Label-Free and Enzyme-Free Colorimetric Detection of Pb2+ Based on RNA Cleavage and Annealing-Accelerated Hybridization Chain Reaction

Label-free and ultrasensitive detection of environmental lead ions based on spatially localized DNA nanomachines driven by hyperbranched hybridization chain reaction

A label-free fluorescent sensing strategy for the rapid and highly sensitive detection of Pb2+ was developed by integrating Pb2+ DNAzyme-specific cleavage activity and a tetrahedral DNA nanostructure (TDN)-enhanced hyperbranched hybridization chain reaction (hHCR). This strategy provides accelerated reaction rates because of the highly effective collision probability and enriched local concentrations from the spatial confinement of the TDN, thus showing a higher detection sensitivity and a more rapid detection process. Moreover, a hairpin probe based on a G-triplex instead of a G-quadruplex or chemical modification makes hybridization chain reaction more controlled and flexible, greatly improving signal amplification capacities and eliminating labeled DNA probes. The enhanced reaction rates and improved signal amplification efficiency endowed the biosensors with high sensitivity and a rapid response. The label-free detection of Pb2+ based on G-triplex combined with thioflavin T can be achieved with a detection limit as low as 1.8 pM in 25 min. The proposed Pb2+-sensing platform was also demonstrated to be applicable for Pb2+ detection in tap water, river water, shrimp, rice, and soil samples, thus showing great potential for food safety and environmental monitoring.

CRISPR/Cas12a-derived ratiometric fluorescence sensor for high-sensitive Pb2+ detection based on CDs@ZIF-8 and DNAzyme

Benefiting from specific target recognition and trans-cleavage capabilities, the CRISPR/Cas12a system has great application prospects in the design of highly sensitive and rapid fluorescence biosensors. The CRISPR/Cas12a-based fluorophore-quencher molecular beacons exhibit single-color emission and are easily exposed to interference from environmental factors. Herein, we design a CRISPR/Cas12a-derived ratiometric fluorescence sensor for Pb2+ detection based on embedded carbon dots@zeolitic imidazolate framework-8 (CDs@ZIF-8) composites and DNAzyme. The functions of ZIF-8 about encapsulating red emissive CDs in the inner cavity and adsorbing DNA on the outer surface are integrated to establish dual fluorescence signals, thereby reducing the possibility of interference and improving sensing accuracy. The presence of Pb2+ is converted into the change of activator by the GR5 DNAzyme to activate the CRISPR/Cas12a system, which provides signal amplification through multiple turnovers of side branch cutting, achieving highly sensitive detection of Pb2+ with a low detection limit of 18 pM. This method has the advantages of simplicity, universality, and excellent quantitative ability, and has broad prospects in sensing applications.

Exonuclease III-propelled DNAzyme walker: an electrochemical strategy for microRNA diagnostics

MicroRNA detection is crucial for early infectious disease diagnosis and rapid cancer screening. However, conventional techniques like reverse transcription-quantitative polymerase chain reaction, requiring specialized training and intricate procedures, are less suitable for point-of-care analyses. To address this, we've developed a straightforward amplifier based on an exonuclease III (exo III)-propelled DNAzyme walker for sensitive and selective microRNA detection. This amplifier employs a specially designed hairpin probe with two exposed segments for strand recognition. Once the target microRNA is identified by the hairpin's extended single-strand DNA, exo III initiates its digestion, allowing microRNA regeneration and subsequent hairpin probe digestion cycles. This cyclical process produces a significant amount of DNAzyme, leading to a marked reduction in electrochemical signals. The biosensor exhibits a detection range from 10 fM to 100 pM and achieves a detection limit of 5 fM (3σ criterion). Importantly, by integrating an "And logic gate," our system gains the capacity for simultaneous diagnosis of multiple microRNAs, enhancing its applicability in RNA-based disease diagnostics.

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.

Recent Advances in Design and Application of Nanomaterials-Based Colorimetric Biosensors for Agri-food Safety Analysis

A colorimetric sensor detects an analyte by utilizing the optical properties of the sensor unit, such as absorption or reflection, to generate a structural color that serves as the output signal to detect an analyte. Detecting the refractive index of an analyte by recording the color change of the sensor structure on its surface has several advantages, including simple operation, low cost, suitability for onsite analysis, and real-time detection. Colorimetric sensors have drawn much attention owing to their rapidity, simplicity, high sensitivity and selectivity. This Review discusses the use of colorimetric sensors in the food industry, including their applications for detecting food contaminants. The Review also provides insight into the scope of future research in this area.

