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Panich W, Puttharugsa C, Tejangkura T, Chontananarth T. A simple color absorption analysis of colorimetric loop-mediated isothermal amplification for detection of Raillietina spp. in clinical samples using a 3D-printed tube holder coupled with a smartphone camera and notebook screen. Mikrochim Acta 2024; 191:603. [PMID: 39284926 DOI: 10.1007/s00604-024-06648-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/21/2024] [Indexed: 10/13/2024]
Abstract
A simple method has been developed for semi-quantitative analysis of the colorimetric output of loop-mediated isothermal amplification (LAMP) using a 3D-printed tube holder with a smartphone and notebook for the detection of Raillietina, which is the cause of Raillietiniasis affecting free-range chicken farming. In this method, a light is directed from a notebook screen to the LAMP products in the tube holder and the color absorption of the LAMP products is measured by using the appropriate smartphone application. It was found that the malachite green dye-coupled LAMP (MaG-LAMP) assay showed the highest sensitivity and specificity for detecting Raillietina without any cross-reaction with other related parasites and hosts. The limit of detection was 10 fg/μL of DNA. A total of 60 fecal samples were infectively confirmed by microscopic examination and the results of microscopy compared with those of MaG-LAMP and triplex PCR assays. Microscopy and MaG-LAMP based on the color absorption demonstrated high agreement in Raillietina detection with kappa = 1. Rapid, simple, cost-effective, and easy interpretation of colorimetric LAMP assays and their high sensitivity make them superior to PCR and morphological investigation, demonstrating the feasibility of this assay in point-of-care screening to support farm management and solve chicken health problems. Our study presents is an alternative diagnostic method using semi-quantitative analysis of colorimetric LAMP based on the differing solution color absorptions between positive and negative reactions for infectious disease diagnosis.
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Affiliation(s)
- Wasin Panich
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Chokchai Puttharugsa
- Department of Physics, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thanawan Tejangkura
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
- Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thapana Chontananarth
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand.
- Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand.
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Adedokun G, Alipanah M, Fan ZH. Sample preparation and detection methods in point-of-care devices towards future at-home testing. LAB ON A CHIP 2024; 24:3626-3650. [PMID: 38952234 PMCID: PMC11270053 DOI: 10.1039/d3lc00943b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Timely and accurate diagnosis is critical for effective healthcare, yet nearly half the global population lacks access to basic diagnostics. Point-of-care (POC) testing offers partial solutions by enabling low-cost, rapid diagnosis at the patient's location. At-home POC devices have the potential to advance preventive care and early disease detection. Nevertheless, effective sample preparation and detection methods are essential for accurate results. This review surveys recent advances in sample preparation and detection methods at POC. The goal is to provide an in-depth understanding of how these technologies can enhance at-home POC devices. Lateral flow assays, nucleic acid tests, and virus detection methods are at the forefront of POC diagnostic technology, offering rapid and sensitive tools for identifying and measuring pathogens, biomarkers, and viral infections. By illuminating cutting-edge research on assay development for POC diagnostics, this review aims to accelerate progress towards widely available, user-friendly, at-home health monitoring tools that empower individuals in personalized healthcare in the future.
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Affiliation(s)
- George Adedokun
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Morteza Alipanah
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL 32611, USA
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611, USA
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3
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Natsuhara D, Miyajima A, Bussho T, Okamoto S, Nagai M, Ihira M, Shibata T. A microfluidic-based quantitative analysis system for the multiplexed genetic diagnosis of human viral infections using colorimetric loop-mediated isothermal amplification. Analyst 2024; 149:3335-3345. [PMID: 38695841 DOI: 10.1039/d4an00215f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In this study, a microfluidic-based system utilizing colorimetric loop-mediated isothermal amplification (LAMP) is introduced for the quantitative analysis of nucleic acid targets. This system offers a user-friendly and cost-effective platform for the multiplexed genetic diagnosis of various infectious diseases across multiple samples. It includes time-lapse imaging equipment for capturing images of the microfluidic device during the LAMP assay and a hue-based quantitative analysis software to analyze the LAMP reaction, streamlining diagnostic procedures. An electric pipette was used to simplify the loading of samples and LAMP reagents into the device, allowing easy operation even by untrained individuals. The hue-based analysis software employs efficient image processing and post-processing techniques to calculate DNA amplification curves based on color changes in multiple reaction chambers. This software automates several tasks, such as identifying reaction chamber areas from time-lapse images, quantifying color information within each chamber, correcting baselines of DNA amplification curves, fitting experimental data to theoretical curves, and determining the threshold time for each curve. To validate the developed system, conventional off-chip LAMP assays were conducted with a 25 μL reaction mixture in 0.2 mL polymerase chain reaction (PCR) tubes using a real-time turbidimeter. The results indicated that the threshold time obtained using the colorimetric LAMP assay in the developed system is comparable to that obtained with real-time turbidity measurements in PCR tubes, demonstrating the system's capability for quantitative analysis of target nucleic acids, including those from human herpesviruses.
