Colorimetric aptasensor for sensitive detection of kanamycin based on target-triggered catalytic hairpin assembly amplification and DNA-gold nanoparticle probes

Triple modal aptasensor arrays driven by CHA-mediated DNAzyme for signal-amplified atrazine pesticide accumulation monitoring in agricultural crops

Developing sensors with high selectivity and sensitivity is of great significance for pesticide analysis in environmental assessment. Herein, a versatile three-way sensor array was designed for the detection of the pesticide atrazine, based on the integration of catalytic hairpin assembly (CHA) amplification and three-mode signal transducers. With atrazine, CHA was triggered to generate abundant G-quadruplex. The produced G-quadruplex hybrid could assemble with thioflavin T (TFT) or hemin to mimic enzyme and induce the fluorescence enhancement by TFT, or the colorimetric increase by the oxidized chromogenic substrate and the naked-eye color change by inhibiting the L-cysteine-mediated aggregation of gold nanoparticles. A distinctive three-mode array was successfully constructed with convenience, on-site accessibility and high sensitivity for enzyme-free practical analysis of atrazine. It is also effective and reliable for analyzing real samples including paddy water, paddy soil and polished rice. The detection limits for atrazine were as low as 7.4 pg/mL by colorimetric observation and 0.25 pg/mL by fluorescent detection. Furthermore, the array was exploited to monitor the residue, distribution and bioaccumulation of atrazine in maize and rice for food security and environmental assessment. Hence, this work presented a versatile example for sensitive and on-site all-in-one pesticide analysis arrays with multiple signal report modes.

A enzyme-free fluorescence quenching sensor for amplified detection of kanamycin in milk based on competitive triggering strategies

In this work, we constructed a FAM fluorescence quenching biosensor based on an aptamer competition recognition and enzyme-free amplification strategy. We design a competing unit consisting of an aptamer chain and a complementary chain, and a catalytic hairpin self-assembly (CHA) unit consisting of two hairpins in which the complementary chain can trigger the catalytic hairpin self-assembly. In the initial state, the aptamer chain is combined with the complementary chain, the catalytic hairpin self-assembly unit is inhibited, the FAM fluorescence group was far away from the BHQ1 quenching group, and the fluorescence is turn-on. In the presence of kanamycin, the aptamer chain recognizes kanamycin and doesn't form double chains, resulting in the free complementary chain triggering hairpin 1 (H1), and then H1 triggering hairpin 2 (H2), FAM fluorophore is close to the BHQ1 quenching group, and the fluorescence is off-on. When H1 and H2 form a cyclic reaction, enzyme-free amplification is achieved and there is significant output of the fluorescence signal. Therefore, the biosensor has good performance in detecting kanamycin, the detection line is 54 nM, the linear range is 54 nM-0.9 μM, and it can achieve highly selective detection of kanamycin. Kanamycin residue may cause serious harm to human health. The high sensitivity detection of kanamycin is urgent, so this project has a great application potential for food detection.

Development of a novel Colorimetric Assay for the rapid diagnosis of Coronavirus disease 2019 from nasopharyngeal samples

Emergence of Coronavirus disease 2019 (COVID-19) pandemic has posed a huge threat to public health. Rapid and reliable test to diagnose infected subjects is crucial for disease spread control. We developed a colorimetric test for COVID-19 detection using a Colorimetric Assay based on thiol-linked RNA modified gold nanoparticles (AuNPs) and oligonucleotide probes. This method was conducted on RNA from 200 pharyngeal swab samples initially tested by Real-Time polymerase chain reaction (RT-PCR) as gold standard. A specific oligonucleotide probe designed based on ORF1ab of COVID-19 was functionalized with AuNPs-probe conjugate. The exposure of AuNP-probe to isolated RNA samples was tested using hybridization. In this comparative study, the colorimetric functionalized AuNPs assay exhibited a detection limit of 25 copies/µL. It was higher in comparison to the RT-PCR method, which could only detect 15 copies/µL. The results demonstrated 100% specificity and 96% sensitivity for the developed method. Herein, we developed an incredibly rapid, simple and cost-effective Colorimetric Assay lasting approximately 30 min which could process considerably higher number of COVID-19 samples compared to the RT-PCR. This AuNP-probe conjugate colorimetric method could be considered the optimum alternatives for conventional diagnostic tools especially in over-populated and/or low-income countries.

