Ultrasensitive Hybridization Chain Reaction-Assisted Multisite Exonuclease III Amplification Strategy Combined with a Direct Quantitative Fluorescence Lateral Flow Technique for Multiple Bacterial 16S rRNA Detection

Magnetic graphene-enhanced exonuclease III assisted amplification strategy driven carbon nanozyme for tri-mode detection of Escherichia coli O157:H7

Ultra-precision point-of-care detection of Escherichia coli O157:H7 in foods is an important issue. Here, the detection sensitivity was improved by a signal cascade amplification strategy synergised by exonuclease III assisted isothermal amplification and reverse magnetic strategy. The double-stranded DNA formed by the aptamer and the target DNA as a sensing switch, avoiding the complex process of specific nucleic acid extraction. Further, the signal display element is a green nanozyme synthesized by co-doping Cu and Cl elements with lignin as precursor, which has excellent peroxidase activity and fluorescence properties. The detection limits of fluorescence, colorimetric, and photothermal modes were 6.1, 8.4, and 9.7 cfu/mL, respectively. In order to enhance the precision of cascade signal amplification and the portability of quantitative detection, we built a neural network BP model installed in a smartphone by measuring multi-component data, which provides flexible and selectable application scenarios for the on-site detection of foodborne pathogens.

Metal and metal oxide nanoparticle-assisted molecular assays for the detection of Salmonella

This paper provides a comprehensive overview of the diverse applications and innovations of nanoparticles in the detection of Salmonella. It encompasses a comprehensive range of novel methods, including efficient enrichment, nucleic acid extraction, immunoassays, nucleic acid tests, biosensors, and emerging strategies with the potential for future applications. The surface modification of specific antibodies or ligands enables nanoparticles to achieve highly selective capture of Salmonella, while optimizing the nucleic acid extraction process and improving detection efficiency. The employment of nanoparticles in immunological and nucleic acid tests markedly enhances the specificity and sensitivity of the reaction, thereby optimizing the determination of detection results. Moreover, the distinctive physicochemical properties of nanoparticles enhance the sensitivity, selectivity, and stability of biosensors, thereby facilitating the rapid advancement of bio-detection technologies. It is particularly noteworthy that there has been significant advancement in the application and innovative research of nanozymes in molecular assays. This progress has not only resulted in enhanced detection efficiency but has also facilitated innovation and improvement in detection technologies. As nanotechnologies continue to advance, the use of metal and metal oxide nanoparticles in Salmonella detection is likely to become a more promising and reliable strategy for ensuring food safety and public health.

A novel photoelectrochemical biosensor for sensitive detection of nucleic acids based on recombinase polymerase amplification and 3D-array titania nanorods

Nucleic acids detection is essential for diagnosing pathogens; however, traditional methods usually face challenges such as low sensitivity, lengthy reaction times, and strict temperature requirements. This study develops a novel photoelectrochemical (PEC) biosensor that integrates recombinase polymerase amplification (RPA) with a 3D-array titania (TiO2) nanorods nanorod electrode, addressing the challenge of achieving sensitive detection of RPA-amplified nucleic acids products, thereby enabling earlier and more reliable pathogen detection. The biosensor utilizes a triple-binding mode involving FITC antibodies, target nucleic acids, and an HRP-streptavidin sandwich structure, significantly improving the bio-functionalization of the electrode surface. The isothermal RPA process amplifies DNA at 37 °C within 20 min, while the TiO2 nanorods ensure efficient photoelectric conversion. The oxidation of 4-chloro-1-naphthol (4-CN) generates a signal-reducing benzo-4-chlorohexadienone (4-CD), enabling precise and sensitive detection. This PEC-RPA biosensor successfully detects Orientia tsutsugamushi (Ot) nucleic acids with a detection limit of 15 copies/μL within 60 min, demonstrating robust performance. The study provides a promising strategy for advancing pathogen nucleic acids diagnostic platforms and offers a versatile approach adaptable for detecting diverse pathogens.

Beyond Traditional Lateral Flow Assays: Enhancing Performance Through Multianalytical Strategies

Multiplex lateral flow assays are one of the greatest advancements in the world of rapid diagnostics, achieving the performance of several tests in one. These tests meet the basic requirements of increasing ease of use, low detection limit, and high specificity, as they combine the use of novel strategies, such as the exploitation of multiple detection labels, and a variety of amplification methods. These tests have proven their usefulness in many different areas, including clinical diagnostics, food, and environmental monitoring. In this review paper, we attempt to highlight and discuss the predominant changes in multianalyte LFAs, as related to their principle, their development, and their combination with other methods. Attention is paid to their flexibility and the challenges associated with the use of LFA arrays, including strategies to improve the detectability, sensitivity, and reliability of the assays. Therefore, this review emphasizes the current advances in the field to underline the possible impact of multiplex LFAs on the future of diagnostics and analytical sciences.