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Affiliation(s)
- Daigo Natsuhara
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Akira Miyajima
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Tomoya Bussho
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Shunya Okamoto
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
- Institute for Research on Next-generation Semiconductor and Sensing Science (IRES2), Toyohashi University of Technology, Aichi 441-8580, Japan
| | - Masaru Ihira
- Faculty of Clinical Science for Biological Monitoring, Fujita Health University, Aichi 470-1192, Japan
| | - Takayuki Shibata
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
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Moehling TJ, Worthington MD, Wong PYG, Wong SS, Meagher RJ. Development of a Colorimetric Loop-Mediated Isothermal Amplification Assay for the Detection of Trypanosoma cruzi in Low-Resource Settings. Diagnostics (Basel) 2024; 14:1193. [PMID: 38893719 PMCID: PMC11172009 DOI: 10.3390/diagnostics14111193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Chagas disease is an inflammatory parasitic infection caused by Trypanosoma cruzi (T. cruzi). Early diagnosis is crucial in guiding treatment and slowing disease progression; however, current diagnostic methods have insufficient detection limits and often require skilled technicians. Molecular tests, especially isothermal nucleic acid assays, are advantageous due to their excellent sensitivity, specificity, speed, and simplicity. Here, we optimized a colorimetric loop-mediated isothermal amplification (LAMP) assay for T. cruzi. We can detect as few as 2 genomic copies/reaction using three different T. cruzi strains. We examined selectivity using other parasitic protozoans and successfully detected T. cruzi DNA extracted from parasites in human whole blood down to 1.2 parasite equivalents/reaction. We also performed a blinded study using canine blood samples and established a 100% sensitivity, specificity, and accuracy for the colorimetric LAMP assay. Finally, we used a heated 3D printer bed and an insulated thermos cup to demonstrate that the LAMP incubation step could be performed with accessible, low-cost materials. Altogether, we have developed a high-performing assay for T. cruzi with a simple colorimetric output that would be ideal for rapid, low-cost screening at the point of use.
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Affiliation(s)
- Taylor J. Moehling
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA 94551, USA; (T.J.M.); (M.D.W.)
| | - Myla D. Worthington
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA 94551, USA; (T.J.M.); (M.D.W.)
| | | | | | - Robert J. Meagher
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA 94551, USA; (T.J.M.); (M.D.W.)
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Panich W, Nak-On S, Sabaijai M, Raksaman A, Puttharugsa C, Tejangkura T, Chontananarth T. Evaluation of semi-quantitative colorimetric assays based on loop-mediated isothermal amplification indicators by using image analysis. Anal Biochem 2024; 688:115481. [PMID: 38360170 DOI: 10.1016/j.ab.2024.115481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Colorimetric assays are some of the most convenient detection methods, creating discoloration in solutions that is visible to the naked eye. However, colorimetric reactions have some limitations regarding the variability in the color perception of individuals caused by factors such as color blindness, experience, and gender. Semi-quantitative chromatic analysis has been used as an alternative method to differentiate between two colors and accurately interpret the results from a numerical value, with high confidence. Therefore, we developed and determined the optimal model between Red-Green-Blue (RGB) and Commission Internationale de l'Eclairage (CIE) Lab color spaces to establish a semi-quantitative colorimetric assay via image analysis by the ImageJ program for loop-mediated isothermal amplification (LAMP), using the dyes malachite green and phenol red. The semi-quantitative colorimetric assays using the color distance values of the CIELab color space (ΔEab) were more suitable than those using the RGB color space (ΔERGB) for chromatic differentiation between positive and negative reactions in both indicator dyes, demonstrating the feasibility of this assay to be applied in the detection of a wide range of pathogens and infectious diseases.
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Affiliation(s)
- Wasin Panich
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Sirapat Nak-On
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Metawee Sabaijai
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Awika Raksaman
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Chokchai Puttharugsa
- Department of Physics, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thanawan Tejangkura
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand; Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thapana Chontananarth
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand; Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand.
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Camargo BD, Cassaboni Stracke M, Soligo Sanchuki HB, de Oliveira VK, Ancelmo HC, Mozaner Bordin D, Klerynton Marchini F, Ribeiro Viana E, Blanes L. Low-Cost Arduino Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) for Sensitive Nucleic Acid Detection. BIOSENSORS 2024; 14:128. [PMID: 38534235 DOI: 10.3390/bios14030128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/05/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
This work presents a low-cost transcription loop-mediated isothermal amplification (RT-LAMP) instrument for nucleic acid detection, employing an Arduino Nano microcontroller. The cooling system includes customized printed circuit boards (PCBs) that serve as electrical resistors and incorporate fans. An aluminum block is designed to accommodate eight vials. The system also includes two PCB heaters-one for sample heating and the other for vial lid heating to prevent condensation. The color detection system comprises a TCS3200 color 8-sensor array coupled to one side of the aluminum heater body and a white 8-LED array coupled to the other side, controlled by two Multiplexer/Demultiplexer devices. LED light passes through the sample, reaching the color sensor and conveying color information crucial for detection. The top board is maintained at 110 ± 2 °C, while the bottom board is held at 65 ± 0.5 °C throughout the RT-LAMP assay. Validation tests successfully demonstrated the efficacy of the colorimetric RT-LAMP reactions using SARS-CoV-2 RNA amplification as a sample viability test, achieving 100% sensitivity and 97.3% specificity with 66 clinical samples. Our instrument offers a cost-effective (USD 100) solution with automated result interpretation and superior sensitivity compared to visual inspection. While the prototype was tested with SARS-CoV-2 RNA samples, its versatility extends to detecting other pathogens using alternative primers, showcasing its potential for broader applications in biosensing.
