Versatile Electrochemiluminescence Biosensing Platform Based on DNA Nanostructures and Catalytic Hairpin Assembly Signal Amplification

Effective multicolor visual biosensor for ochratoxin A detection enabled by DNAzyme catalysis and gold nanorod etching

A novel detection technique is introduced that offers sensitive and reliable ochratoxin A (OTA) detection. The method leverages the etching of gold nanorods (AuNRs) stabilized by hexadecyl trimethyl ammonium bromide (CTAB) using the oxidized form of 3,3',5,5'-tetramethyl benzidine sulfate (TMB2+), creating a susceptible multicolor visual detection system for OTA. The visual detection is enabled by Mg2+-assisted DNAzyme catalysis combined with the catalytic hairpin assembly (CHA) signal amplification strategy. The presence of OTA triggers CHA and signaling responses along with the formation of G-quadruplex-hemin DNAzyme, which promotes the oxidation of TMB with H2O2, leading to the etching of AuNRs and a reduction in their aspect ratio. AuNRs experienced a blue shift in the longitudinal localized surface plasmon resonance peak, resulting in a color change. The technique has been shown to detect OTA with a low detection limit of 0.309 pg/mL, demonstrating high sensitivity and specificity. The detection technique offers versatility by enabling the detection of other pollutants through a simple replacement of the aptamer, expanding the range of detection platforms available for pollutant determinations.

A label-free and rapid fluorometric strategy for microRNA detection using CRISPR-Cas12a coupled with copper nanoparticles

CRISPR-Cas12a with robust trans-cleavage activity were employed to mitigate background fluorescence signal, achieving sensitive detection of miRNA-21. The activation of trans-cleavage activity of Cas12a was achieved by utilizing cDNA as a trigger. Upon the presence of target miRNA-21, cDNA hybridizes with it forming a DNA/RNA double-stranded structure. Exonuclease III (ExoIII) facilitates the degradation of cDNA, releasing the target for subsequent cycles. Due to cDNA degradation, the trans-cleavage activity of Cas12a remains unactivated and does not disrupt the synthesis template of copper nanoparticles. Addition of Cu2+ and AA leads to the formation of highly fluorescent copper nanoparticles. Conversely, in absence of miRNA-21, intact cDNA activates trans-cleavage activity of Cas12a, resulting in degradation of the synthesis template and failure in synthesizing fluorescent copper nanoparticles. This method exhibits excellent selectivity with a low limit of detection (LOD) at 5 pM. Furthermore, we successfully applied this approach to determine miRNA-21 in cell lysates and human serum samples, providing a new approach for sensitive determination of biomarkers in biochemical research and disease diagnosis.

Single-Atom Iron Doped Carbon Dots with Highly Efficient Electrochemiluminescence for Ultrasensitive Detection of MicroRNAs

Herein, single-atom iron doped carbon dots (SA Fe-CDs) were successfully prepared as novel electrochemiluminescence (ECL) emitters with high ECL efficiency, and a biosensor was constructed to ultrasensitively detect microRNA-222 (miRNA-222). Importantly, compared with the conventional without single-atom doped CDs with low ECL efficiency, SA Fe-CDs exhibited strong ECL efficiency, in which single-atom iron as an advanced coreactant accelerator could significantly enhance the generation of reactive oxygen species (ROS) from the coreactant S2O82- for improving the ECL efficiency. Moreover, a neoteric amplification strategy combining the improved strand displacement amplification with Nt.BbvCI enzyme-induced target amplification (ISDA-EITA) could produce 4 output DNAs in every cycle, which greatly improved the amplification efficiency. Thus, a useful ECL biosensor was built with a detection limit of 16.60 aM in the range of 100 aM to 1 nM for detecting traces of miRNA-222. In addition, miRNA-222 in cancer cell lysate (MHCC-97L) was successfully detected by using the ECL biosensor. Therefore, this strategy provides highly efficient single-atom doped ECL emitters for the construction of sensitive ECL biosensing platforms in the biological field and clinical diagnosis.

