DNAzyme-based biosensor for detection of lead ion: A review

Detecting Pb2+ in aqueous environment and live cells by amphiphilic pillar[5]arene-assembled supramolecular sensor based on host-guest charge transfer mechanism

Water-soluble fluorescent chemosensors for lead ion are highly desirable in environmental detection and bioimagery. Based on a water-soluble pillar[5]arene WP5 and imidazolium terminal functionalized 2,2'-bibenzimidazole derivative BIHB, we report a host-guest charge transfer assembly BIHB-2WP5 for sensitive and selective detection of Pb2+ in pure aqueous media. As a result of its high electron-rich cavity, WP5 can bind electron-deficiency guest BIHB with various host/guest stoichiometry to easily tune the microtopography of assembly from nanoparticle to nanocube. In view of the good biocompatibility and sensitivity, the supramolecular assembly BIHB-2WP5 was used as a fluorescent probe for the detection of Pb2+ in living cells and a smartphone Pb2+ detection device was constructed for the in situ test.

Non-Faradaic Impedimetric Detection of Heavy Metal Ions via a Hybrid Nanoparticle-DNAzyme Biosensor

Due to rapid industrialization, novel water-quality monitoring techniques for the detection of highly toxic and hazardous heavy metal ions are essential. Herein, a hybrid noble nanoparticle/DNAzyme electrochemical biosensor is proposed for the simultaneous and label-free detection of Pb2+ and Cr3+ in aqueous solutions. The sensor is based on the combination of a two-dimensional naked-platinum nanoparticle film and DNAzymes, whose double-helix configuration disassembles into smaller fragments in the presence of target-specific heavy metal ions. The electrochemical behavior of the fabricated sensor was investigated with non-faradaic electrochemical impedance spectroscopy (EIS), resulting in the successful detection of Pb2+ and Cr3+ well below their maximum permitted levels in tap water. So far, there has been no report on the successful detection of heavy metal ions utilizing the non-faradaic electrochemical impedance spectroscopy technique based on advanced nanomaterials paired with DNAzymes. This is also one of the few reports on the successful detection of chromium (III) via a sensor incorporating DNAzymes.

Label free electrochemical sensors for Pb(II) detection based on hemicellulose extracted from Opuntia Ficus Indica cactus

We aim to develop an electrochemical sensor for a divalent metal ion (lead II), a highly toxic water contaminant. We explore a sensor formed with a hemicellulose polysaccharide extracted from the Opuntia Ficus Indica cactus associated with agarose as a sensitive layer deposited on a gold electrode. This sensor combines the functional groups of hemicellulose that could form a complex with metal ions and agarose with gelling properties to form a stable membrane. The sensor demonstrated a loading ability of Pb2+, with higher affinity compared to other metal ions such as Hg2+, Ni2+, and Cu2+, thanks to the chemical structure of hemicellulose. The detection was measured by square wave voltammetry based on a well-defined redox peak of the metal ions. The sensor shows high sensitivity towards Pb2+ with a detection limit of 1.3 fM. The application in river and sea water using the standard addition method for lead detection was studied.

Competitive photoelectrochemical aptamer sensor based on a Z-scheme Fe2O3/g-C3N4 heterojunction for sensitive detection of lead ions

Lead ion (Pb2+) is one of the heavy metal contaminants within the environment, which can seriously affect biological health. Thus, it is very important to detect lead ions, especially exceeding the standard concentration (100 ng/mL). In this work, we have developed a photoelectrochemical (PEC) aptamer sensor with Z-scheme Fe2O3/g-C3N4 heterojunction as a substrate material for sensitive detection of Pb2+. Specifically, Fe2O3/g-C3N4 is employed as a substrate with a powerful and stable photocurrent response. Au and DNA-1 connected to the substrate material via the Au-S bond and increased the electron conduction. Marking DNA-2 with ZnO effectively reduced the light absorption intensity resulting in a lower photocurrent response. Surprisingly, the Pb2+ PEC sensor showed good linearity in the detection range of 62 pg/mL to 1 μg/mL with a detection limit as low as 7.9 pg/mL (S/N = 3). The sensor showed stable recovery and low relative standard deviation in real sample detection. Additionally, the sensor exhibited excellent stability, selectivity, and reproducibility. The reproducibility of the electrodes was evaluated, and the accuracy of the individual electrode current values was calculated to range from 0.5% to 2.71% with an RSD of 1.74%. Such PEC sensor guarantees to supply a brand-new approach to the detection of Pb2+.

Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications

The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.

Hybrid Nanoparticle/DNAzyme Electrochemical Biosensor for the Detection of Divalent Heavy Metal Ions and Cr3

A hybrid noble nanoparticle/DNAzyme electrochemical biosensor is proposed for the detection of Pb2+, Cd2+, and Cr3+. The sensor takes advantage of a well-studied material that is known for its selective interaction with heavy metal ions (i.e., DNAzymes), which is combined with metallic nanoparticles. The double-helix structure of DNAzymes is known to dissociate into smaller fragments in the presence of specific heavy metal ions; this results in a measurable change in device resistance due to the collapse of conductive inter-nanoparticle DNAzyme bridging. The paper discusses the effect of DNAzyme anchoring groups (i.e., thiol and amino functionalization groups) on device performance and reports on the successful detection of all three target ions in concentrations that are well below their maximum permitted levels in tap water. While the use of DNAzymes for the detection of lead in particular and, to some extent, cadmium has been studied extensively, this is one of the few reports on the successful detection of chromium (III) via a sensor incorporating DNAzymes. The sensor showed great potential for its future integration in autonomous and remote sensing systems due to its low power characteristics, simple and cost-effective fabrication, and easy automation and measurement.

Aptamer Sensors for the Detection of Antibiotic Residues- A Mini-Review

Food security is a global issue, since it is closely related to human health. Antibiotics play a significant role in animal husbandry owing to their desirable broad-spectrum antibacterial activity. However, irrational use of antibiotics has caused serious environmental pollution and food safety problems; thus, the on-site detection of antibiotics is in high demand in environmental analysis and food safety assessment. Aptamer-based sensors are simple to use, accurate, inexpensive, selective, and are suitable for detecting antibiotics for environmental and food safety analysis. This review summarizes the recent advances in aptamer-based electrochemical, fluorescent, and colorimetric sensors for antibiotics detection. The review focuses on the detection principles of different aptamer sensors and recent achievements in developing electrochemical, fluorescent, and colorimetric aptamer sensors. The advantages and disadvantages of different sensors, current challenges, and future trends of aptamer-based sensors are also discussed.

Overview on the Design of Magnetically Assisted Electrochemical Biosensors

Electrochemical biosensors generally require the immobilization of recognition elements or capture probes on the electrode surface. This may limit their practical applications due to the complex operation procedure and low repeatability and stability. Magnetically assisted biosensors show remarkable advantages in separation and pre-concentration of targets from complex biological samples. More importantly, magnetically assisted sensing systems show high throughput since the magnetic materials can be produced and preserved on a large scale. In this work, we summarized the design of electrochemical biosensors involving magnetic materials as the platforms for recognition reaction and target conversion. The recognition reactions usually include antigen-antibody, DNA hybridization, and aptamer-target interactions. By conjugating an electroactive probe to biomolecules attached to magnetic materials, the complexes can be accumulated near to an electrode surface with the aid of external magnet field, producing an easily measurable redox current. The redox current can be further enhanced by enzymes, nanomaterials, DNA assemblies, and thermal-cycle or isothermal amplification. In magnetically assisted assays, the magnetic substrates are removed by a magnet after the target conversion, and the signal can be monitored through stimuli-response release of signal reporters, enzymatic production of electroactive species, or target-induced generation of messenger DNA.

Fully inkjet-printed paper-based Pb2+ optodes for water analysis without interference from the chloramine disinfectant

We developed a paper-based colorimetric sensor for facile and cost-effective detection of Pb²⁺ in drinking and environmental water samples. The Pb²⁺ ion-selective optodes are fabricated by inkjet printing of ionophore, chromoionophore, and ion exchanger on cellulose paper. Pb²⁺ in water samples induces deprotonation of the pH chromoionophore and changes the optode color, which is acquired and analyzed by a smartphone. The paper-based optode without any plasticizer or polymer has a dynamic range and selectivity comparable to those of traditional optodes using PVC polymer and/or plasticizer. Furthermore, the response time of the plasticizer/polymer-free paper-based optode is much shorter than those of plasticized PVC-based optodes on paper and glass (5 min vs. 15 and 50 min). Moreover, the plasticizer/polymer-free optode preserves the water-wicking capability of porous cellulose paper, allowing for the design of pump-free microfluidic devices. Chloramine, a widely used disinfectant in drinking water, was found to be a strong and generic interference species for heavy metal ion detection via ion-selective optodes. A fully inkjet-printed lateral-flow paper-based device consisting of a sodium thiosulfate-based chloramine elimination zone and a plasticizer/polymer-free sensing zone was designed for Pb²⁺ detection in tap water disinfected by chloramine. The dynamic range of the Pb²⁺ sensor may be shifted from the current 10^-6 to 10^-5 M to lower concentrations by using stronger ionophores, but this work lays a foundation for the design of paper-based heavy metal ion sensors without detrimental interference from disinfectants.

Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes

The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na⁺, K⁺, Ag⁺, Tl⁺, Cu⁺/Cu²⁺, Hg²⁺, and Pb²⁺) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.

On-site detection of fish furunculosis by combining DNAzyme and carboxyl-functionalized graphene

Furunculosis, which is caused by Aeromonas salmonicida, can induce septicemia, leading to the rapid death of fishes belonging to Salmonidae, Cyprinidae, and Fuscheridae, and lamprey. Targeting A. salmonicida, five DNAzyme sequences with the highest enrichment rates were selected through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The enrichment rates were 34.78, 23.60, 8.91, 2.89, and 2.34%, respectively. The DNAzyme with the highest activity, named D-AS-2, showed specificity and sensitivity. D-AS-2 was combined with carboxyl-functionalized graphene to construct a biosensor, which showed good fluorescence response to scabies lesion samples. The diagnostic procedure was completed in <2 min and can be used for the on-site diagnosis of fish diseases. A low-cost, rapid, simple, and highly specific biosensor for the diagnosis of furunculosis was established based on DNAzyme and carboxyl-functionalized graphene.

Signal-on fluorescent sensing strategy for Pb2+ detection based on 8-17 DNAzyme-mediated molecular beacon-type catalytic hairpin assembly circuit

Based on a Pb²⁺-specific 8-17 DNAzyme-induced catalytic hairpin assembly (CHA), a simple signal-on fluorescence strategy for lead ion detection was established. 8-17 DNAzyme was used as the recognition element of Pb²⁺, which catalyzed the cleavage of the RNA base embedded in the DNA substrate strand, while releasing part of the substrate strand (S') as CHA initiator. And two hairpin probes (H1 and H2-FQ) were designed according to the sequence of S' for CHA, in which H2-FQ was labeled with the fluorophore FAM and quencher BHQ-1 as fluorescent "molecular switch" based on fluorescence resonance energy transfer (FRET). In the presence of Pb²⁺, the CHA reaction was triggered to form a large number of H1-H2 complexes, enabling enzyme-free isothermal amplification and a signal-on fluorescence strategy. In the concentration range of 0.5-1000 nM, the fluorescence signal increases with the increase of Pb²⁺ concentration. The quantitative detection limit of Pb²⁺ by this method is 0.5 nM, which has better detection performance compared with the FQ-labeled 8-17 DNAzyme method. The established biosensor exhibits good specificity and can be effectively used for the detection of Pb²⁺ in real samples of river water and grass carp. Through ingenious nucleic acid sequence design, DNAzyme and CHA reactions are integrated to realize the enzyme-free isothermal amplifications and sensitive detection of Pb²⁺, which holds potential versatility in food supervision and environmental monitoring.

DNA-Based Biosensors for the Biochemical Analysis: A Review

In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.

Recent Advances in Chemical Sensors for Soil Analysis: A Review

The continuously rising interest in chemical sensors’ applications in environmental monitoring, for soil analysis in particular, is owed to the sufficient sensitivity and selectivity of these analytical devices, their low costs, their simple measurement setups, and the possibility to perform online and in-field analyses with them. In this review the recent advances in chemical sensors for soil analysis are summarized. The working principles of chemical sensors involved in soil analysis; their benefits and drawbacks; and select applications of both the single selective sensors and multisensor systems for assessments of main plant nutrition components, pollutants, and other important soil parameters (pH, moisture content, salinity, exhaled gases, etc.) of the past two decades with a focus on the last 5 years (from 2017 to 2021) are overviewed.

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%.

