DaimonDNA: A portable, low-cost loop-mediated isothermal amplification platform for naked-eye detection of genetically modified organisms in resource-limited settings

Evaluation of a near-patient SARS-CoV-2 novel rapid diagnostic platform

The goal of this study is to test a novel device and methodology based on the "Pebble" platform and real-time quantitative colorimetric loop-mediated isothermal amplification (qcLAMP) during SARS-CoV-2 detection using crude samples and extracted RNA. The new method employs an inexpensive lightweight device aimed toward rapid point-of-care testing. An extensive evaluation was performed consisting of 1,693 clinical samples across five independent clinical testing centers. Positive colorimetric results were observed within 20 minutes of testing. At a 20-minute time-to-positive cut-off, the specificity is 98.5% with a diagnostic accuracy of 91.9%, compared to qPCR assays. Our findings indicate that the SARS-CoV-2 qcLAMP diagnostic assay in conjunction with the Pebble device is ideal for point-of-care/near-patient testing.IMPORTANCEHere, we describe our analyses and validation of a novel real-time quantitative colorimetric loop-mediated isothermal amplification (qcLAMP) device, available under the name "Pebble" and associated SARS-CoV-2 diagnostic qcLAMP assay for clinical diagnostic use. The analyses were performed in five independent testing sites across Europe using clinical samples from the associated clinical sites and support the use of "pebble" and associated kit in the diagnostic environment.

Customizable Nichrome Wire Heaters for Molecular Diagnostic Applications

Accurate sample heating is vital for nucleic acid extraction and amplification, requiring a sophisticated thermal cycling process in nucleic acid detection. Traditional molecular detection systems with heating capability are bulky, expensive, and primarily designed for lab settings. Consequently, their use is limited where lab systems are unavailable. This study introduces a technique for performing the heating process required in molecular diagnostics applicable for point-of-care testing (POCT), by presenting a method for crafting customized heaters using freely patterned nichrome (NiCr) wire. This technique, fabricating heaters by arranging protrusions on a carbon black-polydimethylsiloxane (PDMS) cast and patterning NiCr wire, utilizes cost-effective materials and is not constrained by shape, thereby enabling customized fabrication in both two-dimensional (2D) and three-dimensional (3D). To illustrate its versatility and practicality, a 2D heater with three temperature zones was developed for a portable device capable of automatic thermocycling for polymerase chain reaction (PCR) to detect Escherichia coli (E. coli) O157:H7 pathogen DNA. Furthermore, the detection of the same pathogen was demonstrated using a customized 3D heater surrounding a microtube for loop-mediated isothermal amplification (LAMP). Successful DNA amplification using the proposed heater suggests that the heating technique introduced in this study can be effectively applied to POCT.

Moving towards on-site detection of Shiga toxin-producing Escherichia coli in ready-to-eat leafy greens

Rapid identification of Shiga toxin-producing Escherichia coli, or STEC, is of utmost importance to assure the innocuousness of the foodstuffs. STEC have been implicated in outbreaks associated with different types of foods however, among them, ready-to-eat (RTE) vegetables are particularly problematic as they are consumed raw, and are rich in compounds that inhibit DNA-based detection methods such as qPCR. In the present study a novel method based on Loop-mediated isothermal amplification (LAMP) to overcome the limitations associated with current molecular methods for the detection of STEC in RTE vegetables targeting stx1 and stx2 genes. In this sense, LAMP demonstrated to be more robust against inhibitory substances in food. In this study, a comprehensive enrichment protocol was combined with four inexpensive DNA extraction protocols. The one based on silica purification enhanced the performance of the method, therefore it was selected for its implementation in the final method. Additionally, three different detection chemistries were compared, namely real-time fluorescence detection, and two end-point colorimetric strategies, one based on the addition of SYBR Green, and the other based on a commercial colorimetric master mix. After optimization, all three chemistries demonstrated suitable for the detection of STEC in spiked RTE salad samples, as it was possible to reach a LOD50 of 0.9, 1.4, and 7.0 CFU/25 g for the real-time, SYBR and CC LAMP assays respectively. All the performance parameters reached values higher than 90 %, when compared to a reference method based on multiplex qPCR. More specifically, the analytical sensitivity was 100, 90.0 and 100 % for real-time, SYBR and CC LAMP respectively, the specificity 100 % for all three assays, and accuracy 100, 96 and 100 %. Finally, a high degree of concordance was also obtained (1, 0.92 and 1 respectively). Considering the current technological advances, the method reported, using any of the three detection strategies, demonstrated suitable for their implementation in decentralized settings, with low equipment resources.

