3D-printed rolling circle amplification chip for on-site colorimetric detection of inorganic mercury in drinking water

Adaptation of a Model Spike Aptamer for Isothermal Amplification-Based Sensing

Isothermal amplification (IA) techniques like rolling circle amplification (RCA) and loop-mediated isothermal amplification (LAMP) have gained significant attention in recent years due to their ability to rapidly amplify DNA or RNA targets at a constant temperature without the need for complex thermal cycling equipment. Such technologies, combined with colorimetric systems rendering visual confirmation of the amplification event, are ideal for the development of point-of-need detection methods suitable for field settings where access to specialized laboratory equipment is limited. The utility of these technologies, thus far limited to DNA and RNA targets, could be broadened to a wide range of targets by using aptamers. Composed of DNA or RNA themselves, aptamers can bind to substances, including proteins, metabolites, and inorganic substances. Their nucleic acid nature can potentially allow them to serve as a bridge, extending the reach of DNA/RNA-centric technologies to the broader molecular world. Indeed, the change in aptamer conformation occurring during ligand interaction can be used to elaborate ligand-responding RCA or LAMP templates. By using an existing aptamer targeting SARS-CoV-2 Spike protein as a model, we explored the possibility of establishing ligand-responsive IA systems. Our study used aptamers with simple sequence modifications as templates in LAMP assays and hyperbranched RCA (HRCA) by exploiting the dynamic nature of the model aptamer to trigger these IA systems. Importantly, our work uniquely demonstrates that this aptamer's dynamic response to ligand binding can regulate both RCA and LAMP processes. This novel approach of using aptamer conformational changes to trigger LAMP paves the way for new aptamer-based detection assays. Our system detects 50 nM of Spike protein, with LAMP occurring within 30 min in the presence of Spike. The colorimetric readout showed clear results, allowing for the detection of Spike protein presence.

MNAzyme-Assisted Nucleic Acid Lateral Flow Assay for Cost-Effective, On-Site Mercury Detection

Mercury ions (Hg2+) are toxic heavy metals present in the environment that pose significant health risks. An advanced detection system could allow for a prompt response and alleviate serious damage to humans. In this study, we developed a cost-effective, on-site detection method for Hg2+ using a multicomponent nucleic acid enzyme (MNAzyme)-assisted nucleic acid lateral flow assay (NALFA). The MNAzyme, which was engineered to contain thymine-thymine mismatches, is responsive only to the presence of Hg2+ and exerts efficient cleavage activity on substrates that can be captured by the NALFA strip, and thus the proposed system enables the visual detection of Hg2+ in the NALFA strip. Our assay demonstrated sufficient detection sensitivity and specificity to meet the WHO standards, offering a good practical alternative for rapid environmental and public health monitoring.

Paper-Based Radial Flow Assay Integrated to Portable Isothermal Amplification Chip Platform for Colorimetric Detection of Target DNA

A novel integrated detection system that introduces a paper-chip-based molecular detection strategy into a polydimethylsiloxane (PDMS) microchip and temperature control system was developed for on-site colorimetric detection of DNA. For the paper chip-based detection strategy, a padlock probe DNA (PLP)-mediated rolling circle amplification (RCA) reaction for signal amplification and a radial flow assay according to the Au-probe labeling strategy for visualization were optimized and applied for DNA detection. In the PDMS chip, the reactions for ligation of target-dependent PLP, RCA, and labeling were performed one-step under isothermal temperature in a single chamber, and one drop of the final reaction solution was loaded onto the paper chip to form a radial colorimetric signal. To create an optimal analysis environment, not only the optimization of molecular reactions for DNA detection but also the chamber shape of the PDMS chip and temperature control system were successfully verified. Our results indicate that a detection limit of 14.7 nM of DNA was achieved, and non-specific DNAs with a single-base mismatch at the target DNA were selectively discriminated. This integrated detection system can be applied not only for single nucleotide polymorphism identification, but also for pathogen gene detection. The adoption of inexpensive paper and PDMS chips allows the fabrication of cost-effective detection systems. Moreover, it is very suitable for operation in various resource-limited locations by adopting a highly portable and user-friendly detection method that minimizes the use of large and expensive equipment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13206-023-00101-7.

