Consumer electronics devices for DNA genotyping based on loop-mediated isothermal amplification and array hybridisation

Massive Screening of Food Extracts for Quality Assessment and Standardization of Allergenic Activity

(1) Background: In drug discovery and pharmaceutical quality control, a challenge is to assess protein extracts used for allergy therapy and in vivo diagnosis, such as prick tests. Indeed, there are significant differences between the features of marketed products due to variations in raw materials, purification processes, and formulation techniques. (2) Methods: A protein array technology has been developed to provide comprehensive information on protein-biomarker interactions on a large scale to support the pharmaceutical industry and clinical research. The biosensing method is based on immobilizing low volumes of protein extracts (40 nL) on thermoplastic chips in array format. The biological activity was estimated by incubating with serum from representative food allergy patients. (3) Results: The reproducible optical signals were registered (deviation lower than 10%) using low-cost technologies such as a smartphone and a reader of digital versatile discs. The method was applied to pharmaceutical products to diagnose ten common food allergies, including barley, kiwi, milk, prawn, egg, peanut, wheat, peach, walnut, and squid. Quality indicators were established from spot intensities, enabling an effective comparison of manufacturers. (4) Conclusions: A biosensing-based strategy for screening pharmaceutical products emerges as a reliable and advantageous alternative to traditional approaches such as electrophoresis, fluorescence chips, and ELISA assays. This high-throughput method can contribute to understanding complex biological processes and evaluate the performance of pharmaceutical products.

Development and validation study of compact biophotonic platform for detection of serum biomarkers

The application of advances in personalized medicine requires the support of in vitro diagnostic techniques aimed at the accurate, fast, sensitive, and precise determination of selected biomarkers. Herein, a novel optical centrifugal microfluidic device is developed for clinical analysis and point-of-care diagnostics. Based on compact disc technology, the integrated biophotonic system enables multiple immunoassays in miniaturized mode. The disposable microfluidic discs are made in cyclic olefin copolymer (COP), containing arrays of immobilized probes. In the developed approach, up to six patient samples can each be tested simultaneously. A portable instrument (<2 kg) controls the assay and the high-sensitive reproducible optical detection in transmission mode. Also, the instrument incorporates specific functionalities for personalized telemedicine. The device (analytical method, disc platform, reader, and software) has been validated to diagnose IgE-mediated drug allergies, such as amoxicillin and penicillin G. The total and specific IgE to β-lactam antibiotics were determined in human serum from patients (25 μL). The excellent analytical performances (detection limit 0.24 ng/mL, standard deviation 7-20 %) demonstrated that the developed system could have the potential for a broader impact beyond the allergy field, as it applies to other IVD tests.

Nanomaterial-based methods for sepsis management

Sepsis is a serious disease caused by an impaired host immune response to infection, resulting in organ dysfunction, tissue damage and is responsible for high in-hospital mortality (approximately 20%). Recently, WHO documented sepsis as a global health priority. Nevertheless, there is still no effective and specific therapy for clinically detecting sepsis. Nanomaterial-based approaches have appeared as promising tools for identifying bacterial infections. In this review, recent biosensors are introduced and summarized as nanomaterial-based platforms for sepsis management and severe complications. Biosensors can be used as tools for the diagnosis and treatment of sepsis and as nanocarriers for drug delivery. In general, diagnostic methods for sepsis-associated bacteria, biosensors developed for this purpose are presented in detail, and their strengths and weaknesses are discussed. In other words, readers of this article will gain a comprehensive understanding of biosensors and their applications in sepsis management.

Nucleotide-selective amplification and array-based detection for identifying multiple somatic mutations

In the context of personalized and cost-effective treatment, knowledge of the mutational status of specific genes is advantageous to predict which patients are responsive to therapies. As an alternative to one-by-one detection or massive sequencing, the presented genotyping tool determines multiple polymorphic sequences that vary a single nucleotide. The biosensing method includes an effective enrichment of mutant variants and selective recognition by colorimetric DNA arrays. The proposed approach is the hybridization between sequence-tailored probes and products from PCR with SuperSelective primers to discriminate specific variants in a single locus. A fluorescence scanner, a documental scanner, or a smartphone captured the chip images to obtain spot intensities. Hence, specific recognition patterns identified any single-nucleotide change in the wild-type sequence overcoming qPCR methods and other array-based approaches. Studied mutational analyses applied to human cell lines provided high discrimination factors, the precision was 95%, and the sensitivity was 1% mutant of total DNA. Also, the methods showed a selective genotyping of the KRAS gene from tumorous samples (tissue and liquid biopsy), corroborating results by NGS. The developed technology supported on low-cost robust chips and optical reading provides an attractive pathway toward implementing fast, cheap, reproducible discrimination of oncological patients.

Isothermal nucleic acid amplification technology for rapid detection of virus

While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.

Discrimination of Single-Nucleotide Variants Based on an Allele-Specific Hybridization Chain Reaction and Smartphone Detection

Massive DNA testing requires novel technologies to support a sustainable health system. In recent years, DNA superstructures have emerged as alternative probes and transducers. We, herein, report a multiplexed and highly sensitive approach based on an allele-specific hybridization chain reaction (AS-HCR) in the array format to detect single-nucleotide variants. Fast isothermal amplification was developed before activating the HCR process on a chip to work with genomic DNA. The assay principle was demonstrated, and the variables for integrating the AS-HCR process and smartphone-based detection were also studied. The results were compared to a conventional polymerase reaction chain (PCR)-based test. The developed multiplex method enabled higher selectivity against single-base mismatch sequences at concentrations as low as 10³ copies with a limit of detection of 0.7% of the mutant DNA percentage and good reproducibility (relative error: 5% for intra-assay and 17% for interassay). As proof of concept, the AS-HCR method was applied to clinical samples, including human cell cultures and biopsied tissues of cancer patients. Accurate identification of single-nucleotide mutations in KRAS and NRAS genes was validated, considering those obtained from the reference sequencing method. To conclude, AS-HCR is a rapid, simple, accurate, and cost-effective isothermal method that detects clinically relevant genetic variants and has a high potential for point-of-care demands.