Gold Nanoparticle-Based Colorimetric Sensors: Properties and Application in Detection of Heavy Metals and Biological Molecules

During the last decade, advances have been made in nanotechnology using nanomaterials, leading to improvements in their performance. Gold nanoparticles (AuNPs) have been widely used in the field of sensor analysis and are also combined with certain materials to obtain the desired characteristics. AuNPs are commonly used as colorimetric sensors in detection methods. In developing an ideal sensor, there are certain characteristics that must be met such as selectivity, sensitivity, accuracy, precision, and linearity, among others. Various methods for the synthesis of AuNPs and conjugation with other components have been carried out in order to obtain good characteristics for their application. AuNPs can be applied in the detection of both heavy metals and biological molecules. This review aimed at observing the role of AuNPs in its application. The synthesis of AuNPs for sensors will also be revealed, along with their characteristics suitable for this role. In the application method, the size and shape of the particles must be considered. AuNPs used in heavy metal detection have a particle size of around 15-50 nm; in the detection of biological molecules, the particle size of AuNPs used is 6-35 nm whereas in pharmaceutical compounds for cancer treatment and the detection of other drugs, the particle size used is 12-30 nm. The particle sizes did not correlate with the type of molecules regardless of whether it was a heavy metal, biological molecule, or pharmaceutical compound but depended on the properties of the molecule itself. In general, the best morphology for application in the detection process is a spherical shape to obtain good sensitivity and selectivity based on previous studies. Functionalization of AuNPs with conjugates/receptors can be carried out to increase the stability, sensitivity, selectivity, solubility, and plays a role in detecting biological compounds through conjugating AuNPs with biological molecules.

A smartphone-based gold nanoparticle colorimetric sensing platform for kanamycin detection in food samples

The misuse of kanamycin in the breeding industry can pose a threat to human health through food exposure. Therefore, it is crucial to monitor kanamycin (Kana) levels in food. This study presents a novel colorimetric approach for detecting kanamycin based on the aggregation of gold nanoparticles (AuNPs) induced by kanamycin. To achieve this, a single-stranded DNA (ssDNA) aptamer was employed to bind the surface of AuNPs and maintain their dispersion under high salt concentrations. Upon adding Kana, the aptamer selectively binds to it and separates from the gold surface, resulting in the aggregation of AuNPs. This leads to a color change in the solution (from red to purple to blue) which can be observed under salt conditions. The proposed sensor demonstrated a linear range of 0.5-3 nM and a limit of detection (LOD) of 0.11 nM under optimal conditions. Its practicability was tested by monitoring kanamycin in six food samples, including milk, honey, vitamin C effervescent tablets, vegetable, and meat with satisfactory spiked recoveries. The sensor's miniaturization, convenience, simplicity, and low cost make it a desirable choice for fast and highly sensitive detection of Kana.

Advancements in nanomaterial-based aptasensors for the detection of emerging organic pollutants in environmental and biological samples

The combination of nanomaterials (NMs) and aptamers into aptasensors enables highly specific and sensitive detection of diverse pollutants. The great potential of aptasensors is recognized for the detection of diverse emerging organic pollutants (EOPs) in different environmental and biological matrices. In addition to high sensitivity and selectivity, NM-based aptasensors have many other advantages such as portability, miniaturization, facile use, and affordability. This work showcases the recent advances achieved in the design and fabrication of NM-based aptasensors for monitoring EOPs (e.g., hormones, phenolic contaminants, pesticides, and pharmaceuticals). On the basis of their sensing mechanisms, the covered aptasensing systems are classified as electrochemical, colorimetric, PEC, fluorescence, SERS, and ECL. Special attention has been paid to the fabrication processes, analytical achievements, and sensing mechanisms of NM-based aptasensors. Further, the practical utility of aptasensing approaches has also been assessed based on their basic performance metrics (e.g., detection limits, sensing ranges, and response times).