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

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

Rolling Circle Amplification-based Copper Nanoparticle Synthesis on Cyclic Olefin Copolymer Substrate and Its Application in Aptasensor

This study aimed to develop a label-free fluorescent aptasensor for the detection of diazinon (DZN) on a cyclic olefin copolymer (COC) substrate. The aptasensor design was based on rolling circle amplification (RCA) technology and the use of self-assembled copper nanoparticles (CuNPs). A dual-function (DF) probe, capable of binding to circular DNA and an aptamer, was designed and immobilized on a COC-bottom 96-well plate. An aptamer was used for selective recognition of DZN, and the specific site of the aptamer that strongly reacted with DZN was successfully identified using circular dichroism (CD) analysis. In presence of DZN, the aptamer and DZN formed a strong complex, thus providing an opportunity for hybridization of the DF probe and circular DNA, thereby initiating an RCA reaction. Repetitive poly thymine (T) sequence with a length of 30-mer, generated in the RCA reaction, served as a template for the synthesis of fluorescent copper nanoparticles, emitting an orange fluorescence signal (at approximately 620 nm) proportional to the amount of RCA product, within 10 min under UV irradiation. The CuNP fluorescence was imaged and quantified using an image analysis software. A linear correlation of the fluorescence signal was confirmed in the DZN concentration range of 0.1–3 ppm, with a detection limit of 0.15 ppm. Adoption of a label-free detection method, utilizing RCA and fluorescent CuNPs on COC substrates, reduced the need for complex equipment and requirements for DZN analysis, thereby representing a simple and rapid sensing method circumventing the limitations of current complex and labor-intensive methods.

Cholesteric Liquid Crystal Photonic Hydrogel Films Immobilized with Urease Used for the Detection of Hg2+

Mercury ion is one of the most widespread heavy metal contaminants which can accumulate in the body through multiple channels, posing a detrimental impact on human health. We demonstrate a simple and low-cost method for the detection of Hg2+ assisted by a cholesteric liquid crystal photonic hydrogel (polyacrylic acid (PAA)) film with immobilized urease (CLC-PAAurease film). In the absence of Hg2+, a significant change in color and an obvious red shift in the reflected light wavelength of the prepared film were observed, since urease can hydrolyze urea to produce NH3, resulting in an increasing pH value of the microenvironment of CLC-PAAurease film. Hg2+ can inhibit the activity of urease so that the color change of the film is not obvious, corresponding to a relatively small variation of the reflected light wavelength. Therefore, Hg2+ can be quantitatively detected by measuring the displacement of the reflected light wavelength of the film. The detection limit of Hg2+ is about 10 nM. This approach has a good application prospect in the monitoring of heavy metal ions in environmental water resources.

A biosensor based on the biomimetic oxidase Fe3O4@MnO2 for colorimetric determination of uric acid

High plasma urate is closely related to gout, cardiovascular and other diseases. Therefore, monitoring the content of uric acid (UA) in plasma is of great significance for the treatment of gout and the prevention of other related diseases. Herein, a biosensor based on the biomimetic oxidase Fe₃O₄ nanoparticles (NPs) @MnO₂ nanosheets (Fe₃O₄@MnO₂ NS) was constructed for colorimetric determination of UA. MnO₂ NS is an efficient biomimetic oxidase, and we found that the intrinsic oxidase activity of MnO₂ NS doped with Fe₃O₄ NPs can be significantly enhanced. The chromogenic substrate TMB can be catalyzed by Fe₃O₄ @MnO₂ NS to generate blue oxidized TMB, and UA can decompose the MnO₂ NS to inhibit the color reaction of TMB selectively, thereby realizing the quantitative detection of UA. In addition, the UA biosensor can perform colorimetric analysis of UA level through three methods: naked eye, smartphone and ultraviolet-visible (UV-vis) spectrophotometer. The linear ranges of UV-vis spectrophotometry and colorimetry with smartphone were 1-70 μM and 200-650 μM, respectively, and the limits of detection (LOD) were 0.27 μM and 21 μM. The analysis results of human plasma samples showed that the method had good selectivity and practicability.