DNA Genotyping Based on Isothermal Amplification and Colorimetric Detection by Consumer Electronics Devices

The point-of-care testing of DNA biomarkers requires compact biosensing systems and consumer electronic technologies provide fascinating opportunities. Their portability, mass-produced components, and high-performance readout capabilities are the main advantages for the development of novel bioanalytical methods.This chapter describes the detection of single nucleotide polymorphisms (SNP) through methods based on user-friendly optical devices (e.g., USB digital microscope, flatbed scanner, smartphone, and DVD drive). Loop mediated isothermal amplification (LAMP) enables the required discrimination of each specific variant prior to the optical reading. In the first method, products are directly hybridized to the allele-specific probes attached to plastic chips in an array format. The second method, allele-specific primers are used, enabling the direct end-point detection based a colorimetric dyer and a microfluidic chamber chip. In both approaches, devices are employed for chip scanning.A representative application to the genotyping of a clinically relevant SNP from human samples is provided, showing the excellent features achieved. Consumer electronic devices are able to register sensitive precise measurements in terms of signal-to-noise ratios, image resolution, and scan-to-scan reproducibility. The integrated DNA-based method lead a low detection limit (100 genomic DNA copies), reproducible (variation <15%), high specificity (genotypes validated by reference method), and cheap assays (<10 €/test). The underlying challenge is the reliable implementation into minimal-specialized clinical laboratories, incorporating additional advantages, such as user-friendly interface, low cost, and connectivity for telemedicine needs.

Electrosprayed mucoadhesive alginate-chitosan microcapsules for gastrointestinal delivery of probiotics

Besides viability protection, a sufficiently prolonged gastrointestinal retention of probiotics has emerged as critically important in improving the functional effectiveness of gastrointestinal delivery of these microorganisms. In this work, we formulated pure, resistant starch-reinforced and chitosan-coated alginate microparticles using an electrospray technique and evaluated their performance as mucoadhesive probiotic formulations for gastrointestinal delivery. In addition, we designed and successfully validated a novel experimental set-up of in vitro wash-off mucoadhesion test, using a portable and low-cost USB microscope for fluorescence imaging. In our test, pure chitosan microparticles (positive control) exhibited the greatest mucoadhesive property, whereas the alginate-resistant starch ones (negative control) were the least retentive on a gastric mucosa. These electrosprayed formulations were spherically shaped, with a size range of 30-600 µm (60-1300 µm with chitosan coating). Moreover, model probiotic Lactobacillus plantarum loaded in alginate-starch formulations was better protected against simulated gastric conditions than in alginate ones, but not better than in the chitosan-coated ones.

All-in-one approaches for rapid and highly specific quantifcation of single nucleotide polymorphisms based on ligase detection reaction using molecular beacons as turn-on probes

Rapid, simple, specific and sensitive approaches for single nucleotide polymorphisms (SNPs) detection are essential for clinical diagnosis. In this study, all-in-one approaches, consisting of the whole detection process including ligase detection reaction (LDR) and real time quantitative polymerase chain reaction performed in one PCR tube by a one-step operation on a real-time PCR system using molecular beacon (MB) as turn-on probe, were developed for rapid, simple, specific and sensitive quantifcation of SNPs. High specificity of the all-in-one approach was achieved by using the LDR, which employs a thermostable and single-base discerning Hifi Taq DNA ligase to ligate adjacently hybridized LDR-specific probes. In addition, a highly specific probe, MB, was used to detect the products of all-in-one approach, which doubly enhances the specificity of the all-in-one approach. The linear dynamic range and high sensitivity of mutant DNA (MutDNA) and wild-type DNA (WtDNA) all-in-one approaches for the detection of MutDNA and WtDNA were studied in vitro, with a broad linear dynamic range of 0.1 fM to 1 pM and detection limits of 65.3 aM and 31.2 aM, respectively. In addition, the MutDNA and WtDNA all-in-one approaches were able to accurately detect allele frequency changes as low as 0.1%. In particular, the epidermal growth factor receptor T790M MutDNA frequency in the tissue of five patients with non-small cell lung cancer detected by all-in-one approaches were in agreement with clinical detection results, indicating the excellent practicability of the developed approaches for the quantification of SNPs in real samples. In summary, the developed all-in-one approaches exhibited promising potential for further applications in clinical diagnosis.

A highly sensitive electrochemical biosensor for protein based on a tetrahedral DNA probe, N- and P-co-doped graphene, and rolling circle amplification

A tetrahedral DNA probe can effectively overcome the steric effects of a single-stranded probe to obtain well-controlled density and minimize nonspecific adsorption. Herein, a highly sensitive electrochemical biosensor is fabricated for determination of protein using a tetrahedral DNA probe and rolling circle amplification (RCA). N- and P-co-doped graphene (NP-rGO) is prepared, and AuNPs are then electrodeposited on it for DNA probe immobilization. Benefitting from the synergistic effects of the excellent electrical conductivity of NP-rGO, the stability of the tetrahedral DNA probe and the signal amplification of RCA, the biosensor achieves a low limit of 3.53 × 10^-14 M for thrombin and a wide linear range from 1 × 10^-13 to 1 × 10^-7 M. This study provides a sensitive and effective method for the detection of protein in peripheral biofluids, and paves the way for future clinical diagnostics and treatment of disease. Graphical abstract.