Rapid and Visual Detection of Urinary Pathogens by Employing Bifunctional Deoxyribonucleic Acid Sensors and Aggregation of Gold Nanoparticles

A simple, rapid, and visual approach is developed to perform diagnosis of urinary tract infection (UTI) and antimicrobial susceptibility testing (AST) by employing smart bifunctional DNA (bfDNA) sensors, exonuclease III, concatermers of CuO nanoparticles (CuONPs), and gold NPs (AuNPs) aggregation [AuNPs agglutination (AA)], namely, the bfDEC-AA method. The bfDNA sensors serve as probes for identifying 16S rRNA genes of bacterium or 18S rRNA of fungus and as mediators connecting the concatermers of CuONPs. The AA as a signal source is triggered by Cu(I)-catalyzed azide-alkyne cycloaddition click chemistry. In this study, the urine samples are analyzed directly, eliminating the need for overnight incubation or bacterial isolation. A crucial color change from red to purple occurs at the UTI diagnostic threshold of 104 CFU mL-1; thus the results of UTI diagnosis can be qualitatively interpreted by the unaided eyes. Similarly, AST was performed visually under our optimal conditions. The color shift can also be quantified using a point-of-care (POC) device. UTI identification, bacteria strain identification, and AST were achieved within 55, 55, and 145 min for 96 samples, respectively. Here, 128 urine samples from suspected UTI patients were tested. Notably, the sensitivity and specificity of our method were 99% and 100% for Gram-negative bacteria (G-) infection, 100% and 100% for Gram-positive bacteria (G+) infection, and 98% and 100% for AST, respectively. Furthermore, the low cost of our POC device (US$156) is friendly to underdeveloped regions.

Enzyme-Assisted Solid-Phase Microextraction Coupled with a DNA Nanowalker for Dual-Amplified Detection of Chloramphenicol in Animal-Derived Food Products

Chloramphenicol (CAP), an aminoalcohol antibiotic, exerts its action on bacterial ribosomes, thereby obstructing protein synthesis. However, the use of CAP in husbandry may lead to its excessive accumulation in animal-derived food products. This presents potential risks to consumer health. This study developed a novel dual-amplification fluorescence detection method by integrating enzyme-assisted solid-phase microextraction (SPME) with a Fe3O4@Au NP-based DNA nanowalker for the detection of CAP in food. The combination of a quartz rod-based SPME biosensor and DNA nanowalker effectively eliminated matrix interference, enabling the conversion of CAP and enhancement of detection signals through two cyclic amplification processes. The strategy demonstrated high sensitivity with a limit of detection of 28.1 aM as well as a wide linear range from 0.1 fM to 1 nM (with R2 > 0.99). This method also demonstrates robust stability and accuracy in detecting trace amounts of CAP in both authentic and prepared positive samples.

Biomedical Utility of Non-Enzymatic DNA Amplification Reaction: From Material Design to Diagnosis and Treatment

Nucleic acid nanotechnology has become a promising strategy for disease diagnosis and treatment, owing to remarkable programmability, precision, and biocompatibility. However, current biosensing and biotherapy approaches by nucleic acids exhibit limitations in sensitivity, specificity, versatility, and real-time monitoring. DNA amplification reactions present an advantageous strategy to enhance the performance of biosensing and biotherapy platforms. Non-enzymatic DNA amplification reaction (NEDAR), such as hybridization chain reaction and catalytic hairpin assembly, operate via strand displacement. NEDAR presents distinct advantages over traditional enzymatic DNA amplification reactions, including simplified procedures, milder reaction conditions, higher specificity, enhanced controllability, and excellent versatility. Consequently, research focusing on NEDAR-based biosensing and biotherapy has garnered significant attention. NEDAR demonstrates high efficacy in detecting multiple types of biomarkers, including nucleic acids, small molecules, and proteins, with high sensitivity and specificity, enabling the parallel detection of multiple targets. Besides, NEDAR can strengthen drug therapy, cellular behavior control, and cell encapsulation. Moreover, NEDAR holds promise for constructing assembled diagnosis-treatment nanoplatforms in the forms of pure DNA nanostructures and hybrid nanomaterials, which offer utility in disease monitoring and precise treatment. Thus, this paper aims to comprehensively elucidate the reaction mechanism of NEDAR and review the substantial advancements in NEDAR-based diagnosis and treatment over the past five years, encompassing NEDAR-based design strategies, applications, and prospects.