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Affiliation(s)
- Bruno Dias Camargo
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | | | - Hellen Cristina Ancelmo
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Dayanne Mozaner Bordin
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Fabricio Klerynton Marchini
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Emilson Ribeiro Viana
- Academic Department of Physics (DAFIS), Federal University of Technology-Paraná (UTFPR), Sete de Setembro 3165 Av., Curitiba 80230-901, Brazil
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
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7
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Layne TR, Scott A, Cunha LL, Turiello R, Landers JP. Three-Dimensional-Printed Instrument for Isothermal Nucleic Acid Amplification with Real-Time Colorimetric Imaging. MICROMACHINES 2024; 15:271. [PMID: 38398999 PMCID: PMC10892149 DOI: 10.3390/mi15020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
Isothermal amplification methods have become popular in research due to the simplicity of the technology needed to run the reactions. Specifically, loop-mediated isothermal amplification (LAMP) has been widely used for various applications since first reported in 2000. LAMP reactions are commonly monitored with the use of colorimetry. Although color changes associated with positive amplification are apparent to the naked eye, this detection method is subjective due to inherent differences in visual perception from person to person. The objectivity of the colorimetric detection method may be improved by programmed image capture over time with simultaneous heating. As such, the development of a novel, one-step, automated, and integrated analysis system capable of performing these tasks in parallel is detailed herein. The device is adaptable to multiple colorimetric dyes, cost-effective, 3D-printed for single-temperature convective heating, and features an easy-to-use LabVIEW software program developed for automated image analysis. The device was optimized and subsequently validated using four messenger-RNA targets and mock forensic samples. The performance of our device was determined to be comparable to that of a conventional thermal cycler and smartphone image analysis, respectively. Moreover, the outlined system is capable of objective colorimetric analysis, with exceptional throughput of up to 96 samples at once.
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Affiliation(s)
- Tiffany R. Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Anchi Scott
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Larissa L. Cunha
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Rachelle Turiello
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - James P. Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22903, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
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Nak-On S, Sabaijai M, Raksaman A, Panich W, Tejangkura T, Chontananarth T. Visualization and development of colorimetric loop-mediated isothermal amplification for the rapid detection and diagnosis of paramphistome infection: colorimetric PAR-LAMP. Parasitol Res 2024; 123:126. [PMID: 38326433 DOI: 10.1007/s00436-024-08150-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Colorimetric detection can be applied to differentiate between positive and negative conditions. It can be coupled with loop-mediated isothermal amplification to diagnose rumen fluke or paramphistome infection, also called colorimetric PAR-LAMP. This study conducted LAMP using three candidate indicator dyes, namely malachite green (MLG), methyl green (MTG), and neutral red (NTR), and the results were observed by the naked eye. The dye concentration was optimized to obtain the most pronounced positive-negative result discrimination. Subsequently, we conducted target sensitivity tests using the DNA of Fischoederius elongatus at different concentrations. To validate the detection accuracy, the result was confirmed by gel electrophoresis. The sensitivity test presented the lowest detectable DNA concentration or limit of detection (LOD), with 1 pg for MLG, 0.5 ng for MTG, and 50 pg for NTR. Different LODs revealed inhibition of LAMP reaction and reduced efficiency of result presentation for colorimetric-based detection, particularly NTR and MTG. For MLG-LAMP, we observed no cross-reaction of non-target DNA and improved reaction with the DNA of Fischoederius cobboldi and Calicophoron sp., with multi-detection. In addition, naked eye observation and agarose gel electrophoresis (AGE) evaluation of the MLG-LAMP results showed a moderate and strong agreement with LAMP-AGE and microscopic examinations. Based on our results, colorimetric PAR-LAMP is a rapid, comfortable, and point-of-care procedure for the diagnosis of paramphistome infection.
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Affiliation(s)
- Sirapat Nak-On
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Metawee Sabaijai
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Awika Raksaman
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Wasin Panich
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thanawan Tejangkura
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
- Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thapana Chontananarth
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand.
- Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand.
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Zhang Y, Shi YE, Wang S, Song Q, Li W, Wang Z. Cobalt oxyhydroxide nanosheet-modulated ratiometric fluorescence platform for the selective detection of malachite green in fish. Mikrochim Acta 2024; 191:119. [PMID: 38300297 DOI: 10.1007/s00604-024-06200-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
A ratiometric fluorescence platform was developed based on the cobalt oxyhydroxide (CoOOH) nanosheet-modulated fluorescence response of blue emissive copper nanoclusters (Cu NCs) and yellow emissive o-phenylenediamine (OPD). CoOOH nanosheets showed dual function of strong absorption and oxidation ability, which can effectively quench the blue fluorescence of Cu NCs, with an excitation and emission peak maximum at 390 and 450 nm, respectively , and transfer the OPD into yellow fluorescence products, with an excitation and emission peak maximum at 390 and 560 nm, respectively. Upon introducing butyrylcholinesterase (BChE) and its substrates, CoOOH nanosheets were decomposed into Co2+, and malachite green (MG) showed strong inhibition ability to this process. This resulted in the obvious difference on the ratio of blue and yellow fluorescence recorded on the system in the presence and absence of MG, which was utilized for the quantitative detection of MG, with a limit of detection of 0.140 μM and a coefficient of variation of 3.5%. The fluorescence ratiometric assay showed excellent detection performances in practical sample analysis.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, Key Laboratory of Chemical Biology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Materials Science, Hebei University, Baoding, 071002, People's Republic of China
| | - Yu-E Shi
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, Key Laboratory of Chemical Biology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Materials Science, Hebei University, Baoding, 071002, People's Republic of China.
| | - Shuaijing Wang
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, People's Republic of China
| | - Qian Song
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, Key Laboratory of Chemical Biology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Materials Science, Hebei University, Baoding, 071002, People's Republic of China
| | - Wei Li
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, People's Republic of China
| | - Zhenguang Wang
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, Key Laboratory of Chemical Biology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Materials Science, Hebei University, Baoding, 071002, People's Republic of China.
