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

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.

Bio-barcode assay: A useful technology for ultrasensitive and logic-controlled specific detection in food safety: A review

Food safety is one of the greatest public health challenges. Developing ultrasensitive detection methods for analytes at ultra-trace levels is, therefore, essential. In recent years, the bio-barcode assay (BCA) has emerged as an effective ultrasensitive detection strategy that is based on the indirect amplification of various DNA probes. This review systematically summarizes the progress of fluorescence, PCR, and colorimetry-based BCA methods for the detection of various contaminants, including pathogenic bacteria, toxins, pesticides, antibiotics, and other chemical substances in food in over 120 research papers. Current challenges, including long experimental times and strict storage conditions, and the prospects for the application of BCA in biomedicine and environmental analyses, have also been discussed herein.

A novel ultrasensitive and fast aptamer biosensor of SEB based on AuNPs-assisted metal-enhanced fluorescence

A fluorescent biosensor strategy was developed in combination with immunomagnetic separation for rapid and sensitive detection of staphylococcal enterotoxin B (SEB). Magnetic nanoparticles (MNPs) modified with aptamer of SEB could capture the SEB. Then the gold nanoparticles (AuNPs) fluorescent probe was added and a "sandwich structure" was formed between AuNPs, SEB and MNPs. The MNPs-SEB-AuNPs structure could be separated with an additional magnetic field, which resulted the lower signals of AuNPs fluorescent probe. In optimal conditions, the current method displayed a broad quantitative range from 100 to 10⁷ fg/mL and the limit of detection was 3.43 fg/mL. The recovery of SEB-spiked milk samples ranged from 92.00 to 119.00 %, which revealed that the developed method had great accuracy. Furthermore, the method was fast and economical for ultrasensitive detection. Therefore, the fluorescent biosensor based on MNPs-AuNPs is promising for the detection of other environmental and food pollutants.

Massively Parallel DNA Computing Based on Domino DNA Strand Displacement Logic Gates

DNA computing has gained considerable attention due to the characteristics of high-density information storage and high parallel computing for solving computational problems. Building addressable logic gates with biomolecules is the basis for establishing biological computers. In the current calculation model, the multiinput AND operation often needs to be realized through a multilevel cascade between logic gates. Through experiments, it was found that the multilevel cascade causes signal leakage and affects the stability of the system. Using DNA strand displacement technology, we constructed a domino-like multiinput AND gate computing system instead of a cascade of operations, realizing multiinput AND computing on one logic gate and abandoning the traditional multilevel cascade of operations. Fluorescence experiments demonstrated that our methods significantly reduce system construction costs and improve the stability and robustness of the system. Finally, we proved stability and robustness of the domino AND gate by simulating the tic-tac-toe process with a massively parallel computing strategy.

Raman enhancement effect of different silver nanoparticles on salbutamol

Salbutamol is a β-adrenergic receptor agonist compound which has been abused as an animal growth promoter to improve carcass lean meat percentage. At present, the detection of salbutamol by SERS mostly uses gold colloid as substrate, which is expensive and has a high detection limit. In this report, Raman enhancement signal of salbutamol was compared with concentrated gold and silver colloids. The results show that the concentrated silver colloid prepared by reducing silver nitrate with hydroxylamine hydrochloride had superior performance. Three silver colloids with different particle sizes were synthesized by the same reducing agent and used as substrates for spectra acquisition of salbutamol to explore the enhancement performance of different silver nanoparticles sizes on salbutamol. The results showed that silver nanoparticles with larger particle sizes were more conducive to the adsorption of salbutamol. Finally, under the optimal conditions (Silver colloid A as enhanced substrate, 0.2 mol/L NaOH aqueous solution as aggregating compound), a better linear relationship between the concentration of salbutamol (ranged from 0.2 to 1 mg/L) and SERS intensity. The linear equation between SERS intensity and salbutamol concentration was C = 0.0023∙I-0.079 (mg/L) with a good linearity (R² =0.994) and lower root mean square error (RMSE_c = 0.022 mg/L), where C (mg/L) was the concentration of salbutamol solution and I was the SERS intensity of salbutamol solution. Validation set correlation coefficient was 0.988 and prediction root mean square error was 0.029 mg/L. This method provides a new idea for further reducing the detection limit of salbutamol. This study is helpful to further develop a simple and low-cost SERS detection method of salbutamol based on silver colloid.

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Raman enhancement signal of salbutamol was compared with concentrated gold and silver colloids.

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The effect of silver nanoparticles sizes on the enhancement effect are in particular broached.

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The methods can realize salbutamol at trace concentrations detection.