Digital E. coli Counter: A Microfluidics and Computer Vision-Based DNAzyme Method for the Isolation and Specific Detection of E. coli from Water Samples

Biological water contamination detection-based assays are essential to test water quality; however, these assays are prone to false-positive results and inaccuracies, are time-consuming, and use complicated procedures to test large water samples. Herein, we show a simple detection and counting method for E. coli in the water samples involving a combination of DNAzyme sensor, microfluidics, and computer vision strategies. We first isolated E. coli into individual droplets containing a DNAzyme mixture using droplet microfluidics. Upon bacterial cell lysis by heating, the DNAzyme mixture reacted with a particular substrate present in the crude intracellular material (CIM) of E. coli. This event triggers the dissociation of the fluorophore-quencher pair present in the DNAzyme mixture leading to a fluorescence signal, indicating the presence of E. coli in the droplets. We developed an algorithm using computer vision to analyze the fluorescent droplets containing E. coli in the presence of non-fluorescent droplets. The algorithm can detect and count fluorescent droplets representing the number of E. coli present in the sample. Finally, we show that the developed method is highly specific to detect and count E. coli in the presence of other bacteria present in the water sample.

DNAzyme-Amplified Electrochemical Biosensor Coupled with pH Meter for Ca2+ Determination at Variable pH Environments

For more than 50% of multiparous cows, it is difficult to adapt to the sudden increase in calcium demand for milk production, which is highly likely to cause hypocalcemia. An electrochemical biosensor is a portable and efficient method to sense Ca²⁺ concentrations, but biomaterial is easily affected by the pH of the analyte solution. Here, an electrochemical biosensor was fabricated using a glassy carbon electrode (GCE) and single-walled carbon nanotube (SWNT), which amplified the impedance signal by changing the structure and length of the DNAzyme. Aiming at the interference of the pH, the electrochemical biosensor (GCE/SWNT/DNAzyme) was coupled with a pH meter to form an electrochemical device. It was used to collect data at different Ca²⁺ concentrations and pH values, and then was processed using different mathematical models, of which GPR showed higher detecting accuracy. After optimizing the detecting parameters, the electrochemical device could determine the Ca²⁺ concentration ranging from 5 μM to 25 mM, with a detection limit of 4.2 μM at pH values ranging from 4.0 to 7.5. Finally, the electrochemical device was used to determine the Ca²⁺ concentrations in different blood and milk samples, which can overcome the influence of the pH.

Ten Years Progress of Electrical Detection of Heavy Metal Ions (HMIs) Using Various Field-Effect Transistor (FET) Nanosensors: A Review

Heavy metal pollution remains a major concern for the public today, in line with the growing population and global industrialization. Heavy metal ion (HMI) is a threat to human and environmental safety, even at low concentrations, thus rapid and continuous HMI monitoring is essential. Among the sensors available for HMI detection, the field-effect transistor (FET) sensor demonstrates promising potential for fast and real-time detection. The aim of this review is to provide a condensed overview of the contribution of certain semiconductor substrates in the development of chemical and biosensor FETs for HMI detection in the past decade. A brief introduction of the FET sensor along with its construction and configuration is presented in the first part of this review. Subsequently, the FET sensor deployment issue and FET intrinsic limitation screening effect are also discussed, and the solutions to overcome these shortcomings are summarized. Later, we summarize the strategies for HMIs' electrical detection, mechanisms, and sensing performance on nanomaterial semiconductor FET transducers, including silicon, carbon nanotubes, graphene, AlGaN/GaN, transition metal dichalcogenides (TMD), black phosphorus, organic and inorganic semiconductor. Finally, concerns and suggestions regarding detection in the real samples using FET sensors are highlighted in the conclusion.

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.

RNA-cleaving DNAzymes as a diagnostic and therapeutic agent against antimicrobial resistant bacteria

The development of nucleic-acid-based antimicrobials such as RNA-cleaving DNAzyme (RCD), a short catalytically active nucleic acid, is a promising alternative to the current antibiotics. The current rapid spread of antimicrobial resistance (AMR) in bacteria renders some antibiotics useless against bacterial infection, thus creating the need for alternative antimicrobials such as DNAzymes. This review summarizes recent advances in the use of RCD as a diagnostic and therapeutic agent against AMR. Firstly, the recent diagnostic application of RCD for the detection of bacterial cells and the associated resistant gene(s) is discussed. The next section summarises the therapeutic application of RCD in AMR bacterial infections which includes direct targeting of the resistant genes and indirect targeting of AMR-associated genes. Finally, this review extends the discussion to challenges of utilizing RCD in real-life applications, and the potential of combining both diagnostic and therapeutic applications of RCD into a single agent as a theranostic agent.