Ultrasensitive Electrochemical Biosensor with Powerful Triple Cascade Signal Amplification for Detection of MicroRNA

In this work, by ingeniously integrating catalytic hairpin assembly (CHA), double-end Mg2+-dependent DNAzyme, and hybridization chain reaction (HCR) as a triple cascade signal amplifier, an efficient concatenated CHA-DNAzyme-HCR (CDH) system was constructed to develop an ultrasensitive electrochemical biosensor with a low-background signal for the detection of microRNA-221 (miRNA-221). In the presence of the target miRNA-221, the CHA cycle was initiated by reacting with hairpins H1 and H2 to form DNAzyme structure H1-H2, which catalyzed the cleavage of the substrate hairpin H0 to release two output DNAs (output 1 and output 2). Subsequently, the double-loop hairpin H fixed on the electrode plate was opened by the output DNAs, to trigger the HCR with the assistance of hairpins Ha and Hb. Finally, methylene blue was intercalated into the long dsDNA polymer of the HCR product, resulting in a significant electrochemical signal. Surprisingly, the double-loop structure of the hairpin H could prominently reduce the background signal for enhancing the signal-to-noise ratio (S/N). As a proof of concept, an ultrasensitive electrochemical biosensor was developed using the CDH system with a detection limit as low as 9.25 aM, achieving favorable application for the detection of miRNA-221 in various cancer cell lysates. Benefiting from its enzyme-free, label-free, low-background, and highly sensitive characteristics, the CDH system showed widespread application potential for analyzing trace amounts of biomarkers in various clinical research studies.

Dual-sensitized heterojunction Ag2S/ZnS/NiS composites with entire visible-light region absorption for ultrasensitive photoelectrochemical detection of tobramycin

In this study, an ultrasensitive photoelectrochemical (PEC) aptasensor based on dual-sensitized heterojunction Ag2S/ZnS/NiS composites as a signal probe was proposed for the detection of tobramycin (TOB) by combining a cascaded quadratic signal amplification strategy. Specifically, compared to the limited visible light-harvesting capability of single sensitized composites, Ag2S/ZnS/NiS composites with p-n and n-n heterojunction could greatly improve the light energy utilization to tremendously strengthen the optical absorption in the entire visible-light region. Moreover, dual-sensitized heterojunction could effectively hinder the rapid recombination of photoelectrons and holes (carriers) to obtain a good photocurrent for improving the sensitivity of the aptasensor. Furthermore, a cascaded quadratic signal amplification strategy was applied to convert trace target TOB into plentiful gold nanoclusters (Au NCs) labelled double-stranded DNA for the construction of PEC aptasensor, with a broad linear detection range from 0.01 to 100 ng mL-1 and a low detection limit of 3.38 pg mL-1. Importantly, this study provided a versatile and sensitive PEC biosensing platform for TOB analysis, and demonstrated its successful application for TOB detection in milk samples. This protocol provides a novel dual-sensitized heterojunction composites to develop a highly efficient and harmfulless PEC aptasensor, which is expected to be used in food safety, environmental monitoring and other areas.

Exonuclease III/Cas12a Cascade Amplification Strategy and Smartphone-Based Portable Fluorescence Detector to Repurpose the Commercial AFP Strip for the POCT of Multiple RNAs

Point of care testing (POCT) of nucleic acid (NA) contributes to the timely disease diagnosis, like bacteria and virus screening in households or resource-constrained areas, but its development has always been stagnant. Herein, we proposed an exonuclease III cascaded with CRISPR/Cas12a (Exo-III/Cas12a) amplification strategy and constructed a smartphone-based portable fluorescence detector (SPFD) to repurpose the commercial alpha-fetoprotein (AFP) strip for the ultrasensitive and hand-held detection of NA samples. In detail, the target-initiated-Exo-III/Cas12a strategy realizes the signal amplification and liberates AFP from magnetic beads through the trans-cleavages of activated Cas12a toward the AFP aptamer. After magnetic separation and migration, the fluorescence signals of the test (FT) and control (FC) lines on the AFP strip were digitally output by the SPFD, and the FT/FC was employed for the quantitative analysis to minimize external disturbances and improve accuracy. We experimentally assessed the universe applicability of the proposed NA-POCT platform toward miRNA-155, 16S rRNA of Staphylococcus aureus, and ORF1a/b RNA of Covid-19 pseudovirus, achieving favorable detection limits of 42 aM, 18 CFU/mL, and 87 copies/μL, respectively. Moreover, its simplicity, universality, and admirable detection performance demonstrate a great potential in the aspect of rapidly transforming the existing POCT devices for multiple new applications at the time of need.

