Semi-quantitative visual detection of loop mediated isothermal amplification (LAMP)-generated DNA by distance-based measurement on a paper device

Hongwarittorrn, Irin; Chaichanawongsaroj, Nuntaree; Laiwattanapaisal, Wanida

doi:10.1016/j.talanta.2017.07.019

Cited by 66 publications

(40 citation statements)

References 34 publications

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“…Non-specific products are expected to be rare due to the requirement for hybridization at six independent sequences in the target. Furthermore, it is likely that paper strip-based readout methods will become available that will facilitate semiquantitative analysis (Hongwarittorrn et al, 2017). Quantitation by such methods, as well as by dilution, will allow at-home students to pursue expanded LAMP-based lab activities, including error analysis and protocol variations, which take advantage of the time and flexibility afforded by flipped lab designs.…”

Section: Discussionmentioning

confidence: 99%

Loop-Mediated Isothermal Amplification (LAMP) as a Rapid, Affordable and Effective Tool to Involve Students in Undergraduate Research

et al. 2020

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Undergraduate research (UR) is a high-impact practice (HIP) to engage undergraduate student in science, technology, engineering and mathematics (STEM), especially from underrepresented groups. UR experiences (UREs) can be integrated into the classroom, making authentic research experiences inclusive and available to all students. However, developing UR pedagogy can be challenging for faculty in resource-limited labs, such as community colleges and small liberal arts colleges. Often molecular biology research methods are expensive, time-consuming and need equipment not readily available or affordable in small schools. Polymerase chain reaction (PCR) is one of the most commonly used techniques in research labs and many UREs. We have investigated loop-mediated isothermal amplification (LAMP) as an inexpensive, accessible alternative to PCR for DNA amplification enabling the identification of microorganisms in the context of UREs. LAMP does not require expensive instrumentation or reagents and uses equipment commonly found in teaching labs. By performing the technique, students learn several key scientific skills that will be useful in their undergraduate or graduate STEM careers. We designed guided independent research experiences for several undergraduates that included the use of LAMP. Students successfully applied the technique to culture samples of common environmental bacteria, including Escherichia coli, Salmonella spp., Staphylococcus aureus, and Enterococcus, and were in addition, able to detect both Salmonella and Enterococcus in directly sampled environmental waters. To highlight the accessibility and affordability of this URE, a simple boiling method was used for DNA preparation from environmental samples. Student response data show positive attitudes toward UR when LAMP is utilized as a research tool to tackle relevant biological questions. The feasibility of using simplified LAMP in UREs points to a potential, more expanded application to public engagement with science and broader and more inclusive interactions with the research community.

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Section: Discussionmentioning

confidence: 99%

Loop-Mediated Isothermal Amplification (LAMP) as a Rapid, Affordable and Effective Tool to Involve Students in Undergraduate Research

et al. 2020

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“…To improve analytical reproducibility, inkjet printing has been proposed to replace manual deposition (e.g., pipetting) to eliminate manual errors . To improve the detection sensitivity, many signal amplification strategies have been integrated on distance‐based paper devices, such as cascade enzymatic reactions, polymerase chain reactions (PCR), and loop mediated isothermal amplification (LAMP) …”

