Recording the Reaction Process of Loop-Mediated Isothermal Amplification (LAMP) by Monitoring the Voltammetric Response of 2′-Deoxyguanosine 5′-Triphosphate

Light Scattering Technology-Combined Ligation-Dependent Loop-Mediated Isothermal Amplification (LL-LAMP) for Sensitive Detection of RNA

Loop-mediated isothermal amplification (LAMP) has been widely used in nucleic acid assay because of its high specificity, sensitivity, and isothermal property. However, the complexity of amplification product detection is still a major challenge for its wide applications. Herein, we developed a light scattering technology-assisted, low-cost, and simple detection manner of LAMP products without expensive reagents and complicated instruments. Only needing to add a kind of strong acid to the amplification products, the amplification products can aggregate into large particles in a strongly acidic medium, and large particles can produce strong light scattering, which shows a good proportional relationship with the number of amplification products in a wide range. The proposed method shows excellent sensitivity and high specificity that can quantify RNA as low as 100 aM with a single-base resolution.

A Review of Isothermal Amplification Methods and Food-Origin Inhibitors against Detecting Food-Borne Pathogens

The isothermal amplification method, a molecular-based diagnostic technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), is widely used as an alternative to the time-consuming and labor-intensive culture-based detection method. However, food matrices or other compounds can inhibit molecular-based diagnostic technologies, causing reduced detection efficiencies, and false-negative results. These inhibitors originating from food are polysaccharides and polyphenolic compounds in berries, seafood, and vegetables. Additionally, magnesium ions needed for amplification reactions can also inhibit molecular-based diagnostics. The successful removal of inhibitors originating from food and molecular amplification reaction is therefore proposed to enhance the efficiency of molecular-based diagnostics and allow accurate detection of food-borne pathogens. Among molecular-based diagnostics, PCR inhibitors have been reported. Nevertheless, reports on the mechanism and removal of isothermal amplification method inhibitors are insufficient. Therefore, this review describes inhibitors originating from food and some compounds inhibiting the detection of food-borne pathogens during isothermal amplification.

Rapid detection of cytochrome cd1-containing nitrite reductase encoding gene nirS of denitrifying bacteria with loop-mediated isothermal amplification assay

The cytochrome cd1-containing nitrite reductase, nirS, plays an important role in biological denitrification. Consequently, investigating the presence and abundance of nirS is a commonly used approach to understand the distribution and potential activity of denitrifying bacteria, in addition to denitrifier communities. Herein, a rapid method for detecting nirS gene with loop-mediated isothermal amplification (LAMP) was developed, using Pseudomonas aeruginosa PAO1 (P. aeruginosa PAO1) as model microorganism to optimize the assay. The LAMP assay relied on a set of four primers that were designed to recognize six target sequence sites, resulting in high target specificity. The limit of detection for the LAMP assay under optimized conditions was 1.87 pg/reaction of genomic DNA, which was an order of magnitude lower than that required by conventional PCR assays. Moreover, it was validated that P. aeruginosa PAO1 cells as well as genomic DNA could be directly used as template. Only 1 h was needed from the addition of bacterial cells to the reaction to the verification of amplification success. The nirS gene of P. aeruginosa PAO1 in spiked seawater samples could be detected with both DNA-template based LAMP assay and cell-template based LAMP assay, demonstrating the practicality of in-field use.

Evaluation of a Loop-Mediated Isothermal Amplification Technique for the Rapid Visual Detection of Hepatozoon canis Infection

BACKGROUND

Laboratory diagnosis of Hepatozoon canis infection is tedious, especially in chronic and/or latent infections.

PURPOSE

The study was planned to develop a simple read out loop mediated isothermal amplification (LAMP) assay targeting a partial 18S rRNA gene of H. canis with naked eye visualisation of LAMP products.

METHODS

A LAMP assay was employed to assess the DNA amplification by adding SYBR Green I dye for naked eye inspection of DNA accumulating in reaction tubes. Positive amplification was read through observation of change in colour of reaction mixture following addition of dye. The visual results were further verified with those of agarose gel electrophoresis. Genomic DNA of other haemoparasites of dog viz. Babesia vogeli, B. gibsoni, Ehrlichia canis and Trypanosoma evansi along with no-template control were used to determine the specificity of assay.