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.

An "Off-On" Rhodamine 6G Hydrazide-Based Output Platform for Fluorescence and Visual Dual-Mode Detection of Lead(II)

In this study, the rhodamine 6G hydrazide (R6GH) complex was synthesized to develop an "off-on" output platform for fluorescence and visual dual-mode analysis of lead(II) (Pb2+). The prepared R6GH complex using the heat to reflux reaction of rhodamine 6G (R6G) and hydrazine hydrate was characterized through FT-IR, MS, 1H NMR, and 13C NMR and demonstrated to have good fluorescence stability and reversibility. The microenvironment for Pb2+ detection has been optimized in detail. Under the optimal conditions, the "off-on" R6GH-based fluorescence output platform showed a good response to Pb2+ in the concentration range of 0.05-6.0 μM (R2 = 0.9851) with a limit of detection (LOD) of 0.02 μM. Furthermore, at three spiked Pb2+ levels in the selected agricultural (tap water, soil) and food (fish, shrimp) samples, the developed R6GH-based fluorescence assays obtained a significant recovery range of 84.0-102.0% (RSD < 5.0%, n = 3), which had a good correlation with the results from ICP-MS (R2 = 0.9915). The developed R6GH immobilized paper-based array sensor can reach the lower LOD (2.5 μM) for Pb2+ through the naked eye. By combining with LAB analysis, a good linear response was obtained in the Pb2+ concentration range of 1.0-50.0 μM. These results indicated that the developed R6GH probe had great application potential in accurate detection of fluorescence and rapid visual and semiquantitative screening for Pb2+.

Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications

The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.

Nanomaterial-based fluorescent sensors for the detection of lead ions

Lead (Pb) poisoning has been a scourge to the human to pose sighnificant health risks (e.g., organ disorders, carcinogenicity, and genotoxicity) as observed from many different parts of the world, especially in developing countries. The demand for accurate sensors for its detection, especially in environmental media (soil, water, food, etc.) has hence been growing steadily over the years. The potential utility of fluorescent nanosensors as an important analytical tool is recognized due to their astonishing characteristics (e.g., high sensitivity/selectivity, enhanced detection performance, low cost, portability, and rapid on-site detection ability). This review is organized to offer insight into the recent developments in fluorescent nanosensing technology for the detection of lead ions (Pb²⁺). To this end, different types of nanomaterials explored for such applications have been classified and evaluated with respect to performance, especially in terms of sensitivity. This review will help researchers gain a better knowledge on the status and importance of optical nanosensors so as to remediate the contamination of lead and associated problems. The technical challenges and prospects in the development of nanosensing systems for Pb²⁺ are also discussed.

G-quadruplex: Flexible conformational changes by cations, pH, crowding and its applications to biosensing

G-quadruplex (G4) is a non-canonical structure that is formed in G-rich sequences of nucleic acids. G4s play important roles in vivo, such as telomere maintenance, transcription, and DNA replication. There are three typical topologies of G4: parallel, anti-parallel, and hybrid. In general, metal cations, such as potassium and sodium, stabilize G4s through coordination in the G-quartet. While G4s have some functions in vivo, there are many reports of developed applications that use G4s. As various conformations of G4s could form from one sequence depending on varying conditions, many researchers have developed G4-based sensors. Furthermore, G4 is a great scaffold of aptamers since many aptamers folded into G4s have also been reported. However, there are some challenges about its practical use due to the difference between practical sample conditions and experimental ones. G4 conformations are dramatically altered by the surrounding conditions, such as metal cations, pH, and crowding. Many studies have been conducted to characterize G4 conformations under various conditions, not only to use G4s in practical applications but also to reveal its function in vivo. In this review, we summarize recent studies that have investigated the effects of surrounding conditions (e.g., metal cations, pH, and crowding) on G4 conformations and the application of G4s mainly in biosensor fields, and in others.

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.