A Self-Assembled G-Quadruplex/Hemin DNAzyme-Driven DNA Walker Strategy for Sensitive and Rapid Detection of Lead Ions Based on Rolling Circle Amplification

Herein, a sensitive biosensor is constructed based on a novel rolling circle amplification (RCA) for colorimetric quantification of lead ion (Pb2+). At the detection system, GR5 DNAzymes are modified on the surface of an immunomagnetic bead, and Pb2+ is captured by the aptamer, inducing the disintegration of the GR5 DNAzyme and the release of the DNA walker. After the introduction of the template DNA, T4 DNA ligase, and phi29 DNA polymerase, an RCA is initiated for the sensitivity improvement of this method. Moreover, a G4-hemin DNAzyme is formed as a colorimetric signal, owing to its peroxide-like activity to catalyze the TMB-H2O2 substrate. Under the optimized conditions, the limit of detection (LOD) of this fabricated biosensor could reach 3.3 pM for Pb2+ with a concentration in the range of 0.01-1000 nM. Furthermore, the results of real samples analysis demonstrate its satisfactory accuracy, implying its great potential in the rapid detection of heavy metals in the environment.

The development of a paper-based distance sensor for the detection of Pb2+ assisted with the target-responsive DNA hydrogel

Due to the serious risks of lead pollution to human health, it plays a great role in constructing a simple, inexpensive, portable, and user-friendly strategy for Pb²⁺ detection in environmental samples. Herein, a paper-based distance sensor is developed to detect Pb²⁺ assisted with the target-responsive DNA hydrogel. Pb²⁺ can activate DNAzyme to cleave its substrate strand, which results in the hydrolysis of the DNA hydrogel. The released water molecules trapped in the hydrogel can flow along the patterned pH paper due to the capillary force. The water flow distance (WFD) is significantly influenced by the amount of water released from the collapsed DNA hydrogel triggered by the addition of various Pb²⁺ concentrations. In this way, Pb²⁺ can be quantitatively detected without using specialized instruments and labeled molecules, and the limit of detection (LOD) of Pb²⁺ is 3.0 nM. Additionally, the Pb²⁺ sensor works well in lake water and tap water. Overall, this simple, inexpensive, portable, and user-friendly method is very promising for quantitative and in-field detection of Pb²⁺ with excellent sensitivity and selectivity.

A novel highly sensitive compilation-detachment fluorescence sensing strategy based on RNA-cleavage DNAzyme for MDA-MB-231 breast cancer biomarker determination

Herein, we designed a novel and highly sensitive fluorescence multicomponent detachable platform for MDA-MB-231 breast cancer cell detection as a model. The RNA cleavage DNAzyme was used as a central operator of the multicomponent probe through which compilation and induced detachment of probe was done. During the compilation step, the dsDNA-Sybr green 1 complexes on gold nanoparticles (GNP@dsDNA@SG1) were assembled. The intercalated Sybr green in the DNA structure has been used as an amplified signal generator on one site of DNAzyme and magnetic nanoparticles (MNP) act as a biological carrier and probe collector on the opposite side. The enzyme activator co-factor (MDA-MB-231 cell cytoplasmic protein) provokes the activation of the catalytic core of enzyme sequence in the DNAzyme molecule, followed by cleavage reaction in the substrate sequence and releasing GNP@ dsDNA@SG1 into the solution. The results indicate that the Sybr green emission fluorescence (520 nm) increases with the increment of MDA-MB-231 protein concentration in the linear dynamic range of 8.10 × 10^-2 to 1.95 ng ml^-1 (0.77 × 10^-3-0.019 cell ml^-1) with a detection limit (LOD) of 1/72 × 10^-2 pg ml^-1 under optimal conditions. The proposed immunosensor has great potential in developing ultrasensitive and rapid diagnostic platforms.

Colorimetric detection of heavy metal ions with various chromogenic materials: Strategies and applications

Detection of heavy metal ions has drawn significant attention in environmental and food area due to their threats to the human health and ecosystem. Colorimetry is one of the most frequently-used methods for the detection of heavy metal ions owing to its simplicity, easy operation and rapid on-site detection. The development of chromogenic materials and their sensing mechanisms are the key research direction in the area of colorimetric method. Since each chromogenic material has their unique optical and chemical properties, they have totally different colorimetric sensing mechanisms. This review focuses on the chromogenic materials and their sensing strategies for the colorimetric detection of heavy metal ions. We divide the chromogenic materials into three types, including organic materials, inorganic materials, and other materials. As for each type of chromogenic material, we discuss their detailed sensing strategies, sensing performance, and real sample applications. Moreover, current challenges and perspectives related to the colorimetry of heavy metal ions are also discussed in this review. The aim of this review is to help readers to better understand the principles of colorimetric methods for heavy metal ions and push the development of rapid detection of heavy metal ions.

