Highly efficient fluorescence sensing of kanamycin using Endo IV-powered DNA walker and hybridization chain reaction amplification

Application and development of signal amplification strategy in detection of antibiotic residues in food

Food is essential for the proper functioning of the human body, and small molecule contaminants, such as antibiotics, have become a growing concern due to their harmful effects on both biological systems and the environment. These contaminants can enter the food supply through the use of antibiotics in animals, potentially causing significant health and ecological damage. As a result, detecting these pollutants, especially at trace levels, has become increasingly important. Aptamer sensors have gained popularity for this purpose because of their high stability, specificity, ease of modification, and low cost. To improve the sensitivity of these sensors, various signal enhancement strategies are used. These strategies aim to better detect small molecule contaminants, with many relying on nanomaterials and nucleic acid amplification techniques to amplify signals. Nanomaterials, which come in different forms such as zero-dimensional, one-dimensional, two-dimensional, and three-dimensional, play a crucial role in improving the performance of these sensors. This article provides an overview of these signal enhancement approaches, discussing the challenges and potential future directions for the development of aptamers in food contamination detection.

Ethylenediamine assist preparation of carbon dots with novel biomass for highly sensitive detection of levodopa

Levodopa (l-Dopa), a precursor drug for dopamine has been widely used to treat Parkinson's disease. However, excess accumulation of l-Dopa in the body may cause movement disorders and uncontrollable emotions. Therefore, it is vital to monitor l-Dopa levels in patients. In this study, a carbon dot (CD)-based fluorescence sensing system was developed for sensitive detection of l-Dopa. The CDs were prepared using a novel biomass, Pandanus amaryllifolius Roxb., as a carbon source via a simple hydrothermal method. Interestingly, it was found that ethylenediamine doping in the preparation system increased the quantum yield of CDs, as well as their fluorescence response sensitivity to l-Dopa. After optimizing the preparation and sensing conditions, the detection limit of l-Dopa decreased from 1.54 μM to 0.05 μM. A complete methodological validation was conducted and the probe was successfully applied to the determination of l-Dopa in fetal bovine serum with excellent precision (RSD ≤ 2.99%) and recoveries of 88.50-99.71%. Overall, this work provides an effective strategy for the regulation of properties of CDs derived from biomass and an innovative method for clinical l-Dopa monitoring.

Aptamer-Based fluorescent DNA biosensor in antibiotics detection

The inappropriate employment of antibiotics across diverse industries has engendered profound apprehensions concerning their cumulative presence within human bodies and food commodities. Consequently, many nations have instituted stringent measures limiting the admissible quantities of antibiotics in food items. Nonetheless, conventional techniques employed for antibiotic detection prove protracted and laborious, prompting a dire necessity for facile, expeditious, and uncomplicated detection methodologies. In this regard, aptamer-based fluorescent DNA biosensors (AFBs) have emerged as a sanguine panacea to surmount the limitations of traditional detection modalities. These ingenious biosensors harness the binding prowess of aptamers, singular strands of DNA/RNA, to selectively adhere to specific target antibiotics. Notably, the AFBs demonstrate unparalleled selectivity, affinity, and sensitivity in detecting antibiotics. This comprehensive review meticulously expounds upon the strides achieved in AFBs for antibiotic detection, particularly emphasizing the labeling modality and the innovative free-label approach. It also elucidates the design principles behind a diverse array of AFBs. Additionally, a succinct survey of signal amplification strategies deployed within these biosensors is provided. The central objective of this review is to apprise researchers from diverse disciplines of the contemporary trends in AFBs for antibiotic detection. By doing so, it aspires to instigate a concerted endeavor toward the development of heightened sensitivity and pioneering AFBs, thereby contributing to the perpetual advancement of antibiotic detection methodologies.

The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology

DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.