DNAzyme recognition triggered cascade signal amplification for rapid and highly sensitive visual detection of uranyl ions

A 40 min rapid and highly sensitive assay for visualized detection of UO22+ in water samples is reported. A dynamic range 1~50 nM and a LOD of 0.48 nM were obtained. Concentrations as low as 5 nM UO22+ could be distinguished by the naked eye.

Functional nucleic acid biosensors utilizing rolling circle amplification

Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.

Label-free Hg(II) electrochemiluminescence sensor based on silica nanoparticles doped with a self-enhanced Ru(bpy)32+-carbon nitride quantum dot luminophore

Herein, a label-free, self-enhanced electrochemiluminescence (ECL) sensing strategy for divalent mercury (Hg(II)) detection was presented. First, a novel self-enhanced ECL luminophore was prepared by combining the ECL reagent tris(2, 2'-bipyridyl) dichlororuthenium(II) hexahydrate (Ru(bpy)₃²⁺) and its co-reactant carbon nitride quantum dots (CNQDs) via electrostatic interactions. In contrast to traditional ECL systems where the emitter and its co-reactant underwent an intermolecular reaction, the self-enhanced ECL system exhibited a shortened electron-transfer distance and enhanced luminous efficiency because the electrons transferred from CNQDs to oxidized Ru(bpy)₃²⁺ via an intramolecular pathway. Furthermore, the as-prepared self-enhanced ECL material was encapsulated in silica (SiO₂) nanoparticles to generate a Ru-QDs@SiO₂ luminophore. Based on the different affinity of Ru-QDs@SiO₂ nanoparticles for single-stranded DNA (ssDNA) and Hg(II)-triggered double-stranded DNA (dsDNA), a label-free ECL biosensor for Hg(II) detection was developed as follows: in the absence of Hg(II), ssDNA was adsorbed on Ru-QDs@SiO₂ surface via hydrogen bond, electrostatic, and hydrophobic interaction. Thus, quenched ECL signal was observed. On the contrary, in the presence of Hg(II), stable dsDNA was formed and carried the ssDNA separating from Ru-QDs@SiO₂ surface, resulting in most of Ru-QDs@SiO₂ existing in their free state. Therefore, a recovered ECL intensity was obtained. On this basis, Hg(II) was measured by the proposed method in the range of 0.1 nM-10 μM, with a detection limit of 33 pM. Finally, Hg(II) spiked in water samples was measured to evaluate the practicality of the fabricated biosensor.

Au nanoparticle-hydrogel nanozyme-based colorimetric detection for on-site monitoring of mercury in river water

A sensitive on-site mercury sensing platform was developed for simple and effective monitoring of mercury levels in the field. The simple and practical mercury detection system was designed by integrating an Au nanoparticle-PEG hydrogel block nanozyme (Au-HBNz) into a polymer film-based colorimetric device. Upon addition of Hg²⁺ ions, Au-HBNz exhibited excellent peroxidase-like activity, catalyzing the oxidation of 3,3',5,5'-tetramethylbenzidine into a blue-colored product, which has a maximum absorbance at 652 nm. The resulting color intensity change was evaluated using a smartphone for simple and rapid Hg²⁺ detection with a broad detection range (0.008-20 μg∙mL^-1) and a linear concentration-response relationship (R² = 0.96). The detection limit (1.10 ng∙mL^-1) was lower than the maximum permissible Hg²⁺ levels in drinking water set by the World Health Organization (6 ng∙mL^-1) and U.S. Environmental Protection Agency (2 ng∙mL^-1). The recoveries of Hg²⁺ determination in river water by spiking Hg²⁺ samples ranged from 92 to 106%, which indicated high validity and applicability of the Hg²⁺ detection system for field measurements. Thus, the developed sensor enables highly selective and efficient real-time monitoring of Hg²⁺.