Target biorecognition-triggered assembly of a G-quadruplex DNAzyme-decorated nanotree for the convenient and ultrasensitive detection of antibiotic residues

The abuse of kanamycin (Kana) in many fields has led to increasing antibiotic pollution problems and serious threats to public health. Therefore, determining how to develop methods to realize the convenient detection of antibiotics in complicated environmental matrices is highly desirable. In this study, we utilized a target biorecognition-triggered hybridization chain reaction (HCR) assembly of a G-quadruplex DNAzyme (G-DNAzyme)-decorated nanotree to develop a novel homogeneous colorimetric biosensing method for the convenient and ultrasensitive detection of Kana antibiotic residues in real samples. Through the designed aptamer-recognition reaction, an Mg²⁺-dependent DNAzyme (MNAzyme) strand can be liberated. Thus, its catalyzed cleavage of the hairpin substrates anchored at a DNA nanowire will cause the assembled formation of an HCR-initiator; this process can be greatly amplified by the exonuclease III-assisted target recycling and the MNAzyme-catalyzed release of another MNAzyme strand. Based on the DNA-nanowire-accelerated HCR assembly of many G-DNAzyme-decorated DNA duplexes on the two sides of the nanowire, a DNA nanotree decorated by numerous G-DNAzymes will form to realize the ultrasensitive colorimetric signal output. Under the optimal conditions, this method exhibited a wide five-order-of-magnitude linear range and a very low detection limit of 28 fg mL^-1. In addition, excellent selectivity, repeatability, and reliability were also demonstrated for this homogeneous bioassay method. These unique features along with its automatic manipulation and low assay cost show promise for practical applications.

Current Advances in Immunoassays for the Detection of β2-Agonists

β2-agonists are a group of synthetic phenylethanolamine compounds which are traditionally used for treating bronchospasm. These compounds can also increase skeletal muscle mass and decrease body fat. The illegal use of β2-agonists in food-producing animals results in residue of β2-agonists in edible tissues and causes adverse health effects in humans. Thus, the detection of β2-agonists at trace level in complex sample matrices is of great importance for monitoring the abuse of β2-agonists. Many methods have been developed to detect β2-agonists. Among them, a variety of antigen–antibody interaction-based techniques have been established to detect β2-agonists in various samples, including animal feed, urine, serum, milk, tissues and hair. In this review, we summarized current achievement in the extraction of β2-agonists from testing samples and detection of β2-agonists using immunological techniques. Future perspectives were briefly discussed.

Target-Dependent Protection of DNA Aptamers against Nucleolytic Digestion Enables Signal-On Biosensing with Toehold-Mediated Rolling Circle Amplification

We report a generalizable strategy for biosensing that takes advantage of the resistance of DNA aptamers against nuclease digestion when bound with their targets, coupled with toehold mediated strand displacement (TMSD) and rolling circle amplification (RCA). A DNA aptamer containing a toehold extension at its 5'-end protects it from 3'-exonuclease digestion by phi29 DNA polymerase (phi29 DP) in a concentration-dependent manner. The protected aptamer can participate in RCA in the presence of a circular template that is designed to free the aptamer from its target via TMSD. The absence of the target leads to aptamer digestion, and thus no RCA product is produced, resulting in a turn-on sensor. Using two different DNA aptamers, we demonstrate rapid and quantitative real-time fluorescence detection of two human proteins: platelet-derived growth factor (PDGF) and thrombin. Sensitive detection of PDGF was also achieved in human serum and human plasma, demonstrating the selectivity of the assay.

Immunochromatographic Assay Based on Polydopamine-Decorated Iridium Oxide Nanoparticles for the Rapid Detection of Salbutamol in Food Samples

Salbutamol (SAL), a β-2 adrenoreceptor agonist, is an unpopular addition to livestock and poultry, causing several side effects to human health. Thus, it is very important to develop a simple and rapid analytical method to screen SAL in the field of food safety. Here, we present an immunochromatographic assay (ICA) method for sensitively detecting SAL with polydopamine-decorated iridium oxide nanoparticles (IrO₂@PDA NPs) as a signal tag. The IrO₂@PDA with excellent hydrophilicity, biocompatibility, and stability was synthesized by oxidating self-polymerization of dopamine hydrochloride (DAH) on the surface of IrO₂ NPs and used to label monoclonal antibodies (mAbs) through simple physical adsorption. Compared with IrO₂ NPs, the IrO₂@PDA also possessed superior optical properties and higher affinity with mAbs. With the proposed method, the limit of detection for SAL was 0.002 ng/mL, which was improved at least 24-fold and 180-fold compared with the IrO₂ NPs-based ICA and conventional gold nanoparticles-based ICA, respectively. Furthermore, the SAL residuals in pork, pork liver, and beef were successfully detected by the developed biosensor and the recoveries ranged from 85.56% to 115.56%. Briefly, this work indicated that the powerful IrO₂@PDA-based ICA can significantly improve detection sensitivity and has huge potential for accurate and sensitive detection of harmful small molecules analytes in food safety fields.

Biocomputing Based on DNA Strand Displacement Reactions

The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.