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10
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Wu X, Yuan X, Liang E, Liu L, Lin Y, Xie L, Chai X, Xu K, Du G, Zhang L. A flavonol-labelled cellulose fluorescent probe combined with composite fluorescent film imaging and smartphone technology for the detection of Fe 3. Int J Biol Macromol 2024; 259:129373. [PMID: 38216010 DOI: 10.1016/j.ijbiomac.2024.129373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024]
Abstract
Fe3+ is one of the most widely distributed and abundant elements on earth. Realizing efficient and real-time monitoring of Fe3+ is of great significance for the natural environment and the health of living organisms. In this paper, a flavonol-labelled cellulose-based fluorescent probe (ACHM) was synthesized by using dialdehyde cellulose (DAC) as the backbone and combining with flavonol derivatives (AHM - 1). The mechanism of recognizing Fe3+ was verified by characterizing the structure of ACHM by NMR, HRMS (High Resolution Mass Spectrometry), FTIR (Fourier Transform Infrared Spectroscopy), XRD (X-ray Diffraction), TG (Thermogravimetry) and SEM (Scanning Electron Microscopy). The H2O solution of the probe ACHM showed good fluorescence properties. It has quenching fluorescence properties for Fe3+, with a low limit of detection (LOD) of 0.10 μM and a fast response time of only 20 s. In addition, in order to expand the application range of the probe, ACHM was prepared as a fluorescent composite film with an average tensile strength of 32.9 MPa and an average elongation at break of 3.39 %. It shows its superiority in mechanical properties. The probe also demonstrated its practical application value for detecting Fe3+ in smartphone imaging applications.
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Affiliation(s)
- Xiaoxiao Wu
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Xushuo Yuan
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Entong Liang
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Li Liu
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Yanfei Lin
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, Zhejiang, China.
| | - Linkun Xie
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Xijuan Chai
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Kaimeng Xu
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China
| | - Guanben Du
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China.
| | - Lianpeng Zhang
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, Yunnan, China.
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11
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Alsaeed M, Alhamid G, Tombuloglu H, Kabanja JH, Karagoz A, Tombuloglu G, Rabaan AA, Al-Suhaimi E, Unver T. Ultrasensitive and fast detection of SARS-CoV-2 using RT-LAMP without pH-dependent dye. Funct Integr Genomics 2024; 24:16. [PMID: 38242999 DOI: 10.1007/s10142-024-01297-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
This study investigates the performance of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the colorimetric detection of SARS-CoV-2 using fluorometric dye, namely, calcein. The detection limit (LoD) with the N-ID1 primer set resulted in superior performance, corresponding to ~ 2 copies/reaction or ~ 0.1 copies/μL of the RNA sample. The color development can be observed by the naked eye, using an ultraviolet (UV) transilluminator or a hand-UV light without the requirement of expensive devices. The average time-to-reaction (TTR) value was 26.2 min in high-copy number samples, while it was about 50 min in rRT-PCR. A mobile application was proposed to quantify the positive and negative results based on the three-color spaces (RGB, Lab, and HSB). Compared to rRT-PCR (n = 67), this assay allows fast and sensitive visual detection of SARS-CoV-2, with high sensitivity (90.9%), selectivity (100%), and accuracy (94.03%). Besides, the assay was sensitive regardless of variants. Since this assay uses a fluorescent dye for visual observation, it can be easily adapted in RT-LAMP assays with high sensitivity. Thus, it can be utilized in low-source centers and field testing such as conferences, sports meetings, refugee camps, companies, and schools.
