A visual Hg2+ detection strategy based on distance as readout by G-quadruplex DNAzyme on microfluidic paper

Self-protective DNAzyme-based dual-responsive three-way Y-probe for simultaneous determination of multiple pathogenic bacteria

Foodborne pathogens, a major cause of foodborne illness due to their high virulence, pose a serious threat to public health. Consequently, identification of foodborne pathogens is essential for the prevention and treatment of foodborne infections. Consequently, there is an immediate need to establish a highly specific and precise approach for the concurrent detection of several foodborne pathogens. Herein, we developed a DNAzyme-based self-protecting dual-response nanoprobe for the simultaneous detection of two foodborne pathogens. The technique utilizes nanostructures to achieve logical signal input and output. In the presence of the target pathogen, the pathogen binds to the arch probe and releases the activation chain, which in turn activates a strand-displacement reaction and DNAzyme for signal amplification, producing different output signals to complete the simultaneous detection of multiple pathogens. The limits of detection for E. coli O157:H7 and S. typhimurium were determined to be 3.7 cfu/mL and 3.2 cfu/mL, with a measurement response time of 2 h. This approach enables ultrasensitive, specific, and simultaneous detection of two foodborne pathogens and is applicable for identifying foodborne pathogens in actual biological samples. The fluorescence detection of foodborne pathogens with a three-way Y-probe and DNAzyme coupling represents a novel approach for the concurrent identification of several foodborne diseases.

Multiple DNA cycle amplification for highly efficient detection of mercury pollution in food

Mercury ion (Hg2+), a highly toxic metal pollutant, is widely found in the environment and can enter the human body through the food chain, causing various health issues. Sensitive and accurate methods for monitoring Hg2+ are highly desirable for ensuring food safety. Herein, we propose a self-sustainable multiple amplification system (MAS) for Hg2+ determination through the reciprocal activation between catalytic hairpin assembly (CHA) and rolling circle amplification (RCA). The thymine-encoded recognition element specifically recognizes Hg2+, triggering the exposure of the initiator. The initiator then motivates the mutual activation of CHA and RCA to accelerate the production of an exponentially amplified signal. The MAS method achieved a low detection limit of 11 pM. Due to its reliable target recognition and robust amplification efficiency, the MAS circuit facilitated the highly efficient and accurate analysis of low-abundance Hg2+ in milk and snakehead samples, thus providing a potentially new tool for food safety control.

Microfluidics in environmental analysis: advancements, challenges, and future prospects for rapid and efficient monitoring

Microfluidic devices have emerged as advantageous tools for detecting environmental contaminants due to their portability, ease of use, cost-effectiveness, and rapid response capabilities. These devices have wide-ranging applications in environmental monitoring of air, water, and soil matrices, and have also been applied to agricultural monitoring. Although several previous reviews have explored microfluidic devices' utility, this paper presents an up-to-date account of the latest advancements in this field for environmental monitoring, looking back at the past five years. In this review, we discuss devices for prominent contaminants such as heavy metals, pesticides, nutrients, microorganisms, per- and polyfluoroalkyl substances (PFAS), etc. We cover numerous detection methods (electrochemical, colorimetric, fluorescent, etc.) and critically assess the current state of microfluidic devices for environmental monitoring, highlighting both their successes and limitations. Moreover, we propose potential strategies to mitigate these limitations and offer valuable insights into future research and development directions.

One-step and real-time detection of Hg2+ in brown rice flour using a biosensor integrated with AC electrothermal enrichment

Mercury (Hg²⁺) is one of the most toxic heavy metals in farm products, so rapid detection of trace Hg²⁺ has always been sought after with high interest. Herein, we report a biosensor to specifically recognize Hg²⁺ in leaching solutions of brown rice flour. This sensor is simple and of low cost, with a very short assay time of 30 s. Another merit is the ultra-low limit of detection (LOD) at fM level. In addition, the specific aptamer probe realizes a good selectivity above 10⁵: 1 against the interferences. This sensor is developed based on an aptamer-modified gold electrode array (GEA) for capacitive sensing. Alternating current electrothermal (ACET) enrichment is induced during the AC capacitance acquirement. Thus, the enrichment and detection are coupled as a single step, and pre-concentration is needless. Owing to the sensing mechanism of solid-liquid interfacial capacitance and ACET enrichment, Hg²⁺ level can be sensitively and rapidly reflected. Also, the sensor has a wide linear range from 1 fM to 0.1 nM and a shelf life of 15 days. This biosensor shows advantages on overall performance, enabling easy-to-operate, real-time, and large-scale Hg²⁺ detection in farm products.

