A sensitive biosensor with a DNAzyme for lead(II) detection based on fluorescence turn-on

Pb2+ Ion Sensors Employing Gold Etching Process: Comparative Investigation on Au Nanorods and Au Nanotriangles

The leaching phenomenon of gold (Au) nanomaterials by Pb2+ ions in the presence of 2-mercaptoethanol (2-ME) and thiosulfate (S2O32- ion) has been systematically applied to a Pb2+ ion sensor. To further investigate the role of Pb2+ ions in sensors containing Au nanomaterials, we revisited the leaching conditions for Au nanorods and compared them with the results for Au nanotriangles. By monitoring the etching rate, it was revealed that Pb2+ ions were important for the acceleration of the etching rate mainly driven by 2-ME and S2O32- pairs, and nanomolar detection of Pb2+ ions were shown to be promoted through this catalytic effect. Using the etchant, the overall size of the Au nanorods decreased but showed an unusual red-shift in UV-Vis spectrum indicating increase of aspect ratio. Indeed, the length of Au nanorods decreased by 9.4% with the width decreasing by 17.4% over a 30-min reaction time. On the other hand, the Au nanotriangles with both flat sides surrounded mostly by dense Au{111} planes showed ordinary blue-shift in UV-Vis spectrum as the length of one side was reduced by 21.3%. By observing the changes in the two types of Au nanomaterials, we inferred that there was facet-dependent alloy formation with lead, and this difference resulted in Au nanotriangles showing good sensitivity, but lower detection limits compared to the Au nanorods.

Advancing biological investigations using portable sensors for detection of sensitive samples

Portable biosensors are emerged as powerful diagnostic tools for analyzing intricately complex biological samples. These biosensors offer sensitive detection capabilities by utilizing biomolecules such as proteins, nucleic acids, microbes or microbial products, antibodies, and enzymes. Their speed, accuracy, stability, specificity, and low cost make them indispensable in forensic investigations and criminal cases. Notably, portable biosensors have been developed to rapidly detect toxins, poisons, body fluids, and explosives; they have proven invaluable in forensic examinations of suspected samples, generating efficient results that enable effective and fair trials. One of the key advantages of portable biosensors is their ability to provide sensitive and non-destructive detection of forensic samples without requiring extensive sample preparation, thereby reducing the possibility of false results. This comprehensive review provides an overview of the current advancements in portable biosensors for the detection of sensitive materials, highlighting their significance in advancing investigations and enhancing sensitive sample detection capabilities.

Engineering DNAzyme strategies for fluorescent detection of lead ions based on RNA cleavage-propelled signal amplification

Based on the high recognition ability and flexible programmability of GR5 DNAzyme, two fluorescent biosensors were engineered for amplified detection of Pb²⁺ via incorporating Ti₃C₂T_X MXenes and embedding 2-aminopurine (2-AP), respectively. The quencher-required approach relied on the DNA affinity and fluorescence quenching ability of Ti₃C₂T_X MXenes. Benefiting from the low background signal modulated by Ti₃C₂T_X MXenes, the sensitive determination of Pb²⁺ was achieved in the linear range of 0.2-10 ng mL^-1 with the limit of detection (LOD) of 0.05 ng mL^-1. The quencher-free approach combined the fluorescent trait of 2-AP embedded in DNA structure, and the RNA cleavage-propelled digestion process of Exonuclease I (Exo I) for signal amplification, indicating the sensitive detection of Pb²⁺ with the LOD as low as 0.02 ng mL^-1 in the linear range of 0.1-10 ng mL^-1. Both DNAzyme assays exhibited simple procedures, favorable specificity, rapid analysis, and satisfactory application in standard reference materials (lead in drinking water) and spiked water samples. The two fluorescent biosensors established in this work would not only provide theoretic fundament for DNA adsorption of Ti₃C₂T_X MXenes and the design of 2-AP-embedded DNAzyme assays, but also hold a great potential for on-site monitoring of lead pollution in water samples.

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.