Ratiometric fluorometric assay triggered by alkaline phosphatase: Proof-of-concept toward a split-type biosensing strategy for DNA detection

Herein, a sensitive ratiometric and split-type fluorescent sensing platform has been constructed for DNA detection based on one signal precursor and two fluorescent signal indicators. In this assay, o-phenylenediamine (OPD) was selected as the signal precursor. On one hand, Cu2+ can oxidize OPD to produce 2, 3-diaminophenazine (DAP), which with an emission peak at 555 nm. On the other hand, ascorbic acid (AA) could react with Cu2+ to generate dehydroascorbic acid (DHAA), which could further react with OPD to form 3-(1, 2-dihydroxy ethyl)furo[3, 4-b]quinoxalin-1 (3H)-on (DFQ) with a strong emission peak at 420 nm. As a result, the formation of DAP was inhibited, and leading to the decrease of fluorescence intensity at 555 nm. Alkaline phosphatase (ALP) could catalyze the substrate l-ascorbic acid-2-phosphate (AA2P) to produce AA in situ. Inspired by the successful use of ALP as a biocatalytic marker in bioassay, a split-type ratiometric fluorescent assay has been designed for DNA detection by using H1N1 DNA as the target model. It was realized for ratiometric fluorescent determination of H1N1 in a linear ranging from 50 pM to 1.5 nM with a limit of detection of 10 pM. The novel strategy could reduce the mutual interferences between the biomolecular recognition system and the fluorescence signal conversion system, which improving the accuracy of detection and effectively reducing the background signal. Furthermore, the strategy provided a promising platform for biomarkers detection in the fields of ratiometric fluorescent biosensors and bioanalysis.

Dumbbell hybridization chain reaction coupled with positively charged Au@luminol nanoparticles for enhanced electrochemiluminescent sensing of exosomal miRNA-21

MicroRNAs (miRNAs) are important cancer biomarkers in cancer cell-derived exosomes. Herein, positively charged Au@luminol nanoparticles ((+)Au@luminol NPs) with enhanced electrochemiluminescence (ECL) and extreme stability were firstly established for the sensitive detection of miRNA-21 in exosome. In the presence of miRNA-21, dumbbell hybridization chain reaction (DHCR) happened at gold nanoparticles and ZIF-67 metal-organic framework modified glass carbon electrode (AuNP/ZIF-MOF/GCE) with the help of dumbbell DNA fuel strands (DHP1 and DHP2). The formed DHCR polymers were negatively charged and could electrostatically adsorb numbers of (+)Au@luminol NPs to produce strong ECL signal. Combing DHCR signal amplification with (+)Au@luminol NPs enhancer, sensitive detection of miRNA-21 realized with a detection limit of 0.43 fM. Moreover, the proposed method was successfully applied for the analysis of miRNA-21 in serum samples of healthy individuals and breast cancer patients, indicating a potential application value in early clinical diagnosis.

Flexible Self-Powered Sensing System Based on Novel DNA Circuit Strategy and Graphdiyne for Thalassemia Gene by Rapid Naked-Eye Tracking and Open-Circuit Voltage

Based on the controllable instantaneous self-assembly ability of long-chain branched DNA nanostructures and the synergistic effect between nucleic acid amplification without enzymes, a highly sensitive and highly specific self-powered biosensing platform is developed. Two-dimensional graphdiyne is prepared, modified on flexible carbon cloth, and then functionalized with gold nanoparticles. When DNA mi-tubes are applied on it, target thalassemia gene CD122 triggers a dual-catalytic hairpin assembly reaction. The generated nanoscale DNA is precisely captured by the DNA mi-tube, exposing binding sites and activating the hybridization chain reaction to form long-chain branched DNA. Double-stranded DNA, along with dendritic DNA carrying a large number of guanine bases, precisely captures the signal molecule methylene blue (MB), generating a significant electrochemical signal. The redox reaction of MB also causes a proportional change in the system's color, achieving a colorimetric detection functionality. An efficient dual-mode self-powered sensing platform, therefore, is established for detecting the thalassemia gene CD122. The linear response range of target concentration to open-circuit voltage and RGB Blue value is 0.0001-10,000 pM. The detection limit under electrochemical mode is 36.3 aM (S/N = 3), and under colorimetric mode, it is as low as 12.1 aM (S/N = 3). The new method exhibits high sensitivity, excellent selectivity, and high accuracy, providing a universal strategy for designing novel biosensing platforms that can be extended to the detection of other biomolecules.

