Microfluidic Biosensor for Rapid Nucleic Acid Quantitation Based on Hyperspectral Interferometric Amplicon-Complex Analysis

A compact microfluidic platform for rapid multiplex detection of respiratory viruses via centrifugal polar-absorbance spectroscopy

Nucleic acid detection technology has become a crucial tool in cutting-edge research within the life sciences and clinical diagnosis domains. Its significance is particularly highlighted during the respiratory virus pandemic, where nucleic acid testing plays a pivotal role in accurately detecting the virus. Isothermal amplification technologies have been developed and offer advantages such as rapidity, mild reaction conditions and excellent stability. Among these methods, recombinase polymerase amplification (RPA) has gained significant attention due to its simple primer design and resistance to multiple reaction inhibitors. However, the detection of RPA amplicons hinders the widespread adoption of this technology, leading to a research focus on cost-effective and convenient detection methods for RPA nucleic acid testing. In this study, we propose a novel computational absorption spectrum approach that utilizes the polar GelRed dye to efficiently detect RPA amplicons. By exploiting the asymmetry of GelRed molecules upon binding with DNA, polar electric dipoles are formed, leading to precipitate formation through centrifugal vibration and electrostatic interaction. The quantification of amplicon content is achieved by measuring the residual GelRed concentration in the supernatant. Our proposed portable and integrated microfluidic device successfully detected five respiratory virus genes simultaneously. The optimized linear detection was achieved and the sensitivity for all the targets reached 100 copies/μL. The total experiment could be finished in 27 min. The clinical experiments demonstrated the practicality and accuracy. This cost-effective and convenient detection scheme presents a promising biosensor for rapid virus detection, contributing to the advancement of RPA technology.

Rapid and multi-target genotyping of Helicobacter pylori with digital microfluidics

Helicobacter pylori (H. pylori) infection correlates closely with gastric diseases such as gastritis, ulcers, and cancer, influencing more than half of the world's population. Establishing a rapid, precise, and automated platform for H. pylori diagnosis is an urgent clinical need and would significantly benefit therapeutic intervention. Recombinase polymerase amplification (RPA)-CRISPR recently emerged as a promising molecular diagnostic assay due to its rapid detection capability, high specificity, and mild reaction conditions. In this work, we adapted the RPA-CRISPR assay on a digital microfluidics (DMF) system for automated H. pylori detection and genotyping. The system can achieve multi-target parallel detection of H. pylori nucleotide conservative genes (ureB) and virulence genes (cagA and vacA) across different samples within 30 min, exhibiting a detection limit of 10 copies/rxn and no false positives. We further conducted tests on 80 clinical saliva samples and compared the results with those derived from real-time quantitative polymerase chain reaction, demonstrating 100% diagnostic sensitivity and specificity for the RPA-CRISPR/DMF method. By automating the assay process on a single chip, the DMF system can significantly reduce the usage of reagents and samples, minimize the cross-contamination effect, and shorten the reaction time, with the additional benefit of losing the chance of experiment failure/inconsistency due to manual operations. The DMF system together with the RPA-CRISPR assay can be used for early detection and genotyping of H. pylori with high sensitivity and specificity, and has the potential to become a universal molecular diagnostic platform.

Rapid and Sensitive Quantification of Bacterial Viability Using Ratiometric Fluorescence Sensing

Bacterial viability assessment plays an important role in food-borne pathogen detection and antimicrobial drug development. Here, we first used GelRed as a DNA-binding stain for a bacterial viability assessment. It was found that live bacteria were able to exclude GelRed, which however could easily penetrate dead ones and be absorbed nonspecifically on the bacterial periplasm. Cations were used to reduce the nonspecific adsorption and greatly increase the red fluorescence ratio of dead to live bacteria. Combined with SYTO 9 (a membrane-permeable dye) for double-staining, a ratiometric fluorescent method was established. Using Escherichia coli O157:H7 as a bacteria model, the ratiometric fluorescent method can probe dead bacteria as low as 0.1%. A linear correlation between the ratiometric fluorescence and the theoretical ratio of dead bacteria was acquired, with a correlation coefficient R2 of 0.97. Advantages in sensitivity, accuracy, and safety of the GelRed/SYTO9-based ratiometric fluorescent method against traditional methods were demonstrated. The established method was successfully applied to the assessment of germicidal efficacy of different heat treatments. It was found that even 50 °C treatment could lead to the death of minor bacteria. The as-developed method has many potential applications in microbial researches, and we believe it could be expanded to the viability assessment of mammalian cells.