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.

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.

Trends in sensor development toward next-generation point-of-care testing for mercury

Mercury is one of the most common heavy metals and a major environmental pollutant that affects ecosystems. Since mercury and its compounds are toxic to humans, even at low concentrations, it is very important to monitor mercury contamination in water and foods. Although conventional mercury detection methods, including inductively coupled plasma mass spectrometry, atomic absorption spectroscopy, and gas chromatography-mass spectrometry, exhibit excellent sensitivity and accuracy, they require operation by an expert in a sophisticated and fully controlled laboratory environment. To overcome these limitations and realize point-of-care testing, many novel methods for direct sample analysis in the field have recently been developed by improving the speed and simplicity of detection. Commonly, these unconventional sensors rely on colorimetric, fluorescence, or electrochemical mechanisms to transduce signals from mercury. In the case of colorimetric and fluorescent sensors, benchtop methods have gradually evolved through technology convergence to give standalone platforms, such as paper-based assays and lab-on-a-chip systems, and portable measurement devices, such as smartphones. Electrochemical sensors that use screen-printed electrodes with carbon or metal nanomaterials or hybrid materials to improve sensitivity and stability also provide promising detection platforms. This review summarizes the current state of sensor platforms for the on-field detection of mercury with a focus on key features and recent developments. Furthermore, trends for next-generation mercury sensors are suggested based on a paradigm shift to the active integration of cutting-edge technologies, such as drones, systems based on artificial intelligence, machine learning, and three-dimensional printing, and high-quality smartphones.

Sequential colorimetric sensing of cupric and mercuric ions by regulating the etching process of triangular gold nanoplates

A triangular gold nanoplate (AuNPL)-based colorimetric assay is presented for ultrasensitive determination of cupric ions (Cu²⁺⁾ and mercuric ions (Hg²⁺) in sequence. AuNPLs were found to be etched efficiently when producing triiodide ions (I₃^-) by a redox reaction between Cu²⁺ and iodide ions (I^-), leading to a change of the shape of AuNPLs from triangular to sphere along with a color change from blue to pink. In the presence of Hg²⁺ the etching of AuNPLs was suppressed due to the consumption of I^- by the formation of HgI₂. With an increase of the concentration of the Hg²⁺ a transformation from sphere to triangular in the shape of AuNPLs occurred with a color change from pink to blue. The evolution of AuNPLs from etching to anti-etching state by sequential addition of Cu²⁺ and Hg²⁺ was accompanied with color variations and band shifts of localized surface plasmon resonance (LSPR), allowing for visual and spectroscopic determination of Cu²⁺ and Hg²⁺ successively within 15 min. In the range 0.01-1.5 μM for Cu²⁺ and 0.02-3.0 μM for Hg²⁺, the linear relationship between the band shift values and the target ions concentration was found good (R² > 0.996). The limit of detections (3S/k) was 19 nM for Cu²⁺ and 9 nM for Hg²⁺, respectively. The lowest visual estimation concentration was 80 nM for both Cu²⁺ and Hg²⁺ through the distinguishable color changes. This system exhibited desirable selectivity for Cu²⁺ and Hg²⁺ over other common ions tested. The method has been successfully applied to sequential determination of Cu²⁺ and Hg²⁺ in real water and food samples. Graphical abstract Scheme 1 Schematic illustration for sequential detection of Cu²⁺ and Hg²⁺ based on etching of AuNPLs.