Improving the selective naked-eye detection of COVID-19 mediated by simultaneously using three different target oligonucleotides coated on plasmonic AuNPs/hexagonal Ag@AuNPs

The localized surface plasmon resonance (LSPR) phenomenon provides a versatile property in biosensor technology. This uncommon feature was utilized to produce a homogeneous optical biosensor to detect COVID-19 by the naked-eye readout. In this work, we synthesized two types of plasmonic nanoparticles: (i) AuNPs and (ii) hexagonal core-shell nanoparticles-Au shell on AgNPs (Au@AgNPs). We report herein the development of two colorimetric biosensors employing the efficient targeting and the binding ability for three regions of the COVID-19 genome, that is, S-gene, N-gene and E-gene, at the same time. Two AuNPs and Ag@AuNPs individually coated with three different targets oligonucleotide sequence (TOs) (AuNPs-TOs-mix and Ag@AuNPs-TOs-mix) for simultaneous detection of S-gene, N-gene and E-gene of the COVID-19 virus, using the LSPR and naked-eye methods in the laboratory and biological samples. The target COVID-19 genome RNA detected using the AuNPs-TOs-mix and Ag@AuNPs-TOs-mix can achieve the same sensitivity. The detection ranges by the AuNPs-TOs-mix and Ag@AuNPs-TOs-mix are both sufficiently improved in equal amounts in comparison to any of the AuNPs-TOs and Ag@AuNPs-TOs. The sensitivity of the current COVID-19 biosensors were 94% and 96% based on the number of positive samples detected for AuNPs-TOs-mix and Ag@AuNPs-TOs-mix, respectively. Moreover, all the real-time PCR confirmed negative samples obtained the same results by the biosensor; accordingly, the specificity of this approach got to 100%. The current study reports a selective, reliable, reproducible and visual 'naked-eye' detection of COVID-19, devoid of the requirement of any sophisticated instrumental techniques.Communicated by Ramaswamy H. Sarma.

An inner filter effect-based fluorescent aptasensor for sensitive detection of kanamycin in complex samples using gold nanoparticles and graphene oxide quantum dots

In this work, a label-free fluorescent aptasensor based on the inner filter effect (IFE) between gold nanoparticles (AuNPs) and graphene oxide quantum dots (GOQDs) was developed for the detection of kanamycin in complex samples. AuNPs are capable of functioning as the fluorescence absorber of GOQDs because of the complementary overlap between their absorption spectra and the emission spectra of GOQDs. AuNPs can effectively quench the fluorescence of GOQDs via the IFE and modulate it with their aggregation state. In the presence of kanamycin, the aptamer is released from the surface of AuNPs, leading to their salt-induced aggregation and the fluorescence recovery of GOQDs. Under the optimum conditions, the fluorescence intensity of GOQDs was linearly proportional to the concentration of kanamycin over the range from 5 to 600 nM, with a detection limit of 3.6 nM. Moreover, the fluorescent aptasensor was successfully applied for kanamycin detection in complex samples (milk, honey and serum), which might hold great promise for kanamycin detection in food safety control and clinical research.