Clarity improvement of the discoloration boundary and detection of Hg2+ ions by using a polystyrene nanoparticle-modified paper-based microdevice

Distance-based microfluidic paper-based analytical devices (μPADs) can be used to calculate the analyte content by reading the length of the discolored area in the channel. A blurred discoloration boundary is difficult to distinguish, resulting in reading errors. In this study, we constructed a μPAD modified with carboxyl-containing polystyrene nanoparticles (PS-μPAD) to improve the discoloration-boundary clarity. The filling of the pores of the fibers with the deposited polystyrene nanoparticles (PS NPs) caused a decrease in the paper porosity, resulting in a flow delay. Meanwhile, the carboxyl groups carried by PS NPs were able to form hydrogen bonds with hydroxyl-containing compounds FLPI, a Hg²⁺ probe, and the two factors acted synergistically to fix the FLPI to react in situ, raising the discoloration-boundary clarity. Compared with the unmodified μPAD, the detection of Hg²⁺ ions using the PS-μPAD still had a good linear relationship. Importantly, the color-depth difference inside and outside the discoloration boundary improved by about four times and showed excellent reproducibility in different populations. The method was simple and easy to expand, thereby providing an idea for more widespread application of distance-based μPADs.

Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing

DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.

Colorimetric Sensors for Chemical and Biological Sensing Applications

Colorimetric sensors have been widely used to detect numerous analytes due to their cost-effectiveness, high sensitivity and specificity, and clear visibility, even with the naked eye. In recent years, the emergence of advanced nanomaterials has greatly improved the development of colorimetric sensors. This review focuses on the recent (from the years 2015 to 2022) advances in the design, fabrication, and applications of colorimetric sensors. First, the classification and sensing mechanisms of colorimetric sensors are briefly described, and the design of colorimetric sensors based on several typical nanomaterials, including graphene and its derivatives, metal and metal oxide nanoparticles, DNA nanomaterials, quantum dots, and some other materials are discussed. Then the applications, especially for the detection of metallic and non-metallic ions, proteins, small molecules, gas, virus and bacteria, and DNA/RNA are summarized. Finally, the remaining challenges and future trends in the development of colorimetric sensors are also discussed.

A Synergistic Dual-Channel Sensor for Ultrasensitive Detection of Pseudomonas aeruginosa by DNA Nanostructure and G-Quadruplex

Pseudomonas aeruginosa is one of the foodborne pathogenic bacteria that greatly threatens human health. An ultrasensitive technology for P. aeruginosa detection is urgently demanded. Herein, based on the mechanism of aptamer-specific recognition, an electrochemical-colorimetric dual-mode ultrasensitive sensing strategy for P. aeruginosa is proposed. The vertices of DNA tetrahedral nanoprobes (DTNPs), that immobilized on the gold electrode were modified with P. aeruginosa aptamers. Furthermore, the G-quadruplex, which was conjugated with a P. aeruginosa aptamer, was synthesized via rolling circle amplification (RCA). Once P. aeruginosa is captured, a hemin/G-quadruplex, which possesses peroxidase-mimicking activity, will separate from the P. aeruginosa aptamer. Then, the exfoliated hemin/G-quadruplexes are collected for oxidation of the 3,3',5',5'-tetramethylbenzidine for colorimetric sensing. In the electrochemical mode, the hemin/G-quadruplex that is still bound to the aptamer catalyzes polyaniline (PANI) deposition and leads to a measurable electrochemical signal. The colorimetric and electrochemical channels demonstrated a good forward and reverse linear response for P. aeruginosa within the range of 1-10⁸ CFU mL^-1, respectively. Overall, compared with a traditional single-mode sensor for P. aeruginosa, the proposed dual-mode sensor featuring self-calibration not only avoids false positive results but also improves accuracy and sensitivity. Furthermore, the consistency of the electrochemical/colorimetric assay was verified in practical meat samples and showed great potential for applications in bioanalysis.