Platform Formed from ZIF-8 and DNAzyme: "Turn-On" Fluorescence Assay for Simple, High-Sensitivity, and High-Selectivity Detection of Pb2

Lead contamination has posed a potential threat to the environment and food safety, arousing extensive concern. In this work, we fabricated a novel fluorescent sensing platform based on zeolitic imidazolate framework-8 (ZIF-8) and DNAzyme for monitoring Pb²⁺ in water and fish samples. ZIF-8 was proposed as a fluorescence quencher with the advantages of simple synthesis, low cost, and high quenching efficiency. The Pb²⁺-dependent GR5 DNAzyme containing the large ssDNA loop can be adsorbed onto ZIF-8 accompanied by fluorescence quenching. Upon binding with Pb²⁺, GR5 DNAzyme was activated and cleaved, leading to the release of FAM-labeled 5-base ssDNA, which restored the fluorescence. The "turn-on" assay can detect Pb²⁺ through the one-pot procedure in the range of 0.01-10.0 nM with a detection limit of 7.1 pM. The platform is promising for on-site monitoring of Pb²⁺ owing to the excellent performance of high sensitivity, low background, strong anti-interference ability, and simple operation.

Amplification of the Fluorescence Signal with Clustered Regularly Interspaced Short Palindromic Repeats-Cas12a Based on Au Nanoparticle-DNAzyme Probe and On-Site Detection of Pb2+ Via the Photonic Crystal Chip

Although great headway has been made in DNAzyme-based detection of Pb²⁺, its adaptability, sensitivity, and accessibility in complex media still need to be improved. For this, we introduce new ways to surmount these hurdles. First, a spherical nucleic acid (SNA) fluorescence probe (Au nanoparticles-DNAzyme probe) is utilized to specifically identify Pb²⁺ and its suitability for precise detection of Pb²⁺ in complex samples due to its excellent nuclease resistance. Second, the sensitivity of Pb²⁺ detection is greatly enhanced via the use of a clustered regularly interspaced short palindromic repeats-Cas12a with target recognition accuracy to amplify the fluorescent signal upon the trans cleavage of the SNA (signal probe), and the limit of detection reaches as low as 86 fM. Third, we boost the fluorescence on photonic crystal chips with a bionic periodic arrangement by employing a straightforward detection device (smartphone and portable UV lamp) to achieve on-site detection of Pb²⁺ with the limit of detection as low as 24 pM. Based on the abovementioned efforts, the modified Pb²⁺ fluorescence sensor has the advantages of higher sensitivity, better specificity, accessibility, less sample consumption, and so forth. Moreover, it can be applied to accurately detect Pb²⁺ in complex biological or environmental samples, which is of great promise for widespread applications.

Stabilization of Gold Nanoparticles by Hairpin DNA and Implications for Label-Free Colorimetric Biosensors

With extremely high extinction coefficients and other unique optical properties, gold nanoparticles (AuNPs) have received growing interest in developing biosensors. DNA hairpin structures are very popular probes for the detection of not only complementary DNA or RNA but also aptamer targets. This work aims to understand the effect of the structure and sequence of hairpin DNA for the stabilization of AuNPs and its implications in AuNP-based label-free colorimetric biosensors. A series of hairpin DNA with various loop sizes from 4 to 26 bases and sequences (random sequences, poly-A and poly-T) were tested, but they showed similar abilities to protect AuNPs from aggregation. Using hairpin DNA with a tail under the same conditions, optimal protection was achieved with a six-base or longer tail. DNA hairpins are likely adsorbed via their tail regions or with their terminal bases if no tail is present. Molecular dynamics simulations showed that the rigidity of the hairpin loop region disfavored its adsorption to AuNPs, while the flexible tail region is favored. Finally, a DNA sensing assay was conducted using different structured DNA, where hairpin DNA with a tail doubled the sensitivity compared to the tail-free hairpin.

DNAzyme-based cascade signal amplification strategy for highly sensitive detection of lead ions in the environment

Lead ions are one of many common environmental pollutants, that can cause posing a serious threat to people's health, thus, their efficient and sensitive detection is important. We propose a cascade signal amplification sensor using a DNAzyme-based strand displacement amplification (SDA) and hybridization chain reaction (HCR) for the high-sensitivity detection of Pb²⁺. In the demonstrated sensor system, the target metal ion can activate DNAzyme to cause a strand displacement reaction. Under the synergistic action of polymerase and nickase, large numbers of DNA strands are generated that can initiate HCR. The subsequent HCR can restore the fluorescence intensity of the FAM quenched for the fluorescence resonance energy transfer effect, which exhibits a strong fluorescence signal. The DNAzyme-based sensor allowed the detection of Pb²⁺ down to 16.8 pM and resulted in a good dynamic line relationship ranging from 50 pM to 500 nM, and the biosensor also showed good selectivity. Furthermore, we confirmed that the proposed sensor can still detect lead ions in complex environments such as lake water, milk, and serum. We believe these findings will provide new ideas for the detection of toxic elements ions in the environment and food.