Engineering DNA walkers for bioanalysis: A review

Considerable advances have been made in the design, modularization, functionalization, and regulation of DNA nanostructures over the past 40 years. These advances have accelerated the development of DNA nanomachines such as DNA walkers, dynamic nanomachines with walking feet, tracks, and driven forces, which have highly sensitive detection and signal amplification abilities that can be applied to various bioanalytical contexts and therapeutic strategies. Here, we describe a rational design of the nano-bio interface, the kinetics of DNA walkers and the strategies for improving their efficiency and sensitivity. We also outline the various bioanalytic and imaging applications to which DNA walkers have been applied, such as electrochemical and optical measurements, when integrated with other simulation and activation tools. Finally, we compare the performances of novel DNA walker-based strategies for bioanalysis and propose a method to improve DNA walker design.

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.

A three-dimensional dynamic DNA walker-mediated branching hybridization chain reaction for the ultrasensitive fluorescence sensing of ampicillin

In this study, a novel, rapid and ultrasensitive fluorescence strategy using the three-dimensional (3D) dynamic DNA walker (DW)-induced branched hybridization chain reaction (bHCR) has been proposed for the detection of ampicillin (AMP). The sensing system was composed of an Nt·Bbvcl-powered DNA walker blocked by an AMP aptamer, hairpin-shaped DNA track probe (TP) and four kinds of metastable hairpin probes as the substrates of bHCR, which triggered the formation of the split G-quadruplex as the signal molecule. Due to the reasonable design, the specific binding between AMP and its aptamer activated the DW, and the DW moved on the surface of the gold nanoparticles (AuNPs) with the help of Nt·Bbvcl to produce primer probes (PPs), which induced bHCR. The products of the bHCR gathered two split G-quadruplex sequences together to form one complete G-quadruplex. The formed G-quadruplex emitted a strong fluorescence signal in the presence of thioflavin-T (ThT) to achieve the purpose of detecting AMP. The sensitivity of this method was greatly improved by the use of the 3D DNA walker and bHCR. The split G-quadruplex enhanced the signal-to-noise ratio (SNR). Under the optimal experimental conditions, a good correlation was obtained between the fluorescence intensity of the sensing system and the concentration of AMP ranging from 5 pM to 500 nM with a limit of detection (LOD) of 3.68 pM. Simultaneously, the method has been applied to the detection of antibiotics in spiked milk samples with satisfactory results.

Nucleic Acid Amplification Techniques in Immunoassay: An Integrated Approach with Hybrid Performance

An immunoassay is mostly employed for the direct detection of food contaminants, and a molecular assay for targeting nucleic acids employs amplification techniques for distinguishing genes. The integration of an immunoassay with nucleic acid amplification techniques inherits the direct and rapid performance of an immunoassay and the ultrasensitive merit of a molecular assay. Enthusiastic attention has been attracted in recent years on the utilization of isothermal amplification techniques in an immunoassay, as well as the employment of a lateral flow immunoassay in a molecular assay. Thus, this Review discussed these kinds of approaches from two categories: immuno-nucleic acid amplification (I-NAA) and nucleic acid amplification-immunoassay (NAA-I). The advantages, drawbacks, and future developments were discussed for a comprehensive understanding.

Enzyme-powered cascade three-dimensional DNA machine for the ultrasensitive determination of kanamycin

DNA walking machines have been widely used in rapid and sensitive detection. In this work, we develop a single enzyme-powered DNA cascade machine for the ultrasensitive determination of kanamycin. To construct the cascade manner, two types of single-legged three-dimensional DNA walking machine are employed to implement integrated target recognition, signal transduction and signal amplification. Upon adding kanamycin to trigger the upstream machine, the sequential enzymatic cleavage drives the autonomous movement of the walking strand and produces plenty of dye-labeled fragments with fluorescence recovery. Meanwhile, these fragments also serve as walking strands to activate the downstream machine for cascade signal amplification. Taking advantage of this cascade DNA machine, ultrasensitive determination can be accomplished in 60 min. Under the optimum conditions, this method was highly selective toward kanamycin with a detection limit of 28 fM. This cascade signal amplification shows great potential for the rapid screening of antibiotics in food.