The Road to Unconventional Detections: Paper-Based Microfluidic Chips

Conventional detectors are mostly made up of complicated structures that are hard to use. A paper-based microfluidic chip, however, combines the advantages of being small, efficient, easy to process, and environmentally friendly. The paper-based microfluidic chips for biomedical applications focus on efficiency, accuracy, integration, and innovation. Therefore, continuous progress is observed in the transition from single-channel detection to multi-channel detection and in the shift from qualitative detection to quantitative detection. These developments improved the efficiency and accuracy of single-cell substance detection. Paper-based microfluidic chips can provide insight into a variety of fields, including biomedicine and other related fields. This review looks at how paper-based microfluidic chips are prepared, analyzed, and used to help with both biomedical development and functional integration, ideally at the same time.

Real-Time Visual Sensing of Heat or Mass Transfer Processes for Microfluids via Tamm Plasmon Polaritons

Heat or mass transfer processes of microfluids are very important in bioscience, environmental engineering, and food science, which are still hard to detect in real time. To overcome this difficulty, we try to use Tamm plasmon polaritons to enhance the interaction of light with microfluids. The main structure of the proposed configuration is Ag-photonic crystal (PhC) cavity, which can generate strong photonic localization by exciting Tamm plasmon polaritons. The results show that the enhancement of light intensity reaches ∼90 times in the cavity and the reflectance spectrum of the proposed structure exists in a narrow valley near 632.8 nm. This illustrates the generation of Tamm plasmon polaritons in the proposed structure. By injecting the microfluids into the cavity, the heat and mass transfer processes of the microfluids will have considerable influence on the reflectance of the proposed structure. Simulation results show that the concentration or temperature distributions of the microfluids can be effectively detected by analyzing the brightness of the imaging pictures, which is real-time and visible. Meanwhile, the sensitivity of the proposed configuration can be tuned by setting proper base parameters. This proposed configuration will have great potential in the study of microfluids, especially for the dynamic processes.

DNAzyme-based biosensors for mercury (Ⅱ) detection: Rational construction, advances and perspectives

Mercury contamination is one of the most severe issues in society due to its threats to public health and the ecological system. However, traditional methods for mercury ion detection are still limited by their time-consuming procedures, requirement of expensive instruments, and low selectivity. In recent decades, tremendous progress has been made in the development of functional nucleic acid-based, especially DNAzyme sensors for mercury (Ⅱ) (Hg²⁺) determination, including RNA-cleaving DNAzymes and G-quadruplex-based DNAzymes in particular. Researchers have heavily studied the construction of Hg²⁺ sensors, mainly originating from in vitro selection-derived DNAzymes, by incorporating T-Hg²⁺-T recognition moieties in existing DNAzyme scaffolds, and interfacing Hg²⁺-sensitive sequences with nanomaterials. In the last case, the employment of materials (as quenchers, signal transducers and DNA immobilizers) enriches the application scenarios of current Hg²⁺-DNAzymes, due to a combination of their functions. We summarize a broad range of sensing approaches, including optical, electrochemical, and other sensing methods, and compare their features. This review elaborates on the rational design strategies for engineering DNAzymes to selectively sense Hg²⁺, critically discusses their properties in different application scenarios, and summarizes recent advances in this field. Additionally, current progress, challenges and future perspectives are also discussed. This minireview provides deeper insights into the chemistry of these functional nucleic acids when working with Hg²⁺, explains the design ideas of DNAzyme-sensors in each platform, and reveals potential opportunities in developing more advanced DNAzyme sensors for the highly selective and sensitive recognition of Hg²⁺. ENVIRONMENTAL IMPLICATION: Mercury is one of the most toxic metallic contaminants due to its high toxicity, non-biodegradability, and serious human health risks when accumulated in the body. In the recent decade, intensive studies have focused on exploring mercury sensors by combining DNAzymes with various sensing methods, paving a promising avenue to gain ultra-high sensitivity and selectivity. However, so far, no review has introduced the recent advances on DNAzyme-based sensors for mercury detection in a critical way. In this review, we comprehensively summarized the studies on DNAzyme-based sensors for mercury detection using various sensing techniques including optical, electrochemical and other sensing methods.