A new Fe/N doped carbon dot naocatalytic amplification-aptamer SERS/RRS/Abs trimode assay platform for ultratrace Pb2

Nanocatalytic amplification of carbon dots is a new way to improve sensitivity. The preparation of the high catalytic activity and stable iron/nitrogen-doped carbon dot (CD_BFe) sol and its application in aptamer (Apt) assay have not been reported yet. In this paper, a simple hydrothermal procedure for the preparation of CD_BFe derived from Fe²⁺-2,2'-bipyridine complex has been developed. It is found that CD_BFe has a strong catalytic effect on the indicator reaction of glyoxal (C₂H₂O₂) reduction of HAuCl₄ to produce gold nanoparticle (AuNP) probe with strong surface enhanced Raman scattering (SERS) at 1617 cm^-1, resonance Rayleigh scattering (RRS) effect at 370 nm and absorption (Abs) at 550 nm. A rapid and sensitive CD_BFe catalytic amplification Apt method for SERS/RRS/Abs trimode detecting ultratrace lead ions was established, based on the Apt reaction mediated the nanocatalytic indicator reaction. The results show that the SERS intensity and Pb(II) concentration have a good linear relationship in the range of 1.3-16 pM, and the detection limit is the lowest. In addition, Hg(II) and As(III) can also be measured by this naocatalytic amplification- Apt assay platform.

Gold nanoparticle-based optical nanosensors for food and health safety monitoring: recent advances and future perspectives

Modern society has been facing serious health-related problems including food safety, diseases and illness. Hence, it is urgent to develop analysis methods for the detection and control of food contaminants, disease biomarkers and pathogens. As the traditional instrumental methods have several disadvantages, including being time consuming, and having high cost and laborious procedures, optical nanosensors have emerged as promising alternative or complementary approaches to those traditional ones. With the advantages of simple preparation, high surface-to-volume ratio, excellent biocompatibility, and especially, unique optical properties, gold nanoparticles (AuNPs) have been demonstrated as excellent transducers for optical sensing systems. Herein, we provide an overview of the synthesis of AuNPs and their excellent optical properties that are ideal for the development of optical nanosensors based on local surface plasmon resonance (LSPR), colorimetry, fluorescence resonance energy transfer (FRET), and surface-enhanced Raman scattering (SERS) phenomena. We also review the sensing strategies and their mechanisms, as well as summarizing the recent advances in the monitoring of food contaminants, disease biomarkers and pathogens using developed AuNP-based optical nanosensors in the past seven years (2015-now). Furthermore, trends and challenges in the application of these nanosensors in the determination of those analytes are discussed to suggest possible directions for future developments.

Applications of hybridization chain reaction optical detection incorporating nanomaterials: A review

The development of powerful, simple and cost-effective signal amplifiers has significant implications for biological research and analysis. Hybridization chain reaction (HCR) has attracted increasing attention because of its enzyme-free, simple, and efficient amplification. In the HCR process, an initiator probe triggered a pair of metastable hairpins through a cross-opening process to propagate a chain reaction of hybridization events, yielding a long-nicked double-stranded nucleic acid structure. To achieve more noticeable signal amplification, nanomaterials, including graphene oxide, quantum dots, gold, silver, magnetic, and other nanoparticles, were integrated with HCR. Various types of colorimetric, fluorescence, plasmonic analyses or chemiluminescence optical sensing strategies incorporating nanomaterials have been developed to analyze various targets, such as nucleic acids, small biomolecules, proteins, and metal ions. This review summarized the recent advances of HCR technology pairing diverse nanomaterials in optical detection and discussed their challenges.