Development of a POCT detection platform based on a locked nucleic acid-enhanced ARMS-RPA-GoldMag lateral flow assay

In this study, a novel genotyping point-of-care testing (POCT) rapid detection device, the locked nucleic acid (LNA)-amplification refractory mutation system (ARMS)-recombinase polymerase amplification (RPA)-GoldMag lateral flow assay (LFA) platform, was provided by mining and synthesis based on prior technology. Research methods based on system-integrated innovation and knowledge-integrated generation have become a new trend in technology development. Here, we exploit the combination of LNA-coupled ARMS-RPA and gold nanoparticle probe technology for detection signal amplification, thus pioneering a new tool for accurate, rapid, and cost-effective genotyping. We also performed SNP typing detection and clinical validation of this new assay platform using common glucose-6-phosphate dehydrogenase (G6PD) gene single nucleotide polymorphism (SNP) loci, and the results demonstrated the high sensitivity, specificity, stability, accuracy and feasibility of the LNA-ARMS-RPA-GoldMag lateral flow assay platform. It is hoped that this new technology will make a significant contribution to the field of POCT rapid diagnosis and aim to expand the application space, reflecting its clinical application value and development prospects.

Nanogels designed for cell-free nucleic acid sequestration

Chronic wounds exhibit over-expression of cell-free deoxyribonucleic acid (cfDNA), leading to a prolonged inflammation and non-healing wounds. Scavenging excessive cfDNA molecules is a promising strategy for chronic wound treatment. Nanoscopic particles act as efficient cfDNA scavengers due to their large surface area, however their efficiency in cfDNA uptake was limited by adsorption solely on the nanoparticle surface. In contrast, nanogels may provide multiple cfDNA binding sites in the nanoparticle interior, however their use for cfDNA scavenging is yet to be explored. Herein, we report cationic nanogels derived from a copolymer of chitosan and poly{2-[(acryloyloxy)ethyl]trimethylammonium chloride} end-grafted to the chitosan backbone as side chains. The nanogels retain their positive charge at the pH and ionic strength of chronic wound exudate, enabling electrostatically driven cfDNA scavenging. The network structure of the nanogels leads to the cfDNA sequestration in the nanogel interior, in addition to surface attachment. A key factor in cfDNA sequestration is the ratio of the pore size of the nanogel-to-cfDNA molecular dimensions. The enhanced cfDNA scavenging efficiency, along with biocompatibility of the nanogels, makes them a promising component of dressings for chronic wound treatment.

A 3D sliding-strip microfluidic device for the simultaneous determination of mta

A simple paper-based microfluidic device was fabricated to simultaneously detect multiple targets. Microfluidic paper-based analytical devices (μPAD) comprise a single-layer moving sliding PAD (SPAD) to control the flow channel switch together with a folding origami PAD (OPAD) to test the target analytes. The facile assembly without any splicing materials avoids cross-contamination and non-specific adsorption of joining materials that may be caused by multi-target detection. The concentration of Fe(III), Ni(II), Cr(VI), and nitrite in standard solutions and actual aqueous solutions was successfully determined using the designed μPAD. The μPAD was able to achieve LOD of 3.3 mg/L, 1.3 mg/L, 0.35 mg/L, 0.28 mg/L for Fe (III), Ni (II), Cr (VI), and nitrite, respectively. The designed SOPAD exhibits improved stability, with a deviation of less than 7% compared to conventional analytical methods (ICP-OES and UV). Our work demonstrates that this 3D PAD holds great promise and a wide scope in environmental monitoring, biochemical analysis, food testing and other testing industries.

Rapid, Highly Sensitive, and Label-Free Pathogen Assay System Using a Solid-Phase Self-Interference Recombinase Polymerase Amplification Chip and Hyperspectral Interferometry

Recombinase polymerase amplification (RPA) is a useful pathogen identification method. Several label-free detection methods for RPA amplicons have been developed in recent years. However, these methods still lack sensitivity, specificity, efficiency, or simplicity. In this study, we propose a rapid, highly sensitive, and label-free pathogen assay system based on a solid-phase self-interference RPA chip (SiSA-chip) and hyperspectral interferometry. The SiSA-chips amplify and capture RPA amplicons on the chips, rather than irrelevant amplicons such as primer dimers, and the SiSA-chips are then analysed by hyperspectral interferometry. Optical length increases of SiSA-chips are used to demonstrate RPA detection results, with a limit of detection of 1.90 nm. This assay system can detect as few as six copies of the target 18S rRNA gene of Plasmodium falciparum within 20 min, with a good linear relationship between the detection results and the concentration of target genes (R² = 0.9903). Single nucleotide polymorphism (SNP) genotyping of the dhfr gene of Plasmodium falciparum is also possible using the SiSA-chip, with as little as 1% of mutant gene distinguished from wild-type loci (m/wt). This system offers a high-efficiency (20 min), high-sensitivity (6 copies/reaction), high-specificity (1% m/wt), and low-cost (∼1/50 of fluorescence assays for RPA) diagnosis method for pathogen DNA identification. Therefore, this system is promising for fast identification of pathogens to help diagnose infectious diseases, including SNP genotyping.

A sample-to-answer DNA detection microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR

We report a microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR, paving the way for low-cost and rapid implementation of PCR diagnostics.