Recent Advances on Functional Nucleic-Acid Biosensors

In the past few decades, biosensors have been gradually developed for the rapid detection and monitoring of human diseases. Recently, functional nucleic-acid (FNA) biosensors have attracted the attention of scholars due to a series of advantages such as high stability and strong specificity, as well as the significant progress they have made in terms of biomedical applications. However, there are few reports that systematically and comprehensively summarize its working principles, classification and application. In this review, we primarily introduce functional modes of biosensors that combine functional nucleic acids with different signal output modes. In addition, the mechanisms of action of several media of the FNA biosensor are introduced. Finally, the practical application and existing problems of FNA sensors are discussed, and the future development directions and application prospects of functional nucleic acid sensors are prospected.

Advances in the Functional Nucleic Acid Biosensors for Detection of Lead Ions

Lead ions (Pb²⁺) are destructive to the natural environment and public health, so the efficient detection of Pb²⁺ is particularly important. Although the instrumental analysis methods have high accuracy, they require high cost and precise operation, which limits their wide application. Therefore, many strategies have been extensively studied for detecting Pb²⁺ by biosensors. Functional nucleic acids have become an efficient tool in this field. This review focuses on the recent biosensors of detecting Pb²⁺ based on functional nucleic acids from 2010 to 2020, in which DNAzyme, DNA G-quadruplex and aptamer will be introduced. The biosensors are divided into three categories that colorimetric, fluorometric and electrochemical biosensors according to the different reported signals. The action mechanism and detection effect of each biosensor are explained. Finally, the present situation of nucleic acid biosensor for the detection of Pb²⁺ is summarized and the future research direction is prospected.

DNAmoreDB, a database of DNAzymes

Deoxyribozymes, DNA enzymes or simply DNAzymes are single-stranded oligo-deoxyribonucleotide molecules that, like proteins and ribozymes, possess the ability to perform catalysis. Although DNAzymes have not yet been found in living organisms, they have been isolated in the laboratory through in vitro selection. The selected DNAzyme sequences have the ability to catalyze a broad range of chemical reactions, utilizing DNA, RNA, peptides or small organic compounds as substrates. DNAmoreDB is a comprehensive database resource for DNAzymes that collects and organizes the following types of information: sequences, conditions of the selection procedure, catalyzed reactions, kinetic parameters, substrates, cofactors, structural information whenever available, and literature references. Currently, DNAmoreDB contains information about DNAzymes that catalyze 20 different reactions. We included a submission form for new data, a REST-based API system that allows users to retrieve the database contents in a machine-readable format, and keyword and BLASTN search features. The database is publicly available at https://www.genesilico.pl/DNAmoreDB/.

Environmental and intercellular Pb2+ ions determination based on encapsulated DNAzyme in nanoscale metal-organic frameworks

With the merits of low cost, simple synthesis procedure, and high affinity for metal ions, deoxyribozyme (DNAzyme) have played important roles in metal ions detection. However, the intracellular applications of DNAzyme are limited because of enzymatic degradation and inefficient cellular uptake. To address these problems, GR-5 as model DNAzyme was encapsulated into zeolitic imidazolate frameworks-8 (ZIF-8) nanoparticles by biomimetic mineralization. The positively charged ZIF-8 with high DNAzyme loading capacity retained their ability to enter cells. Compared with free DNAzyme, the biomimetic mineralization synthesis method has greatly improved the stability of pristine DNAzyme. The as-synthesized DNAzyme@ZIF-8 composite exhibited good stability resisting DNase I, and was used as a sensitive fluorescent nanoprobe for Pb²⁺ determination and successfully achieved selective and sensitive determination for Pb²⁺ at λ_ex/λ_em = 494/522 nm in real samples. The linear range for the determination of Pb²⁺ is 50 to 500 nM. Moreover, the highly active DNAzyme delivered by ZIF-8 allows noninvasive imaging of Pb²⁺ measurement in living cells. This strategy will extend the suitability of functional nucleic acids for in vitro and in vivo bioanalysis and bioimaging. Graphical abstract.