Signal amplification of SiO2 nanoparticle loaded horseradish peroxidase for colorimetric detection of lead ions in water

In this work, we developed an aptamer-based optical assay for the analysis of Pb²⁺, a hazardous heavy metal that may be present in the food chain and harmful to human health. An aptamer targeted against Pb²⁺ was immobilized onto the microplate as the capture probe. SiO₂ nanoparticles (NPs) were synthesized and used as carriers of the signaling horseradish peroxidase (HRP) to achieve amplification of the optical signal. Complementary DNA (cDNA) of the aptamer was also linked to the above mentioned SiO₂ nanoparticle (NPs) as the signal probe. The aptamers were found to be able to capture Pb²⁺, and the unbound aptamers were subsequently hybridized with cDNA-HRP-SiO₂ conjugates. As a result, the addition of TMB-H₂O₂ promoted the formation of blue products in the catalytic system. The assay adopting SiO₂ NPs as an enhancer resulted in higher sensitivity with an LOD of 2.5 nM compared to normal procedures. The feasibility of the aptamer-based colorimetric assay was verified by successful detection of Pb²⁺ in water samples with recoveries in the range of 97.4-103.52%.

Traditional and new applications of the HCR in biosensing and biomedicine

The hybridization chain reaction is a very popular isothermal nucleic acid amplification technology. A single-stranded DNA initiator triggers an alternate hybridization event between two hairpins forming a double helix polymer. Due to isothermal, enzyme-free and high amplification efficiency characteristics, the HCR is often used as a signal amplification technology for various biosensing and biomedicine fields. However, as an enzyme-free self-assembly reaction, it has some inevitable shortcomings of relatively slow kinetics, low cell internalization efficiency, weak biostability of DNA probes and uncontrollable reaction in these applications. More and more researchers use this reaction system to synthesize new materials. New materials can avoid these problems skillfully by virtue of their inherent biological characteristics, molecular recognition ability, sequence programmability and biocompatibility. Here, we summarized the traditional application of the HCR in biosensing and biomedicine in recent years, and also introduced its new application in the synthesis of new materials for biosensing and biomedicine. Finally, we summarized the development and challenges of the HCR in biosensing and biomedicine in recent years. We hope to give readers some enlightenment and help.

Self-extending DNA-Mediated Isothermal Amplification System and Its Biosensing Applications

Signal amplification is critical to achieving sensitive biosensing, but complex strategies often bring problems like system instability, false positive, or narrow target spectrum. Here, a self-extending DNA-mediated isothermal amplification (SEIA) system with simple reaction components is introduced to achieve rapid, robust, and significant signal amplification. In SEIA, based on spontaneous refolding of specific DNA domains and using the previous generation product as a template, a DNA strand can extend continuously in an approximate exponential growth pattern, which was accurately predicted by our formula and well supported by AFM results. Based on a set of proof-of-concept experiments, it was proved that the SEIA system can output different signals and flexibly integrate various functional nucleic acids, which makes it suitable for different scenarios and realizes broad-spectrum target detection. Taking into account the advantages of simplicity, flexibility, and efficiency, the SEIA system as an independent signal amplification module will enrich the toolbox of biosensing design.

Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing

With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.

Biosensing with DNAzymes

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

Hybridization chain reaction and its applications in biosensing

To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.

Self-paired dumbbell DNA -assisted simple preparation of stable circular DNAzyme and its application in Pb2+ sensor

During its development in recent decades, DNAzyme has become a promising candidate for application in biosensor field. However, it still suffers from the problem of thermodynamic and biological instability such as nuclease digestion, which limits its applications in complex samples. Here we have presented a simple and common strategy to resolve this problem by engineering the linear DNAzyme into a circular shape DNAzyme based on the integration of substrate and enzyme parts into one single-stranded sequence. This circular DNAzyme system is indeed endowed with excellent stability due to the stable intramolecular double-stranded formation and extraordinary resistance to nuclease digestion due to the closed structure. We demonstrated that this circular DNAzyme system gained excellent stability and could active under conditions across a broader range of temperature, salt concentrations, and pH. Depending on this circular DNAzyme, combing with Terminal deoxynucleotidyl transferase (TdT)-generated G-quadruplexes, a label free colorimetric sensing platform for Pb²⁺ quantitation was developed, and a detection limit of 0.085 nM was achieved. Then the enzyme digestion cycle amplification was introduced to further improve the sensitivity of the sensing system, an ultralow detection limit of 0.0015 nM for this fluorescence method was achieved. Based on the two sensing platforms, ultrasensitive analysis of Pb²⁺ in environmental water and food samples was successfully realized. It is anticipated that this stable circular DNAzyme design will be helpful for trace detection in complex samples.

A label-free fluorescent biosensor based on a catalyzed hairpin assembly for HIV DNA and lead detection

Herein, a label-free fluorescent signal amplification system based on a catalyzed hairpin assembly (CHA) is reported. In this system, two hairpin probes, H1 and H2, were well-designed in which G-quadruplex sequences were integrated into H2. The CHA reaction was triggered by target/trigger DNA and G-quadruplex sequences were released, which can bind the fluorescent amyloid dye thioflavin T (ThT) to provide fluorescence signals. At the same time, target/trigger DNA was released from the product of the CHA reaction (H1-H2), which continued to initiate the next CHA cycle, and the signal was eventually amplified. This signal amplification approach has been successfully used to develop a label-free fluorescent sensing platform for sensitive detection of human immunodeficiency virus (HIV) DNA and Pb²⁺.