Smart enzyme-free amplification dual-mode self-powered platform designed on two-dimensional networked graphdiyne and DNA nanorods for ultra-sensitive detection of breast cancer biomarkers

Research has shown that microRNAs exhibit regular dysregulation in cancers, making them potential biomarkers for cancer diagnosis. However, achieving specific and sensitive detection of microRNAs has been a challenging task. To address this issue, two-dimensional networked graphdiyne is used to fabricate a self-powered biosensor and establish a new approach for ultra-responsive dual-mode detection of miRNA-141, a breast cancer biomarker. This method detects miRNA-141 using both electrochemical and colorimetric modes by measuring the output electrical signal of an enzyme-based biofuel cell and the RGB blue value of the electrolyte solution. Tetrahedral DNA and DNA nanorods also are immobilized on the electrode as a biocathode and methylene blue is used as the electron acceptor, which is fixed in the DNA phosphate backbone through electrostatic adsorption. The bioanode catalyzes the oxidation of glucose to produce electrons, which reduces methylene blue to its reduced form, resulting in a high open-circuit voltage (EOCV) and a highger RGB Blue value, enabling dual-mode detection. A reliable linear correlation is observed between EOCV values and miRNA-141 concentrations ranging from 0.0001 to 100 pM, with a detection limit of 21.9 aM (S/N = 3). Additionally, the colorimetric mode also demonstrates a reliable linear correlation with a concentration range of 0.0001-10000 pM, and this method can detect a concentration of 22.2 aM (S/N = 3). This innovative research realizes sensitive and accurate determination of miRNA-141 and provides an important new method for cancer diagnosis.

A highly sensitive self-powered sensing method designed on DNA circuit strategy and MoS2 hollow nanorods for detection of thalassemia

Thalassemia is one of the most common monogenic diseases, which seriously affects human growth and development, cardiovascular system, liver, etc. There is currently no effective cure for this disease, making screening for thalassemia particularly important. Herein, a self-powered portable device with high sensitivity and specificity for efficiently screening of low-level thalassemia is developed which is enabled with AuNPs/MoS2@C hollow nanorods and triple nucleic acid amplification technologies. It is noteworthy that AuNPs/MoS2@C electrode shows the advantages of high electrocatalytic activity, fast carrier migration rate and large specific surface area, which can significantly improve the stability and output signal of the platform. Using high-efficiency tetrahedral DNA as the probe, the target CD122 gene associated with thalassemia triggers a catalytic hairpin assembly reaction to achieve CD122 recycling while providing binding sites for subsequent hybridization chain reaction, greatly improving the detection accuracy and sensitivity of the device. A reliable electrochemical/colorimetric dual-mode assay for CD122 is then established, with a linear response range of 0.0001-100 pM for target concentration and open circuit voltage, and the detection limit is 78.7 aM (S/N = 3); a linear range of 0.0001-10000 pM for CD122 level and RGB Blue value, with a detection limit as low as 58.5 aM (S/N = 3). This method achieves ultra-sensitive and accurate detection of CD122, providing a new method for the rapid and accurate screening of thalassemia.

Self-Powered Biosensor Based on DNA Walkers for Ultrasensitive MicroRNA Detection

A novel self-powered biosensor is fabricated for ultrasensitive microRNA-21 (miRNA-21) detection, which includes an enzymatic biofuel cell (EBFC), DNA walkers, a digital multimeter (DMM), and a capacitor. As a novel strategy for signal amplification, DNA walkers are designed in the cathode, while the capacitor stores electrochemical energy from the EBFC to further boost the instantaneous current displayed by the DMM. When miRNA-21 is present, the DNA walkers are provoked to walk from as-opened hairpin structures to other hairpin structures, generating double-strand DNA structures, which stimulate [Ru(NH3)6]3+ to be adsorbed on the cathode surface by electrostatic interaction. Afterward, [Ru(NH3)6]3+ is reduced to [Ru(NH3)6]2+, and the open circuit voltage (EOCV) is significantly increased. Depending on the approach of signal amplification from DNA walkers, this biosensor displays an ultrasensitive assay toward miRNA-21 in the range of 0.5 to 104 fM, with a detection limit of 0.15 fM. In addition, this self-powered biosensor displays high selectivity for miRNA-21 assay in human serum samples.