G-quadruplex based biosensors for the detection of food contaminants

G-quadruplex (G4) is a very interesting DNA structure, commonly associated with cancer and its treatment. With flexible binding ability, G4 has been extended as a significant component in biosensors. On account of its simple operation, high sensitivity and low cost, G4-based biosensors have attracted considerable interest for the detection of food contaminants. In this review, research published in recent 5 years is collated from a principle perspective, that is target recognition and signal transduction. Contaminants with G4 binding capacity are illustrated, emerging G4-based biosensors including colorimetric, electrochemical and fluorescent sensors are also elaborated. The current review indicates that G4 has provided an efficient and effective solution for the rapid detection of food contaminants. A distinctive feature of G4 as recognition unit is the simple composition, but the selectivity is still unsatisfactory. As signal reporter, G4/hemin DNAzyme has not only achieved amplified signals, but also enabled visualized detection, which offers great potential for on-site measurement. With improved selectivity and visualized signal, the combination of aptamer and G4 seems to be an ideal strategy. This promising combination should be developed for the real-time monitor of multiple contaminants in food matrix.

Engineering DNA G-quadruplex assembly for label-free detection of Ochratoxin A in colorimetric and fluorescent dual modes

Colorimetric and fluorescent methods for Ochratoxin A (OTA) detection are convenient and well received. However, the pigments and autofluorescence originated from food matrices often interfere with detection signals. We have developed a strategy with colorimetric and fluorescent dual modes to solve this challenge. In the colorimetric mode, OTA aptamer (AP9) was assembled into a DNA triple-helix switch with a specially designed signal-amplifying sequence. The OTA-induced G-quadruplex (G4) of AP9 would open the switch and release the signal-amplifying sequence for colorimetric signal amplification. The G4 structures of AP9 were further utilized to combine with the fluorogenic dye ThT for fluorescent mode. By skillfully engineering DNA G4 assembly for signal amplification, there was no need for any DNA amplification or nanomaterials labeling. Detections could be carried out in a wide temperature range (22-37 ℃) and finished rapidly (colorimetric mode, 60 min; fluorescent mode, 15 min). Broad linear ranges (colorimetric mode, 10-1.5 ×10³ μg/kg; fluorescent mode, 0.05-1.0 ×10³ μg/kg) were achieved. The limit of detection for colorimetric and fluorescent modes were 4 μg/kg and 0.01 μg/kg, respectively. The two modes have been successfully applied to detect OTA in samples with intrinsic pigments and autofluorescence, showing their applicability and reliability.

Recent Advances and Applications in Paper-Based Devices for Point-of-Care Testing

Point-of-care testing (POCT), as a portable and user-friendly technology, can obtain accurate test results immediately at the sampling point. Nowadays, microfluidic paper-based analysis devices (μPads) have attracted the eye of the public and accelerated the development of POCT. A variety of detection methods are combined with μPads to realize precise, rapid and sensitive POCT. This article mainly introduced the development of electrochemistry and optical detection methods on μPads for POCT and their applications on disease analysis, environmental monitoring and food control in the past 5 years. Finally, the challenges and future development prospects of μPads for POCT were discussed.

DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective

Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.

G-quadruplex DNAzyme as peroxidase mimetic in a colorimetric biosensor for ultrasensitive and selective detection of trace tetracyclines in foods

The colorimetric method can determine the initial results even by the naked eyes, but its main challenge for antibiotics detection in food at present is the relatively low sensitivity. Herein, an ultrasensitive colorimetric biosensor based on G-quadruplex DNAzyme was firstly proposed for the rapid detection of trace tetracycline antibiotics like tetracycline, oxytetracycline, chlortetracycline and doxycycline. DNAzyme composed of hemin and G-quadruplex has peroxidase-like activity, and tetracyclines can combine with hemin to form a stable complex and reduce catalytic activity, making the color of solution changes from yellow to green. The limits of detection (LOD) of the proposed colorimetric biosensor for tetracyclines is determined as low as 3.1 nM, which is lower than most of the other colorimetric methods for antibiotics detection. Moreover, the average recovery range of tetracyclines in actual samples is from 89% to 99%, indicating that such strategy may has bright application prospects for tetracyclines detection in foods.

Development of DNA Biosensors Based on DNAzymes and Nucleases

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.