Sensitive fluorescence detection based on dimeric G-quadruplex combined with enzyme-assisted solid-phase microextraction of streptomycin in honey

Streptomycin (STR), an aminoglycoside antibiotic with the potential to persist in honey and other food products, may induce allergy, toxicity and antibiotic resistance in humans. In this study, we developed a solid-phase microextraction (SPME) biosensor based on a quartz rod that was modified with double-stranded DNA structures consisting of partially complementary G-rich base DNA strand and STR aptamer. The STR isolated by SPME initially bound to the aptamer. Then the remaining double-stranded DNA structures were cleaved by the Nt.BstNBI enzyme, resulting in release of G-quadruplex dimers. The latter formed a complex with thioflain T fluorescent dye, resulting in an amplified fluorescence response. The method exhibited high sensitivity (a limit of detection of 10.84 pM), wide linear range (0.05 nM ∼ 500 nM (with determination coefficient > 0.99)), and simple operation, making it suitable and convenient for STR detection. Successful STR determination in genuine honey samples was demonstrated.

Lateral flow strip assay of a gene segment in the COVID-19 virus with combined dual readout mode and preliminary multisite hybrid chain reaction amplification

The past and present scenario of COVID-19 has revealed the necessity of simple point-of-care tests. When combined with the great advantages of amplification, lateral flow assay nucleic acid analysis represents a more sensitive molecular diagnostic technique compared to universal protein analysis. Room temperature operation, an enzyme-free nature, and in situ elongation make hybrid chain reaction amplification (HCR) a good candidate for amplified combined lateral flow assays (LFAs). Since dual modes of detection can not only satisfy different application scenarios, but also reduce the false-negative rate, in this paper, visual and fluorescent detection based on labelling with colloidal gold nanoparticles and fluorescence labelling were incorporated into a HCR integrated with a LFA. The detection assay was finished in 30 minutes. The linear relationship between the signal and the concentration of the characteristic segment in the COVID-19 ORF gene was demonstrated. The obtained detection limits of as low as 10 fM (6.02 × 103 copies per mL) and 1 fM (6.02 × 102 copies per mL), respectively, were comparable with those in the literature. The multi-site HCR amplification integrated with LFA of a 1053 bp nucleic acid chain was also preliminarily studied, and tri-site amplification was found to exhibit higher signal intensity than single-site amplification. This study provides a promising strategy for simple, sensitive, and wide-ranging detection of pathogenic bacteria.

Rapid Detection of Broad-Spectrum Pathogenic Bacteria Based on Highly Sensitive Proton Response of the Nucleic Acid Amplification SPQC Platform

Pathogenic bacteria significantly contribute to elevated morbidity and mortality rates, highlighting the urgent need for early and precise detection. Currently, there is a paucity of effective broad-spectrum methods for detecting pathogenic bacteria. We have developed an innovative proton-responsive series piezoelectric quartz crystal (PR-SPQC) platform for the broad-spectrum identification of pathogenic bacteria. This was achieved by retrieving and aligning sequences from the NCBI GenBank database to identify and validate 16S rRNA oligonucleotide sequences that are signatures of pathogenic bacteria but absent in humans or fungi. The hyperbranched rolling circle amplification, activated exclusively by the screened target, exponentially generates protons that are detected by SPQC through a 2D polyaniline (PANI) film. The PR-SPQC platform demonstrates broad-spectrum capabilities in detecting pathogenic bacteria, with a detection limit of 2 CFU/mL within 90 min. Clinical testing of blood samples yielded satisfactory results. With its advantages in miniaturization, cost efficiency, and suitability for point-of-care testing, PR-SPQC has the potential to be extensively used for the rapid identification of diverse pathogenic bacteria within clinical practice and public health sectors.

Fluorescent aptasensor for highly sensitive detection of Staphylococcus aureus based on dual-amplification strategy by integrating DNA walking and hybridization chain reaction

Food-borne diseases caused by bacteria threaten human health. Herein, we presented a new fluorescent aptasensor by coupling DNA walking and hybridization chain reaction (HCR) for convenient and sensitive quantification of bacteria. Staphylococcus aureus (S. aureus) was selected as target. When there was target in the system, the binding of S. aureus with its aptamer caused the disintegration of aptamer/DNA walker on the surface of AuNPs and released DNA walker. With the help of Nt.BsmAI, DNA walker moved along the surface of AuNPs and trigger probe was detached from AuNPs. The trigger probe could initiate hybridization chain reaction (HCR) and opened the stems of H1@AuNPs probe and H2@AuNPs probe. After the addition of nicking endonuclease, the adjacent upconversion nanoparticles (UCNPs, NaYF4:Yb3+, Er3+) were further away from the quenchers (AuNPs) of H1 and H2. Therefore, the fluorescence intensity of UCNPs could be restored via fluorescence resonance energy transfer (FRET). Bacteria were thus detected by recording the fluorescence intensity of UCNPs. This method is simple, rapid and sensitive. It can directly detect bacteria in a low background signal. The limit of detection (LOD) was 10 CFU/mL, detection time was less than 3 h. Recovery rates in simulated milk, honey and human serum samples ranged from 93.6 % to 105.8 %. The strategy opens up new paths for early diagnosis of diseases and food monitoring.