Functionalized magnetic composites based on the aptamer serve as novel bio-adsorbent for the separation and preconcentration of trace lead

A magnetic functionalized bio-sorbent based on aptamer was designed for the selective separation of ultra-trace Pb²⁺, shortly termed as Fe₃O₄@Au@DNA. Pb(II) specific aptamer attached to the magnetic solid substrate served as affinity probe to capture and separate trace lead. Oligonucleotides with a polyA block were employed for the immobilization on the surface of AuNPs, with adenine sequences (polyA) as the part of effective anchoring block. The prepared Fe₃O₄@Au@DNA composites were characterized by FT-IR, SEM and XPS. The binding of lead on Fe₃O₄@Au@DNA composites surface was pH-dependent, the adsorption follows Langmuir model, and the adsorption dynamic fits the pseudo-second-order kinetics model. Procedure for lead separation and preconcentration was explored and combined with detection of graphite furnace atomic absorption spectrometry (GFAAS). Under the optimum condition, an enrichment factor of 17.73 was obtained with a sample volume of 1.0 mL. The limit of detection (LOD) was 57 ng L^-1 along with a relative standard deviation (RSD) of 2.06 (n = 9). The procedure was further validated by a certified reference material GBW08608 and several environmental and blood samples.

Coordination-induced structural changes of DNA-based optical and electrochemical sensors for metal ions detection

Metal ions play a critical role in human health and abnormal levels are closely related to various diseases. Therefore, the detection of metal ions with high selectivity, sensitivity and accuracy is particularly important. This article highlights and comments on the coordination-induced structural changes of DNA-based optical, electrochemical and optical-electrochemical-combined sensors for metal ions detection. Challenges and potential solutions of DNA-based sensors for the simultaneous detection of multiple metal ions are also discussed for further development and exploitation.

Protamine-stabilized gold nanoclusters as a fluorescent nanoprobe for lead(II) via Pb(II)-Au(I) interaction

The authors report on a one-pot approach for synthesizing highly fluorescent protamine-stabilized gold nanoclusters. These are shown to be a viable nanoprobe for selective and sensitive fluorometric determination of lead(II) via quenching of fluorescence via Pb(II)-Au(I) interaction. Under optimized conditions, fluorescence measured at excitation/emission peaks of 300/599 nm drops in the 80 nM-15 μM lead(II) concentration range. The detection limit is 24 nM, and relative standard deviations (for n = 11) at concentrations of 0.10, 4.0 and 15 μM are 1.6, 2.5 and 1.9%, respectively. The relative recoveries of added lead(II) in the water samples ranged from 97.9 ± 2.29% to 101.2 ± 1.83%. Graphical abstract Lead(II) ions are found to be able to selectively and sensitively quench the fluorescence of the protamine-gold nanoclusters (PRT-AuNCs). Thereby, an inexpensive, selective and sensitive lead(II) assay was established.

Simultaneous detection and determination of mercury (II) and lead (II) ions through the achievement of novel functional nucleic acid-based biosensors

The serious threats of mercury (Hg²⁺) and lead (Pb²⁺) ions for the public health makes it important to achieve the detection methods of the ions with high affinity and specificity. Metal ions usually coexist in some environment and foodstuff or clinical samples. Therefore, it is very necessary to develop a fast and simple method for simultaneous monitoring the amount of metal ions, especially when Hg²⁺ and Pb²⁺ coexist. DNAzyme-based biosensors and aptasensors have been highly regarded for this purpose as two main groups of the functional nucleic acid (FNA)-based biosensors. In this review, we summarize the recent achievements of functional nucleic acid-based biosensors for the simultaneous detection of Hg²⁺ and Pb²⁺ ions in two main optical and electrochemical groups. The tremendous interest in utilizing the various nanomaterials is also highlighted in the fabrication of the FNA-based biosensors. Finally, some results are presented based on the advantages and disadvantages of the studied FNA-based biosensors to compare their validation.