A Simple Distance Paper-Based Analytical Device for the Screening of Lead in Food Matrices

A simple and rapid distance paper-based analytical device (dPAD) for the detection of lead (Pb) in foods is proposed herein. The assay principle is based on competitive binding between carminic acid (CA) and polyethyleneimine (PEI) to Pb in a food sample. The paper channels were pre-immobilized with PEI, before reacting with a mixture of the sample and CA. Pb can strongly bind to the CA; hence, the length of the red color deposition on the flow channel decreased as a lower amount of free CA bound to PEI. The dPAD exhibited good linear correlation, with ranges of 5-100 µg·mL-1 (R2 = 0.974) of Pb. Although, the limit of detection (LOD) of this platform was rather high, at 12.3 µg·mL-1, a series of standard additions (8.0, 9.0, and 10.0 µg·mL-1) can be used to interpret the cutoff of Pb concentrations at higher or lower than 2 µg·mL-1. The presence of common metal ions such as calcium, magnesium, nickel, and zinc did not interfere with the color distance readout. The validity of the developed dPAD was demonstrated by its applicability to screen the contamination of Pb in century egg samples. The results obtained from the dPAD are in accordance with the concentration measured by atomic absorption spectroscopy (AAS) (n = 9). In conclusion, this proposed dPAD, combined with the standard addition method, could be applied for screening Pb contamination in food matrices. This platform is, therefore, potentially applicable for field measurements of Pb in developing countries, because it is cheap and rapid, and it requires no significant laborious instruments.

Construction of DNA Biosensors for Mercury (II) Ion Detection Based on Enzyme-Driven Signal Amplification Strategy

Mercury ion (Hg²⁺) is a well-known toxic heavy metal ion. It is harmful for human health even at low concentrations in the environment. Therefore, it is very important to measure the level of Hg²⁺. Many methods, reviewed in several papers, have been established on DNA biosensors for detecting Hg²⁺. However, few reviews on the strategy of enzyme-driven signal amplification have been reported. In this paper, we reviewed this topic by dividing the enzymes into nucleases and DNAzymes according to their chemical nature. Initially, we introduce the nucleases including Exo III, Exo I, Nickase, DSN, and DNase I. In this section, the Exo III-driven signal amplification strategy was described in detail. Because Hg²⁺ can help ssDNA fold into dsDNA by T-Hg-T, and the substrate of Exo III is dsDNA, Exo III can be used to design Hg²⁺ biosensor very flexibly. Then, the DNAzyme-assisted signal amplification strategies were reviewed in three categories, including UO₂²⁺-specific DNAzymes, Cu²⁺-specific DNAzymes and Mg²⁺-specific DNAzymes. In this section, the Mg²⁺-specific DNAzyme was introduced in detail, because this DNAzyme has highly catalytic activity, and Mg²⁺ is very common ion which is not harmful to the environment. Finally, the challenges and future perspectives were discussed.

Research progress on the applications of paper chips

Due to the modern pursuit of the quality of life, science and technology have rapidly developed, resulting in higher requirements for various detection methods based on analytical technology. Herein, the development, fabrication, detection and application of paper-based microfluidic chips (μPAD) are summarized. We aim to provide a comprehensive understanding of paper chips, and then discuss challenges and future prospects in this field.

Silver ion-doped CdTe quantum dots as fluorescent probe for Hg2+ detection

Mercury(ii), which is a well-known toxic species, exists in the industrial waste water in many cases. In the present work, CdTe quantum dots (QDs) are studied as a fluorescence probe for Hg²⁺ detection. Ag ions are induced to QDs to enlarge their detection concentration range. l-cysteine is employed in the QD-based fluorescence probe to connect QDs with Hg²⁺. X-ray diffraction, transmission electron microscopy and X-ray photoelectron spectroscopy results indicate the formation of zinc blende CdTe QDs with sizes of ∼5 nm and the existence of Ag⁺ in crystalline CdTe. Photoluminescence (PL) spectra and PL decay spectra were acquired to investigate the emission mechanism of Ag-doped CdTe QDs, revealing multi-emission in QD samples with higher concentrations of Ag⁺ doping. The highest PL quantum yield of the QD samples was 59.4%. Furthermore, the relationship between the fluorescence intensity and the concentration of Hg²⁺ has been established. Two linear relationships were obtained for the plot of F/F₀ against Hg²⁺ concentration, enlarging the detection concentration range of Hg²⁺.

Ag-doped CdTe QDs emit multiple-fluorescence peaks, and the relationship between fluorescence intensity and the concentration of Hg²⁺ is established. Two linear relationships are obtained, which is benefit to the extension of detection range.