Platform- and label-free detection of lead ions in environmental and laboratory samples using G-quadraplex probes by circular dichroism spectroscopy

Guanine-rich quadruplex (G-QD) are formed by conversion of nucleotides with specific sequences by stabilization of positively charged K⁺ or Na⁺. These G-QD structures differentially absorb two-directional (right- and left-handed) circularly polarized light, which can discriminate the parallel or anti-parallel structures of G-QDs. In this study, G-QDs stabilized by Pb²⁺ were analyzed by a circular dichroism (CD) spectroscopy to determine Pb²⁺ concentration in water samples. Thrombin aptamer (TBA), PS2.M, human telomeric DNA (HTG), AGRO 100, and telomeric related sequence (T2) were studied to verify their applicability as probes for platform- and label-free detection of Pb²⁺ in environmental as well as laboratory samples. Among these nucleotides, TBA and PS2.M exhibited higher binding constants for Pb²⁺, 1.20-2.04 × 10⁶/M at and 4.58 × 10⁴-1.09 × 10⁵/M at 100 micromolar and 100 mM K⁺ concentration, respectively. They also exhibited excellent selectivity for Pb²⁺ than for Al³⁺, Cu²⁺, Ni²⁺, Fe³⁺, Co²⁺, and Cr²⁺. When Pb²⁺ was spiked into an effluent sample from a wastewater treatment plant (WWTP), its existence was detected by CD spectroscopy following a simple addition of TBA or PS2.M. By the addition of TBA and PS2.M, the Pb²⁺ signals were observed in effluent samples over 0.5 micromolar (100 ppb) concentration. Furthermore, PS2.M caused a Pb²⁺-specific absorption band in the effluent sample without spiking of Pb²⁺, and could be induced to G-QD structure by the background Pb²⁺ concentration in the effluent, 0.159 micromolar concentration (3.30 ppb). Taken together, we propose that TBA and PS2.M are applicable as platform- and label-free detection probes for monitoring Pb²⁺ in environmental samples such as discharged effluent from local WWTPs, using CD spectroscopy.

Advances in Optical Biosensors and Sensors Using Nanoporous Anodic Alumina

This review paper focuses on recent progress in optical biosensors using self-ordered nanoporous anodic alumina. We present the fabrication of self-ordered nanoporous anodic alumina, surface functionalization, and optical sensor applications. We show that self-ordered nanoporous anodic alumina has good potential for use in the fabrication of antibody-based (immunosensor), aptamer-based (aptasensor), gene-based (genosensor), peptide-based, and enzyme-based optical biosensors. The fabricated optical biosensors presented high sensitivity and selectivity. In addition, we also showed that the performance of the biosensors and the self-ordered nanoporous anodic alumina can be used for assessing biomolecules, heavy ions, and gas molecules.

Recent advances on functional nucleic acid-based biosensors for detection of food contaminants

It has seen increasing development of reliable, robust, and flexible biosensors for rapid food-safety analysis in the past few decades. Recently, functional nucleic acid-based biosensors have attracted attention because of their programmability, bottom-up characteristics, and structural switches. However, few systematic reviews devoted to categorizing the potential of DNA nanostructures and devices were found for detecting food contaminants. Hence, the applications of functional nucleic acid-based biosensors were reviewed for analyzing food contaminants, including foodborne pathogen bacteria, biotoxins, heavy metals, and et al. In addition to categorizing the various biosensors, multiple signal readout strategies, such as optical, electrochemical, and mass-based signals were also examined. Finally, the future changes and potential opportunities, as well as practical applications of functional nucleic acid-based biosensors were discussed.

A label-free lead(II) ion sensor based on surface plasmon resonance and DNAzyme-gold nanoparticle conjugates

Detection of lead(II) (Pb²⁺) ions in water is important for the protection of human health and environment. The growing demand for onsite detection still faces challenges for sensitive and easy-to-use methods. In this work, a novel surface plasmon resonance (SPR) biosensor based on GR-5 DNAzyme and gold nanoparticles (AuNPs) was developed. Thiolated DNAzyme was immobilized on the gold surface of the sensor chip followed by anchoring the substrate-functionalized AuNPs through the DNAzyme-substrate hybridization. The coupling between the localized surface plasmon (LSP) of AuNPs and the surface plasmon polaritons (SPP) on the gold sensor surface was used to improve the sensitivity. The substrate cleavage in the presence of Pb²⁺ ions was catalyzed by DNAzyme, leading to the removal of AuNPs and the diminished LSP-SPP coupling. The optimal detection limit was 80 pM for the sensor fabricated with 1 μM DNAzyme, corresponding to two or three orders of magnitude lower than the toxicity levels of Pb²⁺ in drinking water defined by WHO and USEPA. By tuning the surface coverage of DNAzyme, the sensitivity and dynamic range could be controlled. This sensor also featured high selectivity to Pb²⁺ ions and simple detection procedure. Successful detection of Pb²⁺ ions in groundwater indicates that this method has the prospect in the onsite detection of Pb²⁺ ions in water. Given the variety of AuNPs and metal-specific DNAzymes, this detection strategy would lead to the development of more sensitive and versatile heavy metal sensors. Graphical abstract.