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Affiliation(s)
- Moneerah Alsaeed
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Galyah Alhamid
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Juma H Kabanja
- Department of Pathology & Laboratory Medicine, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Aysel Karagoz
- Quality Assurance Department, Turk Pharmaceutical and Serum Ind. Inc., Ankara, Turkey
| | - Guzin Tombuloglu
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan
| | - Ebtesam Al-Suhaimi
- Vice Presidency for Scientific Research and Innovation, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Turgay Unver
- Ficus Biotechnology, Ankara, Turkey
- Faculty of Engineering, Ostim Technical University, 06374, Ankara, Turkey
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12
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Rioboó-Legaspi P, González-López A, Beltrán-Sánchez JF, Cima-Cabal MD, García-Suárez MM, Sánchez AJG, Fernández-Otero T, Haro JG, Costa-Rama E, Fernández-Abedul MT. Phenol red as electrochemical indicator for highly sensitive quantification of SARS-CoV-2 by loop-mediated isothermal amplification detection. Talanta 2024; 266:124963. [PMID: 37517341 DOI: 10.1016/j.talanta.2023.124963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
The current COVID-19 pandemic has made patent the need for rapid and cost-effective diagnostic tests, crucial for future infectious outbreaks. Loop-mediated isothermal amplification (LAMP) is a promising and decentralized alternative to qPCR. In this work we have developed a sensitive, fast, and simple innovative methodology for quantification of SARS-CoV-2 RNA copies, combining reverse-transcription LAMP with electrochemical detection. This is based on the oxidation of phenol red (PR), a visual and electroactive LAMP indicator, which oxidation peak potential (Ep) changes with the progress of the LAMP reaction. Using that Ep shift as analytical signal, a calibration curve was obtained for fragment N1 copies of SARS-CoV2 (which provided better results than N or S fragments), with a potential shift of 16.2 mV per order of magnitude, and a practical limit of detection of 21 copies·μL-1. Moreover, the precision of Ep is excellent (RSD < 2%): 557 ± 5 mV for negative and 602 ± 7 mV for positive (2148 N fragment RNA copies·µL-1·-1) LAMP controls. This methodology has been applied to the analysis of nasopharyngeal swab samples, resulting in total concordance with clinical RT-qPCR results. Advances towards fully decentralization have been achieved by designing and fabricating a small portable heater for isothermal procedures, obtaining comparable results to those from a commercial benchtop thermal cycler.
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Affiliation(s)
- P Rioboó-Legaspi
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain
| | - A González-López
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain
| | - J F Beltrán-Sánchez
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - M D Cima-Cabal
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Spain.
| | - M M García-Suárez
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Spain
| | - A J García Sánchez
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - T Fernández-Otero
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - J García Haro
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - E Costa-Rama
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain
| | - M T Fernández-Abedul
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain.
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13
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Pauly MD, Ganova-Raeva L. Point-of-Care Testing for Hepatitis Viruses: A Growing Need. Life (Basel) 2023; 13:2271. [PMID: 38137872 PMCID: PMC10744957 DOI: 10.3390/life13122271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Viral hepatitis, caused by hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), or hepatitis E virus (HEV), is a major global public health problem. These viruses cause millions of infections each year, and chronic infections with HBV, HCV, or HDV can lead to severe liver complications; however, they are underdiagnosed. Achieving the World Health Organization's viral hepatitis elimination goals by 2030 will require access to simpler, faster, and less expensive diagnostics. The development and implementation of point-of-care (POC) testing methods that can be performed outside of a laboratory for the diagnosis of viral hepatitis infections is a promising approach to facilitate and expedite WHO's elimination targets. While a few markers of viral hepatitis are already available in POC formats, tests for additional markers or using novel technologies need to be developed and validated for clinical use. Potential methods and uses for the POC testing of antibodies, antigens, and nucleic acids that relate to the diagnosis, monitoring, or surveillance of viral hepatitis infections are discussed here. Unmet needs and areas where additional research is needed are also described.
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Affiliation(s)
| | - Lilia Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., NE, Atlanta, GA 30329, USA;
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14
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Pauly MD, Weis-Torres S, Hayden TM, Ganova-Raeva LM, Kamili S. Development of simple, rapid, and sensitive methods for detection of hepatitis C virus RNA from whole blood using reverse transcription loop-mediated isothermal amplification. J Clin Microbiol 2023; 61:e0077123. [PMID: 37933990 PMCID: PMC10662345 DOI: 10.1128/jcm.00771-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an underdiagnosed global health problem. Diagnosis of current HCV infections typically requires testing for HCV RNA using high-complexity laboratory tests. Methods for the detection of HCV RNA that are simple, inexpensive, rapid, and compatible with use outside of a laboratory setting are very important in order to improve access to hepatitis C diagnostic testing and facilitate accelerated linkage to care. We developed and evaluated three simple workflows for extracting HCV RNA from small volumes of whole blood for use in a sensitive, pan-genotypic RT-LAMP assay. The water workflow uses osmotic stress to release HCV RNA and has a limit of detection of 4.3 log10(IU/mL) (95% CI 4.0-4.9). The heat workflow uses a heating step to release HCV RNA and has a limit of detection of 4.2 log10(IU/mL) (95% CI 3.8-5.1). The bead workflow, which uses chemical lysis of the sample and a streamlined paramagnetic solid phase reversible immobilization bead procedure for nucleic acid purification, has a limit of detection of 2.8 log10(IU/mL) (95% CI 2.5-3.4). When used to test whole blood spiked with HCV RNA-positive plasma samples in which most HCV levels were below 5.0 log10(IU/mL), the water, heat, and bead workflows detected HCV RNA in 69%, 75%, and 94% of samples, respectively. These workflows are compatible with visual lateral flow dipsticks, and each takes less than 60 min from sample to result. Each workflow can be performed with minimal and inexpensive equipment. With further procedural simplifications, these workflows may form the basis of assays for the point-of-care diagnosis of HCV infections.