The mechanism and improvements to the isothermal amplification of nucleic acids, at a glance

A comparative review of the most common isothermal methods is provided. In the last two decades, the challenge of using isothermal amplification systems as an alternate to the most extensive and long-standing nucleic acids-amplifying method-the polymerase chain reaction-has arisen. The main advantage of isothermal amplification is no requirement for expensive laboratory equipment for thermal cycling. Considerable efforts have been made to improve the current techniques of nucleic acid amplification and the development of new approaches based on the main drawbacks of each method. The most important and challenging goal was to achieve a low-cost, straightforward system that is rapid, specific, accurate, and sensitive.

A Fluorescence Sensor for Pb2+ Detection Based on Liquid Crystals and Aggregation-Induced Emission Luminogens

Heavy metals, such as lead ions, are regarded as the main environmental contaminants and have a negative impact on human bodies, making detection technologies of lead ions critical. However, most existing detection methods suffer from time consumption, complicated sample pretreatment, and expensive equipment, which hinder their broad use in real-time detection. Herein, we show a new fluorescence sensor for detecting lead ions derived from liquid crystals doped with an aggregation-induced emission luminogen. The mechanism is based on the variation of fluorescence intensity caused by the disturbance of an ordered liquid crystal configuration in the presence of Pb²⁺, induced by DNAzyme and its catalytic cleavage. The proposed fluorescence sensor exhibits a low detection limit of 0.65 nM, which is 2 orders of magnitude lower than that previously reported in an optical sensor based on liquid crystals. The detection range of the Pb²⁺ fluorescence sensor is broad, from 20 nM to 100 μM, and it also selects lead ions from numerous metal ions exactly, resulting in a highly sensitive, highly selective, simple, and low-cost detection strategy of Pb²⁺ with potential applications in chemical and biological fields. This approach to designing a liquid crystal fluorescence sensor offers an inspiring stage for detecting biomacromolecules or other heavy metal ions by varying decorated molecules.

Fluorescence and electrochemical assay for bimodal detection of lead ions based on Metal-Organic framework nanosheets

The accurate measurement of heavy metal ions is essential for human health and environmental protection. Here, we report the design of a simple and convenient bimodal strategy for signal-on, label-free lead ion detection in environmental samples based on two-dimensional metal-organic framework (2D-MOF) nanosheets. 2D-MOFs have different affinities toward guanine-rich DNA (ssGDNA) and the G-quadruplex, allowing these structures to be distinguished. The nanosheets were also used as quenchers for fluorescent lead ion detection. Using lead ions to induce G-quadruplex formation from ssGDNA, a simple fluorescence resonance energy transfer (FRET) strategy was developed for lead ion detection; the detection limit was 3.3 nM. Based on changes in the GDNA configuration, the FRET system was converted into an electrochemical sensor for lead ion assays using an electrode modified with the 2D-MOF nanosheets. Electrochemical impedance spectroscopy showed a high sensitivity and a low limit of detection (i.e., 8.7 pM) of the electrode. The adaptability of the bimodal mechanism was verified through the successful detection of lead ions in tap water and fertilizer samples, and the method accuracy was demonstrated through inductively coupled plasma analysis. The developed bimodal device is cost-effective, highly sensitive, and allows for convenient operation, thereby rendering it a promising and reliable system for the detection of lead ions in environmental samples.

An enzyme-mediated universal fluorescent biosensor template for pathogen detection based on a three-dimensional DNA walker and catalyzed hairpin assembly

An enzyme-mediated universal fluorescent biosensor template for rapid detection of pathogens was developed based on the strategy of a three-dimensional (3D) DNA walker and catalyzed hairpin assembly (CHA) reaction. In the bacterial recognition step, a strand displacement reaction between bacteria and the double-stranded complex caused the release of the walker strand. The walker strand triggered the DNA walker to produce an enzyme fragment, and the DNA walker used gold nanoparticles (AuNPs) as the track to provide an excellent DNA ligand anchoring area. In the CHA step, the enzyme fragment induced the CHA cycle to yield fluorescence signals, which greatly enhanced the conversion ratio of trigger DNA and the sensitivity of the fluorescent biosensor. The effect of the distance and density of the DNA ligand was studied by adjusting the length of poly-adenine (PolyA), and was further explored by its reaction kinetics. By comparing the maximum reaction rate (Vmax), Michaelis constant (Km) and turnover number (Kcat), the optimized PolyA probe was assessed and identified. In this work, the optimized PolyA-DNA probe exhibited an outstanding sensitivity in Salmonella typhimurium (S. ty) detection, which is 11.9 times and 4.6 times higher than those of the SH-DNA and the MCH treated SH-DNA. Meanwhile, a detection limit of 28.1 CFU mL-1 was achieved in Escherichia coli (E. coli) detection. Furthermore, the biosensor achieved good selectivity and high repeatability with recoveries of 91%-115% for real sample detection. Considering these advantages, this template has great potential as a routine tool for pathogen detection and has wide applications in the field of global public health and food safety.