One-step electrochemical sensor based on an integrated probe toward sub-ppt level Pb2+ detection by fast scan voltammetry

Herein, a one-step electrochemical sensor for selective and sensitive detection of lead ion Pb²⁺ was developed based on an integrated probe meso-tetra(4-carboxyphenyl) porphine (TCPP)-multi-walled carbon nanotubes (MWCNTs)@Fe₃O₄, which is TCPP-modified magnetic multi-walled carbon nanotubes. In the integrated probe, TCPP is a porphyrin with a specific cavity structure which could selectively chelate with Pb²⁺, MWCNTs with good electric conductivity provide a place to load TCPP and form a specific adsorption state of Pb²⁺ on the electrode surface, and Fe₃O₄ enables the rapid separation and one-step fabrication of the electrochemical sensor. Based on it, the sample pre-enrichment, separation and determination can be integrated, making the whole process very fast and simple. In addition, fast scan voltammetry (FSV) with a scan rate up to 200 V/s could be used to improve the detection sensitivity greatly, benefitting from the specific adsorption state formed. Under the optimal conditions obtained through orthogonal experiments including adsorption time, integrated probe dosage and solution pH, there was a good linear relationship between the peak current and Pb²⁺ concentration ranging from 2.0 × 10^-4 μg L^-1 to 2.0 × 10^-3 μg L^-1, with the limit of detection (LOD) being 6.7 × 10^-5 μg L^-1 (S/N = 3) i.e. 0.067 ppt. Analysis of actual water samples was successful. Therefore, being simple, fast, selective and sensitive, the one-step electrochemical sensor proposed has a good potential in practical applications.

Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution

We perform molecular dynamics simulations, based on recent crystallographic data, on the 8-17 DNAzyme at four states along the reaction pathway to determine the dynamical ensemble for the active state and transition state mimic in solution. A striking finding is the diverse roles played by Na+ and Pb2+ ions in the electrostatically strained active site that impact all four fundamental catalytic strategies, and share commonality with some features recently inferred for naturally occurring hammerhead and pistol ribozymes. The active site Pb2+ ion helps to stabilize in-line nucleophilic attack, provides direct electrostatic transition state stabilization, and facilitates leaving group departure. A conserved guanine residue is positioned to act as the general base, and is assisted by a bridging Na+ ion that tunes the pKa and facilitates in-line fitness. The present work provides insight into how DNA molecules are able to solve the RNA-cleavage problem, and establishes functional relationships between the mechanism of these engineered DNA enzymes with their naturally evolved RNA counterparts. This adds valuable information to our growing body of knowledge on general mechanisms of phosphoryl transfer reactions catalyzed by RNA, proteins and DNA.

DNAzyme-Functionalized R-Phycoerythrin as a Cost-Effective and Environment-Friendly Fluorescent Biosensor for Aqueous Pb2+ Detection

The sensitive detection of Pb²⁺ is of significant importance for food safety, environmental monitoring, and human health care. To this end, a novel fluorescent biosensor, DNAzyme-functionalized R-phycoerythrin (DNAzyme-R-PE), was presented for Pb²⁺ analysis. The biosensor was prepared via the immobilization of Iowa Black^® FQ-modified DNAzyme–substrate complex onto the surface of SPDP-functionalized R-PE. The biosensor produced a minimal fluorescence signal in the absence of Pb²⁺. However, Pb²⁺ recognition can induce the cleavage of substrate, resulting in a fluorescence restoration of R-PE. The fluorescence changes were used to measure sensitively Pb²⁺ and the limit of detection was 0.16 nM with a linear range from 0.5–75 nM. Furthermore, the proposed biosensor showed excellent selectivity towards Pb²⁺ even in the presence of other metal ions interferences and was demonstrated to successfully determine Pb²⁺ in spiked lake water samples.