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Affiliation(s)
- Matthew D. Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Sabrina Weis-Torres
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Tonya M. Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Lilia M. Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
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15
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Ki J, Kwon IH, Lee J, Lim J, Jang S, Son SU, Seo SB, Oh SY, Kang T, Jung J, Lee KG, Hwang J, Lim EK. A portable smartphone-based colorimetric sensor that utilizes dual amplification for the on-site detection of airborne bacteria. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132398. [PMID: 37639787 DOI: 10.1016/j.jhazmat.2023.132398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Over the past few years, infections caused by airborne pathogens have spread worldwide, infecting several people and becoming an increasingly severe threat to public health. Therefore, there is an urgent need for developing airborne pathogen monitoring technology for use in confined environments to enable epidemic prevention. In this study, we designed a colorimetry-based bacterial detection platform that uses a clustered regularly interspaced short palindromic repeat-associated protein 12a system to amplify signals and a urease enzyme to induce color changes. Furthermore, we have developed a smartphone application that can distinguish colors under different illumination conditions based on the HSV model and detect three types of disease-causing bacteria. Even synthetic oligomers of a few picomoles of concentration and genomic DNA of airborne bacteria smaller than several nanograms can be detected with the naked eye and using color analysis systems. Furthermore, in the air capture model system, the bacterial sample generated approximately a 2-fold signal difference compared with that in the control group. This colorimetric detection method can be widely applied for public safety because it is easy to use and does not require complex equipment.
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Affiliation(s)
- Jisun Ki
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ik Hwan Kwon
- Safety Measurement Institute, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Jina Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Jaewoo Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Medical Device Development Center, Osong Medical innovation foundation, 123, Osongsaengmyeong-ro, Chungcheongbuk-do, 28160, Republic of Korea
| | - Soojin Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Seong Uk Son
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Seung Beom Seo
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Cogno-Mechatronics Engineering, Pusan National University, 2 Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Seo Yeong Oh
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), Daejeon 34141, Republic of Korea
| | - Jungho Hwang
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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16
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Novi VT, Abbas A. Naked-eye visualization of nucleic acid amplicons using hierarchical nanoassembly. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4640-4644. [PMID: 37591804 DOI: 10.1039/d3ay01050c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
This study reports the development of a rapid visualization method for DNA amplicons. Oligonucleotide-coated gold nanoparticles hierarchically assemble on DNA networks to form globular nanostructures, which precipitate into a distinct visible red pellet. This aims to overcome challenges associated with nanoparticle aggregation and dye-based colorimetric detection in LAMP assays.
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Affiliation(s)
- Vinni Thekkudan Novi
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN 55108, USA.
| | - Abdennour Abbas
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN 55108, USA.
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17
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Yaren O, McCarter J, Morris AR, Bradley KM, Karalkar NB, McLendon DC, Kim D, Eastmond BH, Burkett-Cadena ND, Alto BW, Benner SA. Multiplex Surveillance Kit Using Sweetened Solid Support to Detect Arboviruses Isothermally in Mosquito Saliva from the Field. Anal Chem 2023; 95:10736-10743. [PMID: 37390024 DOI: 10.1021/acs.analchem.3c01735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Recently reported "displaceable probe" loop amplification (DP-LAMP) architecture has shown to amplify viral RNA from SARS-CoV-2 with little sample processing. The architecture allows signals indicating the presence of target nucleic acids to be spatially separated, and independent in sequence, from the complicated concatemer that LAMP processes create as part of their amplification process. This makes DP-LAMP an attractive molecular strategy to integrate with trap and sampling innovations to detect RNA from arboviruses carried by mosquitoes in the field. These innovations include (a) development of organically produced carbon dioxide with ethylene carbonate as a bait deployable in mosquito trap, avoiding the need for dry ice, propane tanks, or inorganic carbonates and (b) a process that induces mosquitoes to lay virus-infected saliva on a quaternary ammonium-functionalized paper (Q-paper) matrix, where (c) the matrix (i) inactivates the deposited viruses, (ii) releases their RNA, and (iii) captures viral RNA in a form that keeps it stable for days at ambient temperatures. We report this integration here, with a surprisingly simple workflow. DP-LAMP with a reverse transcriptase was found to amplify arboviral RNA directly from Q-paper, without requiring a separate elution step. This capture-amplification-detection architecture can be multiplexed, with the entire system integrated into a device that can support a campaign of surveillance, in the wild outdoors, that reports the prevalence of arboviruses from field-captured mosquitoes.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Jacquelyn McCarter
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Andrew R Morris
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- College of Medicine, University of Florida, Gainesville, Florida 32611,, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Nilesh B Karalkar
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Daniel C McLendon
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Dongmin Kim
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Bradley H Eastmond
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
- Thermo Fisher Scientific, Frederick, Maryland 02451, USA
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Barry W Alto
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
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18
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Li Y, Xue H, Fei Y, Yang Y, Huang D, Wang L, Xiong X, Xiong X. A rapid and closed-tube method based on the dual-color fluorescence loop-mediated isothermal amplification for visual detection of Atlantic salmon (Salmo salar). Food Chem 2023; 405:134975. [PMID: 36410220 DOI: 10.1016/j.foodchem.2022.134975] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/16/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) visual detection based on hydroxyl naphthol blue (HNB) and SYTO 9 is often confounded by the narrow color variation window and the requirement of empirical preset of cutoff intensity value. To improve the suitability for naked-eye inspection, the present work proposed a strategy based on the fluorescence property of SYTO 9 and HNB to enlarge the contrast and a novel dual-color fluorescence LAMP (dfLAMP) assay was developed for visual detection of Atlantic salmon. Specifically, HNB of 26.25 μM, blended with SYTO 9 of 0.75-1.5 μM, was added in the mixture before amplification, producing light green fluorescence for both positive and negative samples. After amplification, green or yellow-green fluorescence was observed for positive samples, while only orange-red fluorescence emitted for negative ones, enabling an easy and rapid distinguish. The optimized dfLAMP assay has proved its specificity and can detect as little as 1 fg Atlantic salmon DNA.