Tributylhexadecylphosphonium Modification Strategy to Construct Gold Nanoprobes for the Detection of Aqueous Cr(III)-Organic Complexes

Most metal probes based on gold nanoparticles (AuNPs) are designed for free metal ions in synthetic waters, and very few are applicable in the detection of metal-organic complexes ubiquitous in real water samples. In this study, we proposed a novel colorimetric nanoprobe strategy for complexed Cr(III) species based on the analyte-induced aggregation of AuNPs, as coated by a cationic surfactant tributylhexadecylphosphonium bromide (THPB) instead of traditional carboxyl modifiers. Such a detection system could be realized via both naked eye and/or UV-vis spectroscopy with detection limits of 8.0 and 0.29 μM, respectively, much lower than its allowable maximum level in industrial effluent as regulated by China EPA (1.5 mg Cr/L, ∼30 μM). The proposed detection system also exhibits high selectivity against various interfering substances including free ions, small organic molecules, and other metal-citrate complexes. The unique hydrolysis and extremely slow decomplexation of Cr(III) are believed to favor the formation of the specific interaction between Cr(III)-citrate and THPB-AuNPs, as verified by X-ray photoelectron spectroscopy characterization, thus endowing the nanoprobe with specific discrimination of the complexed Cr(III) via the aggregation of THPB-AuNPs. Also, the THPB-AuNPs could be stored at room temperature for 30 days and maintain constant detection performance. Moreover, the quantitative detection of Cr(III)-organic complexes with the background of various real water samples agreed well with that based on inductively coupled plasma atomic emission spectrometry, making it an attractive alternative for on-site detection of authentic samples containing Cr(III)-organic species.

A Visual and Ratiometric Chemosensor Using Thiophene Functionalized Hydrazone for the Selective Sensing of Pb2+ and F- Ions

Herein, a simple, efficient ratiometric chemosensor was reported for the selective sensing of Pb²⁺ and F^- ions using thiophene functionalized hydrazone as a chemical probe. Hydrazone moiety was developed by utilizing thiophene/naphthalene as a platform for the particular recognition of cation and anion. The structures of the precursor (Z)-(1-(5-bromothiophen-2-yl)ethylidene)hydrazine (ABTH) and the final probe 1-((Z)-(((Z)-1-(5-bromothiophen-2-yl)ethylidene)hydrazono)methyl)naphthalen-2-ol (NAPABTH) were confirmed by ¹H, ¹³C-NMR and LC-MS spectroscopic methods. The interaction of NAPABTH with Pb²⁺ and F^- ions was visually observed by the formation of pink and dark yellow solutions, respectively. The detection limits were found to be very low for Pb²⁺ as 1.06 ppm and for F^- ions as 3.72 nM. This visual detection of Pb²⁺/F^- ions with satisfactory outcomes obtained from UV-Vis titrations. The sensing mechanistic pathways and stoichiometric ratios were obtained from DFT and Job's plot, respectively. The observed results are highly promising as highly selective chemosensor with lower detection limits for Pb²⁺ and F^- ions. This strategy could exhibit tremendous applications for the selective sensing of heavy metal cations with rapid sensitivity for the design of new devices.

Sensitive and Programmable "Signal-Off" Electrochemiluminescence Sensing Platform Based on Cascade Amplification and Multiple Quenching Mechanisms

A versatile and sensitive quantum dot (QD)-based "signal-off" electrochemiluminescence (ECL) sensing system was constructed using target-initiated dual Mg²⁺-dependent DNAzyme (MNAzyme) recycling and catalytic hairpin assembly (CHA) amplification strategies. After the cascade amplification, numerous ferrocene-labeled Y-shaped DNA complexes generated on the QD-modified electrode surface. In the presence of hemin, moreover, the terminal sequence of the formed complex could assemble into hemin/G-quadruplex. Therefore, the highly efficient ECL quenching was achieved due to the multiple quenching mechanisms, including electron/energy transfer between ferrocene and QDs, the steric hindrance effects, and the horseradish peroxidase-mimicking activity of hemin/G-quadruplex. Furthermore, owing to the flexibility in regulating the recognition sequences of MNAzyme, the assaying targets can be programmed. Based on the cascade amplification and multiple ECL quenching mechanisms, the developed programmable "signal-off" ECL sensing platform demonstrates excellent sensitivity and the detection limits of 35.00 aM, 3.71 fM, and 0.28 pM (S/N = 3) for target DNA, aptamer substrate (ATP as a model), and ion (Ag⁺ as a model), respectively.