Orderly Aggregated Catalytic Hairpin Assembly for Synchronous Ultrasensitive Detecting and High-Efficiency Co-Localization Imaging of Dual-miRNAs in Living Cells

In this work, the orderly aggregated catalytic hairpin assembly (OA-CHA) was developed for synchronous ultrasensitive detection and high-efficiency colocalization imaging of dual-miRNAs by a carefully designed tetrahedral conjugated ladder DNA structure (TCLDS). Exactly, two diverse hairpin probes were fixed on tetrahedron conjugated DNA nanowires to form the TCLDS without fluorescence response, which triggered OA-CHA in the aid of output DNA 1 and output DNA 2 produced by targets miRNA-217 and miRNA-196a cycle to generate TCLDS with remarkable fluorescence response. Impressively, compared with the traditional CHA strategy, OA-CHA avoided the fluorescence group and quenching group from approaching again because of the spatial confinement effect to significantly enhance the fluorescence signal, resulting in the simultaneous ultrasensitive detection of dual-miRNAs with detection limits of 21 and 32 fM for miRNA-217 and miRNA-196a, respectively. Meanwhile, the TCLDS with lower diffusivity could achieve accurate localization imaging for reflecting the spatial distribution of dual-miRNAs in living cells. The strategy based on OA-CHA provided a flexible and programmable nucleic amplification method for the synchronous ultrasensitive detection and precise imaging of multiple biomarkers and had potential in disease diagnostics..

Constructed a self-powered sensing platform based on nitrogen-doped hollow carbon nanospheres for ultra-sensitive detection and real-time tracking of double markers

Acute myocardial infarction (AMI) is acute necrosis of a portion of the myocardium caused by myocardial ischemia, which seriously threatens people's health and life safety. Its early diagnosis is a difficult problem in clinical medicine. Research has found that the abnormal expression of microRNA-199a (miR-199a) and microRNA-499 (miR-499) was closely related to AMI disease. In this work, we took advantage of the structural advantages of nitrogen-doped hollow carbon nanospheres (N-HCNSs) to design an ultra-sensitive, portable real-time monitoring visual self-powered biosensor system, which based on dual-target miRNAs triggered catalytic hairpin assembly (CHA) for sensitive detection of miR-199a and miR-499. In addition, the capacitor and the smartphone are introduced into the system to realize the secondary improvement of system sensitivity and portable real-time visual monitoring. Under optimized conditions, in the linear range of 0.1-100000 aM, the detection limits of miR-199a and miR-499 are 0.031 and 0.027 aM, respectively. At the same time, the ultra-sensitive detection of miRNAs is realized in the serum sample, and the recovery rate of miR-199a and miR-499 are 98.0-106.0% (RSD: 0.6-8.1%) and 94.0-109.7% (RSD: 1.8-7.7%), respectively. The method is simple, sensitive and can be used for real-time tracking and portable monitoring of related diseases.

Fluorescent aptasensor for the ultrasensitive detection of antibiotic residue in food samples based on dumbbell DNA-mediated signal amplification

Sensitive and reliable detection of antibiotics is of great significance for environmental and food safety due to its high risk in trace concentrations. Herein, we developed a fluorescence sensing system for chloramphenicol (CAP) detection based on dumbbell DNA-mediated signal amplification. Two hairpin dimers (2H1 and 2H2) were employed as the building blocks to construct the sensing scaffolds. The CAP-aptamer binding in another hairpin H0 can liberate the trigger DNA, which then activates the cyclic assembly reaction between 2H1 and 2H2. The separation of FAM and BHQ in the formed product of cascaded DNA ladder yields a high fluorescence signal for CAP monitoring. Compared with the monomer hairpin assembly between H1 and H2, the dimer hairpin assembly between 2H1 and 2H2 exhibits enhanced signal amplification efficiency and reduced reaction time. The developed CAP sensor showed a wide linear range from 10 fM to 10 nM with a detection limit of 2 fM. Importantly, this sensing platform has been successfully applied to the determination of CAP in fish, milk, and water samples with satisfactory recovery and accuracy. With the advantages of high sensitivity, mix-and-read pattern, and robustness, our proposed CAP sensor can be used as a simple and routine tool for the detection of trace amounts of antibiotic residues.

