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

Amplified Assembly of G-Quadruplex-Decorated DNA Network Nanostructure toward AIE Signaling-Based Sensitive Biosensing

Aggregation-induced emission (AIE) has offered a promising approach for developing low-background fluorescent methods; however, its applications often suffer from complex probe synthesis and poor biocompatibility. Herein, a novel AIE biosensing method for kanamycin antibiotic assays was developed by utilizing a DNA network nanostructure assembled from an aptamer recognition reaction to capture a large number of tetraphenylethylene fluorogen-labeled signal DNA (DTPE) probes. Due to the excellent hydrophilicity of the oligonucleotides, DTPE exhibited excellent water solubility without obvious background signal emission. Based on an ingenious nucleotide design, an abundance of G-quadruplex blocks neighboring the captured DTPE were formed on the DNA nanostructure. Because of the greatly restricted free motion of DTPE by this unique nanostructure, a strong AIE fluorescence signal response was produced to construct the signal transduction strategy. Together with target recycling and rolling circle amplification-based cascade nucleic acid amplification, this method exhibited a wide linear range from 75 fg mL-1 to 1 ng mL-1 and a detection limit down to 24 fg mL-1. The excellent analytical performance and effective manipulation improvement of the method over previous approaches determine its promising potential for various applications.

Enhancement of telomerase extension via quadruple nucleic acid recycling to develop a novel colorimetric biosensing method for kanamycin assay

BACKGROUND

Colorimetric biosensors have important value for antibiotic residue testing. However, many previous methods were constructed based on the optical density change of certain unstable single-colored products with poor discrimination for visual measurements. Moreover, their low extinction coefficients usually result in low sensitivity of biosensors. In addition, many conventional signal amplification strategies often involve sophisticated nanomaterial preparation, inconvenient multi-step assay manipulation and limited signal amplification ability. Therefore, the development of new colorimetric biosensing strategies with excellent visual discrimination, high sensitivity and convenient manipulation is highly desirable.

RESULTS

We designed a target recycling accelerated cascade DNA walking amplification mechanism to trigger a telomerase extension-related enzymatic reaction, and developed a novel colorimetric biosensing strategy for kanamycin (Kana) assay. The target recycling was induced by an exonuclease III-assisted aptamer recognition reaction, which could also trigger the successive DNA walking at the streptavidin (SA)- and magnetic bead (MB)-based tracks. This not only caused the quantitative exposure of the telomeric substrate primers on MB surfaces but also released another strand to accelerate the SA-based DNA walking. By using the telomerase extension product to link numerous alkaline phosphatases and induce the plasmonic property change of gold nanobipyramids (Au NBPs), a colorimetric signal output strategy was constructed. This method could be applied for the high-resolution visual screening of Kana, and it also showed a very low detection limit of 17.6 fg mL-1 for assaying Kana over a wide, five-order-magnitude linear range.

SIGNIFICANCE

The quadruple nucleic acid recycling-enhanced telomerase extension resulted in the ultrahigh sensitivity of the method and also excluded the sophisticated manipulations involved in conventional biosensing strategies. The multiple enzyme catalysis-induced plasmonic property change of Au NBPs realized the stable and multicolor visual signal transduction. Together with its low cost, simple operation, high selectivity, excellent repeatability, and reliable performances, this method exhibits great potential for use in practical applications.

Fluorescence biosensor for ultrasensitive detection of the available lead based on target biorecognition-induced DNA cyclic assembly

A fluorescence biosensor was developed for the ultrasensitive detection of the available lead in soil samples by coupling with DNAzyme and hairpin DNA cyclic assembly. The biorecognition between lead and 8-17 DNAzyme will cleave the substrate strands (DNA2) and release the trigger DNA (T), which can be used to initiate the DNA assembly reactions among the hairpins (H1, H2, and H3). The formed Y-shaped sensing scaffold (H1-H2-H3) contains active Mg2+-DNAyzmes at three directions. In the presence of Mg2+, the BHQ and FAM modified H4 will be cleaved by the Mg2+-DNAyzme to generate a high fluorescence signal for lead monitoring. The linear range of the fluorescence biosensor is from 1 pM to 100 nM and the detection limit is 0.2 pM. The biosensor also exhibited high selectivity and the nontarget competing heavy metals did not interfere with the detection results. Compare with the traditional method (DTPA+ICP-MS) for the available lead detection, the relative error (Re) is in the range from -8.3 % to 9.5 %. The results indicated that our constructed fluorescence biosensor is robust, accurate, and reliable, and can be applied directly to the detection of the available lead in soil samples without complex extraction steps.