Section: Distance‐based Quantitative Readout Strategymentioning

confidence: 99%

Equipment‐Free Quantitative Readout in Paper‐Based Point‐of‐Care Testing

You

Bai

et al. 2019

Small Methods

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been widely applied in resource-limited settings due to their easy-to-operate and equipment-independent characteristics with minimum user intervention. [9] However, LFAs are often limited to qualitative results readout by providing "yes" or "no" signal, which is insufficient in some application scenarios, e.g., a clinical action will be made in clinics according to the accurate amount of targets. Recently, the emerging µPADs have gained considerable interests due to their excellent capability for outputting quantitative results. [10] Nowadays, quantitative paper-based assays are mainly based on electrochemical detection, [11] electrochemiluminescence detection, [12] and fluorescent detection. [13,14] Although sensitive and quantitative detection can be obtained, special equipment for quantification of detection signal is usually involved. For instance, electrochemical workstation is needed for performing electrochemical detection on paper, while a special light-emitting device is indispensable for fluorescent testing. For addressing these limitations, some handheld equipments, such as glucose meter, [15] multimeter, [16] and smartphone, [17,18] have been introduced as readers for outputting quantitative measurements with improved portability. However, the accessibility and cost of these handheld equipments may still be a big challenge for their application in resource-poor areas, where the quantitative detection in an equipment-free manner is preferred. Hence, the exploitation of equipment-free paper-based analytical devices shows broad practical application prospects in POCT field.Colorimetric detection holds great potential for developing equipment-free detection methods through direct readout by naked eye. [19] Conventionally, the color intensity analysis has been widely used to realize quantification of analytes, whereas a camera is needed to capture images and a computer-based software for image processing. [20] Hence, these quantitative methods based on color intensity analysis are unsatisfactory for exploiting equipment-free quantitative strategies. Fortunately, thanks to the novel signal transformation design in paper-based colorimetric detection, different types of equipment-free quantitative paper devices have already been proposed, where the detection signal has been transformed into the measurement of color change distance, [21] the counting of colored detection zones, [22] the measurement of testing time, [23] and the reading of displayed text. [24] These equipment-free strategies have been demonstrated to be capable of detecting a variety of analytes with acceptable performance, such as metal ions, nucleic acids, bacteria, and cells, whose detection shows great attraction in POCT, thus exhibiting great feasibility and versatility for POCT applications.Equipment-free paper-based devices with quantitative readout have gained considerable interests in recent years, due to the features of remarkable cheapness, prominent portability, and excellent user friendliness. These equipment-free strategies have b...

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“…[7][8][9] These methods often utilize a color-changing reaction that occurs as fluid wicks along a channel, where the length of the colored region corresponds to the concentration of the targeted analyte. [9][10][11][12][13][14][15][16] The specific reaction used depends on the target analyte, requiring each new device to be designed for a different suitable reaction. Other distancebased methods utilize other mechanisms, such as fluid viscosity 17 or blood coagulation, 18 affecting wicking speeds.…”

Section: Introductionmentioning

confidence: 99%

Distance and Microsphere Aggregation-Based DNA Detection in a Paper-Based Microfluidic Device

et al. 2020

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In paper-based microfluidics, the simplest devices are colorimetric, giving qualitative results. However, getting quantitative data can be quite a bit more difficult. Distance-based devices provide a user-friendly means of obtaining quantitative data without the need for any additional equipment, simply by using an included ruler or calibrated markings. This article details the development of a quantitative DNA detection device that utilizes the aggregation of polystyrene microspheres to affect the distance that microspheres wick through filter paper. The microspheres are conjugated to single-stranded DNA (ssDNA) oligomers that are partially complementary to a target strand and, in the presence of the target strand, form a three-strand complex, resulting in the formation of aggregates. The higher the concentration of the target strand, the larger the aggregate, and the shorter the distance wicked by the microspheres. This behavior was investigated across a wide range of target concentrations and under different incubation times to understand aggregate formation. The device was then used to successfully detect a target strand spiked in extracted plant DNA.

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Semi-quantitative visual detection of loop mediated isothermal amplification (LAMP)-generated DNA by distance-based measurement on a paper device

Cited by 66 publications

References 34 publications

Loop-Mediated Isothermal Amplification (LAMP) as a Rapid, Affordable and Effective Tool to Involve Students in Undergraduate Research

Loop-Mediated Isothermal Amplification (LAMP) as a Rapid, Affordable and Effective Tool to Involve Students in Undergraduate Research

Equipment‐Free Quantitative Readout in Paper‐Based Point‐of‐Care Testing

Distance and Microsphere Aggregation-Based DNA Detection in a Paper-Based Microfluidic Device

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