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Affiliation(s)
- Yi Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yanjing Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China.
| | - Danping Huang
- The State Light Industry Food Quality Supervision and Detection Station, Nanjing 210009, China
| | - Libin Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China.
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19
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Yin C, Song Z, Wang X, Li H, Liu Y, Wang Q, Feng X, Song X. Development and clinical application of a rapid, visually interpretable polymerase spiral reaction for tcdB gene of Clostridioides difficile in fecal cultures. FEMS Microbiol Lett 2023; 370:fnad080. [PMID: 37537148 DOI: 10.1093/femsle/fnad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/14/2023] [Accepted: 08/02/2023] [Indexed: 08/05/2023] Open
Abstract
In the surveillance of outbreaks of Clostridioides difficile infection, the rapid detection and diagnosis of C. difficile remain a major challenge. Polymerase spiral reaction (PSR) is a nucleic acid amplification technique that uses mixed primers and the strand displacement activity of Bst DNA polymerase to achieve a pair of primers and a single enzyme in an isothermal environment. The primer design is simple, the reaction is efficient, and a color indicator can be used to visualize the result. In this study, we developed a rapid and visually interpretable PSR to detect C. difficile by analyzing artificially contaminated feces samples and clinical isolates from patient feces samples. We designed two pairs of primers for a PSR that specifically targeted the conserved tcdB gene of C. difficile. The amplification results were visualized with the chromogenic dye hydroxynaphthol blue. The entire process was accomplished in 50 min at 64°C, with high specificity. The limit of detection of C. difficile with PSR was 150 fg/μl genomic DNA or 2 × 10 CFU/ml in artificially contaminated feces samples. With this method, we analyzed four clinical isolates and also compared the PSR with an isolation-and-culture detection method, polymerase chain reaction, and the Sanger sequencing. The four clinical isolates were found positive for tcdB, which confirmed the high specificity of the primers. The positive rates of tcdB in toxigenic C. difficile detected with PSR, PCR, and Sanger sequencing were 100%. The proportions of toxin types in these clinical C. difficile strains were 50% tcdA+tcdB+CDT- and 50% tcdA+tcdB+CDT+. The assay described should extend our understanding of the incidence of C. difficile. This may allow the rapid diagnosis and screening of C. difficile-related disease outbreaks in the field.
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Affiliation(s)
- Caihong Yin
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
| | - Zhanyun Song
- Changchun Customs Technology Center, 4448 Freedom Road, Changchun, China
| | - Xianghui Wang
- Changchun Customs Technology Center, 4448 Freedom Road, Changchun, China
| | - Hui Li
- Changchun Customs Technology Center, 4448 Freedom Road, Changchun, China
| | - Yue Liu
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
| | - Qiulin Wang
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
| | - Xin Feng
- School of Public Health, College of Veterinary Medicine, Jilin University, 5333 Xi 'an Road, Changchun, China
| | - Xiuling Song
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
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20
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Li Q, An Z, Sun T, Ji S, Wang W, Peng Y, Wang Z, Salentijn GIJ, Gao Z, Han D. Sensitive colorimetric detection of antibiotic resistant Staphylococcus aureus on dairy farms using LAMP with pH-responsive polydiacetylene. Biosens Bioelectron 2023; 219:114824. [PMID: 36327562 DOI: 10.1016/j.bios.2022.114824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/29/2022] [Accepted: 10/16/2022] [Indexed: 11/19/2022]
Abstract
Rapidly and accurately detecting antibiotic-resistant pathogens in agriculture and husbandry is important since these represent a major threat to public health. While much attention has been dedicated to detecting now-common resistant bacteria, such as methicillin-resistant Staphylococcus aureus, fewer methods have been developed to assess resistance against macrolides in Staphylococcus aureus (SA). Here, we report a visual on-site detection system for macrolide resistant SA in dairy products. First, metagenomic sequencing in raw milk, cow manure, water and aerosol deposit collected from dairy farms around Tianjin was used to identify the most abundant macrolide resistance gene, which was found to be the macB gene. In parallel, SA housekeeping genes were screened to allow selective identification of SA, which resulted in the selection of the SAOUHSC_01275 gene. Next, LAMP assays targeting the above-mentioned genes were developed and interpreted by agarose gel electrophoresis. For on-site application, different pH-sensitive colorimetric LAMP indicators were compared, which resulted in selection of polydiacetylene (PDA) as the most sensitive candidate. Additionally, a semi-quantitative detection could be realized by analyzing the RGB information via smartphone with a LOD of 1.344 × 10-7 ng/μL of genomic DNA from a milk sample. Finally, the proposed method was successfully carried out at a real farm within 1 h from sample to result by using freeze-dried reagents and portable devices. This is the first instance in which PDA is used to detect LAMP products, and this generic read-out system can be expanded to other antibiotic resistant genes and bacteria.