High-Density N-Vacancy-Induced Multipath Electrochemiluminescence Improvement of 3D g-C3N4 for Ultrasensitive MiRNA-222 Analysis

Using dissolved O₂ as the cathodic co-reactant of three-dimensional (3D) g-C₃N₄ is a convenient method to improve the electrochemiluminescence (ECL) signal, but it still suffers the disadvantages of limited luminous efficiency of 3D g-C₃N₄ and low content, low reactivity, and instability of dissolved O₂. Here, N vacancy with high density was first introduced into the structure of 3D g-C₃N₄ (3D g-C₃N₄-NV), which could conveniently realize multipath ECL improvement by simultaneously solving the above shortcomings effectively. Specifically, N vacancy could change the electronic structure of 3D g-C₃N₄ to broaden its band gap, increase fluorescence (FL) lifetime, and accelerate electron transfer rate, obviously improving the luminous efficiency of 3D g-C₃N₄. Meanwhile, N vacancy made the excitation potential of 3D g-C₃N₄-NV to shift from -1.3 to -0.6 V, effectively weakening the electrode passivation. Moreover, the adsorption capacity of 3D g-C₃N₄-NV was obviously enhanced, which could make the dissolved O₂ enrich around 3D g-C₃N₄-NV. And massive active NV sites of 3D g-C₃N₄-NV could promote O₂ to more efficiently convert to reactive oxygen species (ROS) that were key intermediates in ECL generation. Using the newly proposed 3D g-C₃N₄-NV-dissolved O₂ system as an ECL emitter, an ultrasensitive target conversion biosensor was constructed for miRNA-222 detection. The fabricated ECL biosensor exhibited satisfactory analytical performance for miRNA-222 with a detection limit of 16.6 aM. The strategy achieved multipath ECL improvement by introducing high-density N vacancy simply in the 3D structure of g-C₃N₄ and could open a new horizon for developing a high-performance ECL system.

CRISPR-Cas12a Coupled with DNA Nanosheet-Amplified Fluorescence Anisotropy for Sensitive Detection of Biomolecules

DNA nanosheets (DNSs) have been utilized effectively as a fluorescence anisotropy (FA) amplifier for biosensing. But, their sensitivity needs to be further improved. Herein, CRISPR-Cas12a with strong trans-cleavage activity was utilized to enhance the FA amplification ability of DNSs for the sensitive detection of miRNA-155 (miR-155) as a proof-of-principle target. In this method, the hybrid of the recognition probe of miR-155 (T1) and a blocker sequence (T2) was immobilized on the surface of magnetic beads (MBs). In the presence of miR-155, T2 was released by a strand displacement reaction, which activated the trans-cleavage activity of CRISPR-Cas12a. The single-stranded DNA (ssDNA) probe modified with a carboxytetramethylrhodamine (TAMRA) fluorophore was cleaved in large quantities and could not bind to the handle chain on DNSs, inducing a low FA value. In contrast, in the absence of miR-155, T2 could not be released and the trans-cleavage activity of CRISPR-Cas12a could not be activated. The TAMRA-modified ssDNA probe remained intact and was complementary to the handle chain on the DNSs, and a high FA value was obtained. Thus, miR-155 was detected through the obviously decreased FA value with a low limit of detection (LOD) of 40 pM. Impressively, the sensitivity of this method was greatly improved about 322 times by CRISPR-Cas12a, confirming the amazing signal amplification ability of CRISPR-Cas12a. At the same time, the SARS-CoV-2 nucleocapsid protein was detected by the strategy successfully, indicating that this method was general. Moreover, this method has been applied in the analysis of miR-155 in human serum and the lysates of cells, which provides a new avenue for the sensitive determination of biomarkers in biochemical research and disease diagnosis.

Highly sensitive and specific detection of silver ions using a dual-color fluorescence co-localization strategy

Ag⁺ ions are widely used in various fields of human life due to their unique properties and they threaten the environment and human health. The traditional methods for Ag⁺ detection commonly suffer from disadvantages including limited sensitivity, expensive equipment and complicated operating steps. Herein, we developed a highly specific dual-color fluorescence co-localization (DFC) strategy based on the C-Ag⁺-C structure for Ag⁺ detection. In this strategy, Ag⁺ ions can be captured to form C-Ag⁺-C base pairs, and these ions enable single-stranded DNAs to form double strands. The DFC strategy can exclude nonspecific interaction sites and greatly improve the sensitivity and specificity. By DFC of the QDs and Cy5 linked to the DNA strands, highly sensitive Ag⁺ detection was achieved in the concentration range from 0.14 pM to 200 nM, with a limit of detection (LOD) of 0.14 pM. Moreover, this method has been applied for the detection of Ag⁺ ions in real environmental samples with satisfactory recoveries. We believe that the DFC strategy is promising for Ag⁺ detection.