Progress in rapid optical assays for heavy metal ions based on the use of nanoparticles and receptor molecules

This review (with 230 refs.) covers recent progress in rapid optical assays for heavy metals (primarily lead and mercury as the most relevant) based on the use of nanoparticles and receptor molecules. An introduction surveys the importance, regulatory demands (such as maximum permissible concentrations) and potential and limitations of various existing methods. This is followed by a general discussion on the use of nanoparticles in optical assays of heavy metals (including properties, basic mechanisms of signal generation). The next sections cover methods for the functionalization of nanoparticles with (a) sulfur-containing compounds (used for modification of nanoparticles or added to the reaction medium), (b) nitrogen-containing compounds (such as amino acids, polypeptides, and heterocyclic molecules), and (c) oxygen-containing species (such as hydroxy and carbonyl compounds). This is continued by a specific description of specific assays based on the use of aptamers as receptors, on the use of deoxyribozymes as synthetic reaction catalysts, of G-quadruplex aptamers, of aptamers in logic gate-type of assays of linear (unstructured) aptamers ("hairpins"), and on the use of aptamers in lateral flow assays. A next section covers assays based on the employment of antibodies as receptors (used in the immunoassay development). The properties of various nanoparticles and their applicability in optical assays are also discussed in some detail. Final sections discuss the selectivity of assays, potential interferences by other cations, methods for their elimination, and also matrix effects and approaches for sample pretreatment. A concluding section discusses current challenges and future trends. Analysis based on enzyme inhibition assay is not treated here but enzyme-like action of some receptor molecules such as DNAzymes is discussed. Graphical abstract Schematic presentation of main principles of application of various nanoparticles with receptor molecules (S-, N-, O-containing, heterocyclic compounds, proteins, antibody, aptamers) for heavy metals ions detection. The included methods cover optical assays with description of mechanisms of interactions and signal generation.

Electrochemical Aptasensor Based on Sulfur-Nitrogen Codoped Ordered Mesoporous Carbon and Thymine-Hg2+-Thymine Mismatch Structure for Hg2+ Detection

A renewable electrochemical aptasensor was proposed for super-sensitive determination of Hg²⁺. The novel aptasensor, based on sulfur-nitrogen codoped ordered mesoporous carbon (SN-OMC) and thymine-Hg²⁺-thymine (T-Hg²⁺-T) mismatch structure, used ferrocene as signal molecules to achieve the conversion of current signals. In the absence of Hg²⁺, the thiol-modified T-rich probe 1 spontaneously formed a hairpin structure by base pairing. After being hybridized with the ferrocene-labeled probe 2 in the presence of Hg²⁺, the hairpin structure of probe 1 was opened due to the preferential formation of the T-Hg²⁺-T mismatch structure, and the ferrocene signal molecules approached the modified electrode surface. SN-OMC with high specific surface area and ample active sites acted as a signal amplification element in electrochemical sensing. The sensitive determination of Hg²⁺ can be actualized by analyzing the relationship between the change of oxidation current caused by ferrocene signal molecules and the Hg²⁺ concentrations. The aptasensor had a fine linear correlation in the range of 0.001-1000 nM with a detection limit of 0.45 pM. The aptasensor also displayed a good response in real sample detection and provided a promising possibility for in situ detection.

A sensitive biosensing method for detecting of ultra-trace amounts of AFB1 based on "Aptamer/reduced graphene oxide" nano-bio interaction

A simple, low-cost and sensitive label-free aptasensor assembled with assisting reduced graphene oxide nanosheets as the signal amplifier was fabricated and applied for detecting ultra-low levels of Aflatoxin B1(AFB1) through a nano-bio interaction system. The conditions of different modified glassy carbon electrodes as the base of aptasensor were investigated by cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The performance of the fabricated aptasensor was evaluated by FESEM, HRTEM and AFM images. The proposed biosensor detected AFB1sensitively in a wide linear range (0.5 nM-4μM) by DPV with a considerable low limit of detection (LOD = 0.07 nM) and good repeatability (RSD = 2.9) and stability. Finally, the present aptasensor was applied successfully for monitoring AFB1 with appropriate recoveries in pasteurized cow milk and human blood plasma as real samples.