Electrochemical aptasensor based on exonuclease III-mediated signal amplification for sensitive detection of vomitoxin in cornmeal

Vomitoxin (DON) residues in grains are of great concern to public health. Herein, a label-free aptasensor was constructed to detect DON distributed in grains. Cerium-based metal-organic framework composite gold nanoparticles (CeMOF@Au) were used as substrate materials to facilitate electron transfer and provided more binding sites for DNA. The separation of DON-aptamer (Apt) complex and cDNA was achieved by magnetic separation technique based on magnetic beads (MBs), ensuring the specificity of the aptasensor. Exonuclease III (Exo III)-assisted cDNA cycling process strategy would be triggered when cDNA was separated and introduced to the sensing interface for further signal amplification. Under optimal conditions, the constructed aptasensor presented a wide detection range from 1 × 10^-8 mg·mL^-1 to 5 × 10^-4 mg·mL^-1 for DON, and the detection limit was 1.79 × 10^-9 mg·mL^-1, including a satisfactory recovery in cornmeal sample spiked with DON. The results showed that the proposed aptasensor had high reliability and promising application potential in detecting DON.

Portable biosensor for on-site detection of kanamycin in water samples based on CRISPR-Cas12a and an off-the-shelf glucometer

On-site and cost-effective monitoring of antibiotic residue in water samples using a ubiquitous device that is readily available to the general public is a big challenge. Herein, we developed a portable biosensor for kanamycin (KAN) detection based on a glucometer and CRISPR-Cas12a. The aptamer-KAN interactions liberate the trigger C strand, which can initiate the hairpin assembly to produce numerous double-stranded DNA. After recognition by CRISPR-Cas12a, Cas12a can cleave the magnetic bead and invertase-modified single-stranded DNA. After magnetic separation, the invertase can convert sucrose into glucose, which can be quantified by a glucometer. The linear range of the glucometer biosensor is from 1 pM to 100 nM and the detection limit is 1 pM. The biosensor also exhibited high selectivity and the nontarget antibiotics had no significant interference with KAN detection. The sensing system is robust and can work in complex samples with excellent accuracy and reliability. The recovery values were in the range of 89-107.2 % for water samples and 86-106.5 % for milk samples. The relative standard deviation (RSD) was below 5 %. With the advantages of simple operation, low cost, and easy accessibility to the public, this portable pocket-sized sensor can realize the on-site detection of antibiotic residue in resource-limited settings.

A fluorescent biosensor for Cd2+ detection in water samples based on Cd2+-fueled wheel DNAzyme walker and its logic gate applications

A fluorescent biosensor was developed for Cd²⁺ detection based on a Cd²⁺-fueled wheel DNAzyme walker. Cd²⁺ can activate the wheel to roll along the DNA walking tracks through DNAzyme cleavage and toehold-mediated strand displacement. The substrate strand was modified with BHQ and Cy5. Through continuous cleavage reactions toward the substrate strands, a high fluorescence signal can be obtained. The biosensor is ultrasensitive, and the detection limit is 0.2 pM (S/N = 3). The fluorescent assay is robust and has been applied to the determination of Cd²⁺ in real water samples with good accuracy and reliability. Using Cd²⁺, Pb²⁺, and Hg²⁺ as the three inputs, we also construct a concatenated AND logic gate. The input combination of (111) can produce an output of 1. Other input combinations produce an output of 0. Our proposed detection platform and logic system hold great promise for the ultrasensitive and intelligent sensing of different heavy metal ions in water samples.