Review of recent progress on DNA-based biosensors for Pb2+ detection

Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb²⁺ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb²⁺ has become a rapidly growing topic in the analytical community. Pb²⁺ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb²⁺ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb²⁺ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb²⁺ sensing. In this article, these Pb²⁺ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.

Ultrasensitive ratiometric detection of Pb2+ using DNA tetrahedron-mediated hyperbranched hybridization chain reaction

A fluorescent sensing strategy was developed for rapid, highly sensitive and specific detection of lead (II) ion (Pb²⁺) on the basis of Pb²⁺ DNAzyme-controlled tetrahedral DNA nanostructure (TDN)-mediated hyper-branched hybridization chain reaction (hHCR). In this strategy, DNA hairpins used for HCR amplification are modified on the four vertexes of TDN, which are then used to perform rapid TDN-hHCR in the presence of an initiator strand, producing large-sized cross-linked reaction products and thus giving greatly improved fluorescence resonance energy transfer (FRET) signal output. Pb²⁺ DNAzyme catalyzes the cleavage of the initiator strand, inhibiting the initiation of TDN-hHCR and giving decreased FRET signal. Synergetic signal amplification of Pb²⁺ DNAzyme-catalyzed cleavage reaction and subsequent TDN-hHCR confers the sensing platform with ultrahigh sensitivity. As low as 0.25 pM Pb²⁺ can be detected by using either signal "turn-on" or "turn-off" mode. The whole detection process can be finished within 20 min. Strong anti-interference capacity of FRET-based ratiometric detection and high specificity of Pb²⁺ DNAzyme endow the sensing platform with great practical application potential, which was demonstrated by the accurate detection of Pb²⁺ in real river water, fruit, vegetable and grain samples.

Liquid crystal-based sensing platform for detection of Pb2+ assisted by DNAzyme and rolling circle amplification

Lead ions (Pb²⁺) are one of the most widespread heavy metal contaminants that pose detrimental impact on environment and human health. We demonstrate a highly sensitive and specific liquid crystal (LC)-based sensing platform for detecting Pb²⁺ assisted by DNAzyme and rolling circle amplification (RCA). Magnetic beads (MBs) are functionalized with DNA duplexes of the catalytic strands (DNAzymes) and the substrate strands. In the presence of Pb²⁺, the substrate strands are disassembled due to activation of the DNAzyme, which allows initiation of DNA RCA on MBs. The amplified DNA strands can disrupt arrangement of octadecy trimethyl ammonium bromide monolayers (OTAB), thereby inducing planar orientation of LC molecules at the interface of aqueous and LCs. Thus, LCs exhibit bright appearance. In contrast, RCA cannot be triggered in the absence of Pb²⁺. Therefore, LC molecules adopt perpendicular orientation at the interface, which induces the dark morphology of LCs. The limit of detection reaches as low as 16.7 pM. It is an improvement of more than two orders of magnitude compared to that of previously reported LC-based sensing approaches. This approach also shows excellent performance in monitoring Pb²⁺ in tap water and lake water.

The Recent Development of Hybridization Chain Reaction Strategies in Biosensors

With the continuous development of biosensors, researchers have focused increasing attention on various signal amplification strategies to pursue superior performance for more applications. In comparison with other signal amplification strategies, hybridization chain reaction (HCR) as a powerful signal amplification technique shows its certain charm owing to nonenzymatic and isothermal features. Recently, on the basis of conventional HCR, this technique has been developed and improved rapidly, and a variety of HCR-based biosensors with excellent performance have been reported. Herein, we present a systematic and critical review on the research progress of HCR in biosensors in the last five years, including the newly developed HCR strategies such as multibranched HCR, migration HCR, localized HCR, in situ HCR, netlike HCR, and so on, as well as the combination strategies of HCR with isothermal signal amplification techniques, nanomaterials, and functional DNA molecules. By illustrating some representative works, we also summarize the advantage and challenge of HCR in biosensors, and offer a deep discussion of the latest progress and future development trends of HCR in biosensors.