RESULTS

Among the 109 blood samples presented at Small Animal Clinics, Teaching Veterinary Clinical Complex, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab (India) tested, 39 revealed colour change from orange to green indicating positive reaction while 70 were negative as revealed by no colour change. The results of visual inspection were comparable to those obtained by agarose gel electrophoresis. The LAMP primers specifically amplified H. canis DNA, whereas no amplification was detected in DNA samples of other haemoparasites and no-template control revealing specificity of the assay. The diagnostic sensitivity and specificity (95% CI) of visual LAMP assay with respect to microscopy in detection of H. canis varied from 100% (15.81-100.00%) and 65.42% (55.61-74.35%), respectively.

CONCLUSION

The present investigation has developed a specific and rapid LAMP assay for the detection of H. canis, using SYBR Green I dye, which has practical applications for the screening of field samples.

A Novel One-Step Fabricated, Droplet-Based Electrochemical Sensor for Facile Biochemical Assays

A simple, novel concept for the one-step fabrication of a low-cost, easy-to-use droplet-based electrochemical (EC) sensor is described, in which the EC reagents are contained in a droplet and the droplet assay is operated on a simple planar surface instead of in a complicated closed channel/chamber. In combination with an elegant carbon electrode configuration, screen-printed on a widely available polyethylene terephthalate (PET) substrate, the developed sensor exhibits a stable solution-restriction capacity and acceptable EC response, and thus can be used directly for the detection of different analytes (including ascorbic acid (AA), copper ions (Cu(2+)), 2'-deoxyguanosine 5'-triphosphate (dGTP) and ferulic acid (FA)), without any pretreatment. The obtained, acceptable linear ranges/detection limits for AA, Cu(2+), dGTP and FA are 0.5-10/0.415 mM, (0.0157-0.1574 and 0.1574-1.5736)/0.011 mM, 0.01-0.1/0.008 mM and 0.0257-0.515/0.024 mM, respectively. Finally, the utility of the droplet-based EC sensor was demonstrated for the determination of AA in two commercial beverages, and of Cu(2+) in two water samples, with reliable recovery and good stability. The applicability of the droplet-based sensor demonstrates that the proposed EC strategy is potentially a cost-effective solution for a series of biochemical sensing applications in public health, environmental monitoring, and the developing world.

Emerging Loop-Mediated Isothermal Amplification-Based Microchip and Microdevice Technologies for Nucleic Acid Detection

Rapid, sensitive, and selective pathogen detection is of paramount importance in infectious disease diagnosis and treatment monitoring. Currently available diagnostic assays based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) are time-consuming, complex, and relatively expensive, thus limiting their utility in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been used extensively in the development of rapid and sensitive diagnostic assays for pathogen detection and nucleic acid analysis and hold great promise for revolutionizing point-of-care molecular diagnostics. Here, we review novel LAMP-based lab-on-a-chip (LOC) diagnostic assays developed for pathogen detection over the past several years. We review various LOC platforms based on their design strategies for pathogen detection and discuss LAMP-based platforms still in development and already in the commercial pipeline. This review is intended as a guide to the use of LAMP techniques in LOC platforms for molecular diagnostics and genomic amplifications.

Quantitative determination of target gene with electrical sensor

Integrating loop-mediated isothermal amplification (LAMP) with capacitively coupled contactless conductivity detection (C(4)D), we have developed an electrical sensor for the simultaneous amplification and detection of specific sequence DNA. Using the O26-wzy gene as a model, the amount of initial target gene could be determined via the threshold time obtained by monitoring the progression of the LAMP reaction in real time. Using the optimal conditions, a detection limit of 12.5 copy/μL can be obtained within 30 min. Monitoring the LAMP reaction by C(4)D has not only all the advantages that existing electrochemical methods have, but also additional attractive features including being completely free of carryover contamination risk, high simplicity and extremely low cost. These benefits all arise from the fact that the electrodes are separated from the reaction solution, that is C(4)D is a contactless method. Hence in proof of principle, the new strategy promises a robust, simple, cost-effective and sensitive method for quantitative determination of a target gene, that is applicable either to specialized labs or at point-of-care.

Monitoring the progression of loop-mediated isothermal amplification using conductivity

Loop-mediated isothermal amplification (LAMP) yields a large amount of DNA, as well as magnesium pyrophosphate precipitate, causing a decrease in ionic strength that can be measured with a conductivity meter. There is a clear relationship between the conductivity of the LAMP mixture solution and the duration of biochemical reaction. Moreover, there is also a clear relationship between the change in conductivity and the amount of initial template DNA over the range of 0.08 to 3.2 ng. These results demonstrate the feasibility not only for detecting the LAMP product qualitatively but also for real-time monitoring the biochemical reaction progression quantitatively using conductivity measurements.