A review on the identification of transgenic oilseeds and oils

Transgenic technology can increase the quantity and quality of vegetable oils worldwide. However, people are skeptical about the safety of transgenic oil-bearing crops and the oils they produce. In order to protect consumers' rights and avoid transgenic oils being adulterated or labeled as nontransgenic oils, the transgenic detection technology of oilseeds and oils needs careful consideration. This paper first summarized the current research status of transgenic technologies implemented at oil-bearing crops. Then, an inspection process was proposed to detect a large number of samples to be the subject rapidly, and various inspection strategies for transgenic oilseeds and oils were summarized according to the process sequence. The detection indicators included oil content, fatty acid, triglyceride, tocopherol, and nucleic acid. The detection technologies involved chromatography, spectroscopy, nuclear magnetic resonance, and polymerase chain reaction. It is hoped that this article can provide crucial technical reference and support for staff engaging in the supervision of transgenic food and for researchers developing fast and efficient monitoring methods in the future.

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. In this work, we developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative analysis with the simplicity of point-of-care testing. The device innovation lies on the use of a plastic tube anchored vertically on a hot surface while the side walls are exposed to a mini camera able to take snapshots of the colour change in real time during LAMP amplification. Competitive features are the rapid analysis (< 30 min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (< 5 copies/reaction), smartphone-operation, fast prototyping (3D-printing) and ability to select the dye of interest (Phenol red, HNB). The device’s clinical utility is demonstrated in cancer mutations-analysis during the detection of 0.01% of BRAF-V600E-to-wild-type molecules from tissue samples and COVID-19 testing with 97% (Ct < 36.8) and 98% (Ct < 30) sensitivity when using extracted RNA and nasopharyngeal-swabs, respectively. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.

Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens

Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.

A low-cost, portable, and practical LAMP device for point-of-diagnosis in the field

Transition of rapid, ready-to-use, and low-cost nucleic acid-based detection technologies from laboratories to points of sample collection has drastically accelerated. However, most of these approaches are still incapable of diagnosis starting from sampling, through nucleic acid isolation and detection in the field. Here, we developed a simple, portable, low-cost, colorimetric, and remotely controllable platform for reliable, high-throughput, and rapid diagnosis using loop mediated isothermal amplification (LAMP) assays. It consists of a thermally isolated cup, low-cost electronic components, a polydimethylsiloxane sample well, and a fast prototyped case that covers electronic components. The steady-state temperature error of the system is less than 1%. We performed LAMP, Colony-LAMP, and Colony PCR reactions using the yaiO₂ primer set for Escherichia coli and Pseudomonas aeruginosa samples at 65˚C and 30 min. We detected the end-point colorimetric readouts by the naked eye under day light. We confirmed the specificity and sensitivity of our approach using pure genomic DNA and crude bacterial colonies. We benchmarked our Colony-LAMP detection against Colony PCR. The number of samples tested can easily be modified for higher throughput in our system. We strongly believe that our platform can greatly contribute rapid and reliable diagnosis in versatile operational environments. This article is protected by copyright. All rights reserved.

Optimization of Loop-Mediated Isothermal Amplification (LAMP) reaction mixture for biosensor applications

Genetically Modified (GM) foods are becoming the future of agriculture on surviving global natural disasters and climate change by their enhanced production efficiency and improved functional properties. On the other hand, their adverse health and environmental effects, ample evidence on transgene leakage of Genetically Modified Organisms (GMOs) to crops have raised questions on their benefits and risks. Consequently, low-cost, reliable, rapid, and practical detection of GMOs have been important. GMO-detection platforms should be capable of stably storing detection reagents for long-delivery distances with varying ambient temperatures. In this study, we developed an event-specific, closed tube colorimetric GMO detection method based on Loop-Mediated Isothermal Amplification (LAMP) technique which can be integrated into GMO-detection platforms. The entire detection process optimized to 30 min and isothermally at 65 °C. The durability of the LAMP mixture in the test tubes showed that the LAMP reaction mixture, in which Bst polymerase and DNA sample was later included, yielded DNA amplicons for 3 days at room temperature, and for 6 days at 4 °C.•Simple, stable, and cheap storage method of LAMP reaction mixture for GMO-detection technologies.•GMO-detection platforms can stably store detection reagents for long-delivery distances with varying ambient temperatures.•Any DNA sample can be used in the field or resource-limited setting by untrained personnel.

