpin probe 1 (Hp1) with a toehold region was modified with a 5'-thiol group (5'-SH) and self-assembled onto the surface of a gold electrode. Upon addition of EpCAM, the probe A (a 15-mer) is liberated from the aptamer/probe A complex and then hybridizes with the toehold domain of Hp1. This results in the exposure of another toehold for further hybridizing with hairpin probe 2 (Hp2) to displace probe A in the presence of Hp2 that was labeled with the electrochemical probe Methylene Blue (MB). Subsequently, liberated probe A is hybridized again with another Hp1 to start the next round of DNA recycling amplification by reusing probe A. This leads to the formation of plenty of MB-labeled DNA strands on the electrode surface and generates an amplified current. This 1:N probe-response amplification results in ultrasensitive and specific detection of EpCAM, with a 20 pg·mL^-1 detection limit. The electrode is highly stable and regenerable. It was successfully applied to the determination of EpCAM in spiked human serum, urine and saliva, and thus provides a promising tool for early clinical diagnosis. Graphical abstract Schematic illustration of the electrochemical detection for EpCAM. The method is based on aptamer-based recognition and EpCAM-driven toehold-mediated DNA recycling amplification. Hp1: Hairpin probe 1; Hp2: Hairpin probe 2; MB: Methylene blue; MCH: 6-Mercapto-1-hexanol; EpCAM: Epithelial cell adhesion molecule.