A DNAzyme assay coupled with effective magnetic separation and rolling circle amplification for detection of lead cations with a smartphone camera

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%.

Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments

Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring.

Lead Assays with Smartphone Detection Using a Monolithic Rod with 4-(2-Pyridylazo) Resorcinol

A monolithic rod of polyurethane foam-[4-(2-pyridylazo) resorcinol] (PUF-PAR) as a simple chemical sensor for lead assays with smartphone detection and image processing was developed. With readily available simple apparatus such as a plastic cup and a stirrer rod, the monolithic PUF rod was synthesized in a glass tube. The monolithic PUF-PAR rod could be directly loaded by standard/sample solution without sample preparation. A one-shot image in G/B value from a profile plot in ImageJ for a sample with triplicate results via a single standard calibration approach was obtained. A linear single standard calibration was: [G/B value] = -0.038[µg Pb2+] + 2.827, R2 = 0.95 for 10-30 µg Pb2+ with a limit of quantitation (LOQ) of 33 µg L-1. The precision was lower than 15% RSD. The proposed method was tested by an assay for Pb2+ contents in drinking water samples from Bangkok. The results obtained by the proposed method agree with those of ICP-OES and with 100-120% recovery, demonstrating that the method is useful for screening on-site water monitoring.

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.

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.

DNA branched junctions induced the enhanced fluorescence recovery of FAM-labeled probes on rGO for detecting Pb2

The reduced graphene oxide (rGO) could strongly adsorb and quench the fluorescence of dye-labeled single-stranded DNA (ssDNA); thus, it is widely applied in fluorescent sensors. However, these sensors may suffer from a limited sensitivity due to the low fluorescence recovery when adding the complementary DNA (cDNA) sequence. In this work, the powerful DNA branched junctions were constructed to improve the fluorescence recovery of FAM-labeled probe on rGO. In the presence of target Pb²⁺, the ribonucleotide (rA) in the substrate was cleaved specifically and the catalytic hairpin assembly of three metastable hairpins was further initiated, accompanied by the formation of DNA branched junctions. Then, the liberated Pb²⁺ could be recyclable. Impressively, the DNA branched junctions not only hybridize with the FAM-labeled probes with a high efficiency, but also are significantly undesirable for the rGO. Thus, a high fluorescence recovery of FAM-labeled probe on rGO was expected. The integration of the high fluorescence recovery and dual-cycle signal amplification endows the sensing strategy with a good performance for Pb²⁺ detection, including low detection limit (0.17 nM), good selectivity, and satisfactory practical applicability. The proposed DNA branched junctions offer a novel avenue to improve the fluorescence recovery of the dye-labeled probes on rGO for biological analysis.