Electrochemical biosensor for detection of MON89788 gene fragments with spiny trisoctahedron gold nanocrystal and target DNA recycling amplification

The shape-controlled synthesis of gold nanocrystals via shape induction of hexadecyltrimethylammonium chloride, potassium bromide, and potassium iodide and enantioselective direction of L-cysteine is reported. The resulting gold nanocrystals (STO-Au) offer spiny trisoctahedron nanostructures with good monodispersity and enhanced exposed high-index facets and high catalytic activity. Construction of the electrochemical sensing platform for MON89788 gene involves the modification of STO-Au, thionine (Thi), and labeled bipedal DNA probe 1 or 2 (P1 or P2) for target DNA-induced recycling amplification. In the detection, two surface DNA probes were immobilized on gold electrode via the Au-S bond. Then, hairpin DNA 1 (H1), Thi-STO-Au-P1, and Thi-STO-Au-P2 self-assemble into two-dimensional DNA nanopores (DNPs) on the electrode surface. Target DNA hybridizes with hairpin DNA 2 (H2) to open hairpin structure of H2. The opened H2 binds with H1 in the DNPs to release Thi-STO-Au-P1, Thi-STO-Au-P2, and target DNA by toehold-mediated strand-displacement. The utilization of target DNA-induced recycling allows one target DNA to release 2N STO-Au-labeled DNA strands, promoting significant signal amplification. The detection signal is further enhanced by the catalyzed redox reaction of Thi with STO-Au. The differential pulse voltammetric signal, best measured at - 0.18 V vs. Ag/AgCl, decreases linearly with increasing concentration of MON89788 in the range 0.02-8 × 104 fM, and the detection limit is 0.0048 fM (S/N = 3). The proposed method was successfully applied for electrochemical detection of MON89788 gene fragments in the PCR products from genetically modified soybean. Graphical Abstract We develop l-cysteine controlled synthesis of spiny trisoctahedron gold nanocrystals with good monodispersity and highly exposed high-index facets. The architecture achieves to ultrahigh catalytic activity. The electrochemical biosensor based on gold nanocrystals and target DNA recycling amplification provides advantage of sensitivity, repeatability, and regeneration-free.

Colorimetric biosensing of nopaline synthase terminator using Fe3O4@Au and hemin-functionalized reduced graphene oxide

In this paper, we present a simple and label-free colorimetric biosensor for detection of the nopaline synthase (NOS) terminator in genetically modified (GM) plants. The "signal on" colorimetric biosensor was developed using a nanocomposite consisted of gold nanoparticles doped magnetic Fe₃O₄ nanoparticles (Fe₃O₄@Au NP), capture probe DNA (cDNA), and hemin-functionalized reduced graphene oxide nanosheets (H-GN). The nanocomposite was successfully prepared by means of Au-S bonds and the strong π interactions between cDNA and H-GN. The sensing approach is based on the excellent peroxidase-mimicking activity of H-GN and its different electrostatic interactions with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). In presence of the target NOS, the cDNA in the nanocomposite will hybridize with its complementary sequence, and form dsDNA structure. Due to the weak π interactions between dsDNA and H-GN, a portion of H-GN will be released from the surface of Fe₃O₄@Au NPs and transferred into solution. After magnetic separation was performed, the supernatant was incubated with 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H₂O₂. The released H-GN can catalyze the oxidation reaction of TMB and turn the colorless solution blue. This "signal-on" colorimetric biosensor shows a broad linear range of 0.5-100 nM for the target NOS, with a 0.19 nM detection limit. The application of the biosensor for determination of NOS segments in samples of GM and non-GM tomatoes shows that it can discriminate between GM and non-GM plants. The reliability of the method for samples of NOS-spiked GM tomato suggests satisfactory recoveries in the range of 93.6%-94.2%.