Recent Advances and Perspectives on the Sources and Detection of Antibiotics in Aquatic Environments

Water quality and safety are vital to the ecological environment, social development, and ecological susceptibility. The extensive use and continuous discharge of antibiotics have caused serious water pollution; antibiotics are widely found in freshwater, drinking water, and reservoirs; and this pollution has become a common phenomenon and challenge in global water ecosystems, as water polluted by antibiotics poses serious risks to human health and the ecological environment. Therefore, the antibiotic content in water should be identified, monitored, and eliminated. Nevertheless, there is no single method that can detect all different types of antibiotics, so various techniques are often combined to produce reliable results. This review summarizes the sources of antibiotic pollution in water, covering three main aspects: (1) wastewater discharges from domestic sewage, (2) medical wastewater, and (3) animal physiology and aquaculture. The existing analytical techniques, including extraction techniques, conventional detection methods, and biosensors, are reviewed. The electrochemical biosensors have become a research hotspot in recent years because of their rapid detection, high efficiency, and portability, and the use of nanoparticles contributes to these outstanding qualities. Additionally, the comprehensive quality evaluation of various detection methods, including the linear detection range, detection limit (LOD), and recovery rate, is discussed, and the future of this research field is also prospected.

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

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

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

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

A Colorimetric Strategy Based on Aptamer-Catalyzed Hairpin Assembly for the On-Site Detection of Salmonella typhimurium in Milk

Salmonella typhimurium (S. typhimurium) is a foodborne pathogen that has caused numerous outbreaks worldwide, necessitating the development of on-site strategy to prevent early contamination. Here, we set up an enzyme-free strategy for aptamer-catalyzed hairpin assembly in which salt-induced aggregation of unmodified gold nanoparticles (AuNPs) served as a colorimetric signal output, allowing on-site detection of S. typhimurium in milk. The aptamer-functionalized magnetic beads were used as a vehicle of specifically enriching target bacteria which conjugated with target aptamer to trigger the “Y” shape catalytic hairpin assembly (Y-CHA) circuit. Due to the hairpins desorbing from the surface of AuNPs to the formation of a large amount of double-stranded DNA (dsDNA), AuNPs turned from dispersion to aggregation in the presence of S. typhimurium, resulting in a change of the colorimetric signal from red to blue-gray. The signal output showed a linear relationship for S. typhimurium over a concentration range of 10² to 10⁶ CFU/mL, with a sensitivity of 2.4 × 10² CFU/mL under optimal conditions. The visual protocol has excellent selectivity even in the presence of other competitive bacteria and has been validated in real milk samples with a sensitivity of 2.8 × 10³ CFU/mL.

Advances in Colorimetric Assay Based on AuNPs Modified by Proteins and Nucleic Acid Aptamers

This review is focused on the biosensing assay based on AuNPs (AuNPs) modified by proteins, peptides and nucleic acid aptamers. The unique physical properties of AuNPs allow their modification by proteins, peptides or nucleic acid aptamers by chemisorption as well as other methods including physical adsorption and covalent immobilization using carbodiimide chemistry or based on strong binding of biotinylated receptors on neutravidin, streptavidin or avidin. The methods of AuNPs preparation, their chemical modification and application in several biosensing assays are presented with focus on application of nucleic acid aptamers for colorimetry assay for determination of antibiotics and bacteria in food samples.

Transcription-Based Amplified Colorimetric Thrombin Sensor Using Non-Crosslinking Aggregation of DNA-Modified Gold Nanoparticles

Gold nanoparticles (AuNPs) have been employed as colorimetric biosensors due to the color difference between their dispersed (red) and aggregated (blue) states. Although signal amplification reactions triggered by structural changes of the ligands on AuNPs have been widely used to improve measurement sensitivity, the use of ligands is limited. In this study, we designed a AuNP-based signal-amplifying sandwich biosensor, which does not require a conformational change in the ligands. Thrombin was used as a model target, which is recognized by two different probes. In the presence of the target, an extension reaction occurs as a result of hybridization of the two probes. Then RNA synthesis is started by RNA polymerase activation due to RNA promoter duplex formation. The amplified RNA drives aggregation or dispersion of the AuNPs, and a difference of the color if the AuNP solution is observed. As this detection system does not require a conformational change in the ligand, it can be generically applied to a wide range ligands.