Highly sensitive and selective detection of Pb2+ using a turn-on fluorescent aptamer DNA silver nanoclusters sensor

A novel turn-on fluorescent biosensor has been constructed using C-PS2.M-DNA-templated silver nanoclusters (Ag NCs) with an average diameter of about 1 nm. The proposed approach presents a low-toxic, simple, sensitive, and selective detection for Pb²⁺. The fluorescence intensity of C-PS2.M-DNA-Ag NCs enhances significantly in the presence of Pb²⁺, which is attributed to the special interaction between Pb²⁺ and its aptamer DNA PS2.M. Pb²⁺ induces the aptamer to form G-quadruplex and makes two darkish DNA/Ag NCs located at the 3' and 5' terminus close, resulting in the fluorescence light-up. Moreover, Pb²⁺ can be detected as low as 3.0 nM within a good linear range from 5 to 50 nM (R = 0.9862). Furthermore, the application for detection of Pb²⁺ in real water samples further demonstrates the reliability of the sensor. Thus, this sensor system shows a potential application for monitoring Pb²⁺ in environmental samples.

The Triple Roles of Glutathione for a DNA-Cleaving DNAzyme and Development of a Fluorescent Glutathione/Cu2+-Dependent DNAzyme Sensor for Detection of Cu2+ in Drinking Water

Pistol-like DNAzyme (PLDz) is an oxidative DNA-cleaving catalytic DNA with ascorbic acid as cofactor. Herein, glutathione was induced into the reaction system to maintain reduced ascorbic acid levels for higher efficient cleavage. However, data indicated that glutathione played triple roles in PLDz-catalyzed reactions. Glutathione alone had no effect on PLDz, and showed inhibitory effect on ascorbic acid-induced PLDz catalysis, but exhibited stimulating effect on Cu²⁺-promoted self-cleavage of PLDz. Further analysis of the effect of glutathione/Cu²⁺ on PLDz indicated that H₂O₂ played a key role in PLDz catalysis. Finally, we developed a fluorescent Cu²⁺ sensor (PL-Cu 1.0) based on the relationship between glutathione/Cu²⁺ and catalytic activity of PLDz. The fluorescent intensity showed a linear response toward the logarithm concentration of Cu²⁺ over the range from 80 nM to 30 μM, with a detection limit of 21.1 nM. PL-Cu 1.0 provided only detection of Cu²⁺ over other divalent metal ions. Ca²⁺ and Mg²⁺ could not interfere with Cu²⁺ detection even at a 1000-fold concentration. We further applied PL-Cu 1.0 for Cu²⁺ detection in tap and bottled water. Water stored in copper taps overnight had relatively high Cu²⁺ concentrations, with a maximum 22.3 μM. Trace Cu²⁺ (52.2 nM) in deep spring was detected among the tested bottled water. Therefore, PL-Cu 1.0 is feasible to detect Cu²⁺ in drinking water, with a practical application.

Designing a Biostable L-DNAzyme for Lead(II) Ion Detection in Practical Samples

A promising biosensor for effectively lead (II) ion detection in practical applications was developed by constructing a Pb2+-specific L-DNAzyme, the enantiomer of the natural nucleic acid-constructed D-DNAzyme. This fluorescent sensor contains the L-enzyme strand with a quencher at the 3' end, and the L-substrate strand with a fluorophore at the 5' and a quencher at the 3' ends that formed a complex. In the presence of Pb2+, the L-substrate is cut into two fragments, leading to the recovery of fluorescence. The sensor shows high sensitivity and selectivity for Pb2+ detection with a linear response in the range of 5-100 nM and a detection limit of 3 nM in aqueous solution. Importantly, based on that L-DNAzyme consists of non-natural nucleic acids, which is insensitive to nuclease digestion, protein adsorption and D-DNA hybridization, our sensor shows specific response to Pb2+ in practical water and serum samples. Therefore, it is expected that our L-DNAzyme-based strategy may offer a new method for developing simple, rapid and sensitive sensors in complex systems.

Highly sensitive and selective optical detection of lead(ii) using a label-free fluorescent aptasensor

Configurations and measurement principles of a label-free fluorescence aptamer-based PG assay for Pb²⁺ detection.