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Affiliation(s)
- Qiaofeng Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Wageningen Food Safety Research, Wageningen University & Research, P.O. Box 230, 6700, AE, Wageningen, the Netherlands
| | - Zhaoxia An
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Tieqiang Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shuaifeng Ji
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Weiya Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Gert I J Salentijn
- Wageningen Food Safety Research, Wageningen University & Research, P.O. Box 230, 6700, AE, Wageningen, the Netherlands; Laboratory of Organic Chemistry, Wageningen University, Wageningen, 6708, WE, the Netherlands.
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
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21
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Abstract
INTRODUCTION The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis. AREAS COVERED This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications. EXPERT OPINION RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.
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Affiliation(s)
- Gihoon Choi
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Taylor J Moehling
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J Meagher
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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22
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Shirshikov FV, Bespyatykh JA. Loop-Mediated Isothermal Amplification: From Theory to Practice. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1159-1174. [PMID: 36590469 PMCID: PMC9788664 DOI: 10.1134/s106816202206022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022]
Abstract
Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.
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Affiliation(s)
- F. V. Shirshikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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23
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Development of an optimized colorimetric RT-LAMP for SARS-CoV-2 assay with enhanced procedure controls for remote diagnostics. Sci Rep 2022; 12:21424. [PMID: 36503901 PMCID: PMC9741705 DOI: 10.1038/s41598-022-25872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
The coronavirus pandemic accentuated the need for molecular diagnostic tests. A technique highly used to this end is the Polymerase Chain Reaction (PCR)-a sensitive and specific technique commonly used as the gold standard for molecular diagnostics. However, it demands highly trained personnel and high-maintenance equipment and is relatively time-consuming. An alternative is the Loop-Mediated Isothermal Amplification (LAMP) technique, which doesn't need sample purification or expensive equipment, and is similar to PCR when compared in sensitivity and specificity. In this paper, we developed an optimized colorimetric Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) Point-of-Care test using a portable device to diagnose COVID-19. Variables such as concentration of primers, magnesium sulfate, betaine, hydrochloride guanidine, Bst, and temperature of the reactions were tested. We also created a pipetting quality control system-using a combination of dyes-to avoid false negatives due to a lack of samples added to the reaction test tube. Mineral oil was incorporated in the composition of the RT-LAMP reactions to avoid evaporation when a heating lid isn't available. The final RT-LAMP test is tenfold more sensitive when compared to the WarmStart Colorimetric Master mix from New England Biolabs with a sensitivity of 5 copies per μL.
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24
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Wang J, Davidson JL, Kaur S, Dextre AA, Ranjbaran M, Kamel MS, Athalye SM, Verma MS. Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens. BIOSENSORS 2022; 12:bios12121094. [PMID: 36551061 PMCID: PMC9776365 DOI: 10.3390/bios12121094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 05/17/2023]
Abstract
Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Simerdeep Kaur
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Andres A. Dextre
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohamed S. Kamel
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Shreya Milind Athalye
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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25
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Kim GR, Hwang JS, Kim JD, Kim YS, Park CY. Electrochemical Gene Amplification Signal Detection of Disposable Biochips Using Electrodes. SENSORS (BASEL, SWITZERLAND) 2022; 22:8624. [PMID: 36433221 PMCID: PMC9693005 DOI: 10.3390/s22228624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Real-time Polymerase Chain Reaction (RT-PCR), a molecular diagnostic technology, is spotlighted as one of the quickest and fastest diagnostic methods for the actual coronavirus (SARS-CoV-2). However, the fluorescent label-based technology of the RT-PCR technique requires expensive equipment and a sample pretreatment process for analysis. Therefore, this paper proposes a biochip based on Electrochemical Impedance Spectroscopy (EIS). In this paper, it was possible to see the change according to the concentration by measuring the impedance with a chip made of two electrodes with different shapes of sample DNA.
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Affiliation(s)
- Gyo-Rim Kim
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Ji-Soo Hwang
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Jong-Dae Kim
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Yu-Seop Kim
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Chan-Young Park
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
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26
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Xiao B, Zhao R, Wang N, Zhang J, Sun X, Chen A. Recent advances in centrifugal microfluidic chip-based loop-mediated isothermal amplification. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Park JW. Principles and Applications of Loop-Mediated Isothermal Amplification to Point-of-Care Tests. BIOSENSORS 2022; 12:bios12100857. [PMID: 36290994 PMCID: PMC9599884 DOI: 10.3390/bios12100857] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 05/03/2023]
Abstract
For the identification of nucleic acids, which are important biomarkers of pathogen-mediated diseases and viruses, the gold standard for NA-based diagnostic applications is polymerase chain reaction (PCR). However, the requirements of PCR limit its application as a rapid point-of-care diagnostic technique. To address the challenges associated with regular PCR, many isothermal amplification methods have been developed to accurately detect NAs. Isothermal amplification methods enable NA amplification without changes in temperature with simple devices, as well as faster amplification times compared with regular PCR. Of the isothermal amplifications, loop-mediated isothermal amplification (LAMP) is the most studied because it amplifies NAs rapidly and specifically. This review describes the principles of LAMP, the methods used to monitor the process of LAMP, and examples of biosensors that detect the amplicons of LAMP. In addition, current trends in the application of LAMP to smartphones and self-diagnosis systems for point-of-care tests are also discussed.
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Affiliation(s)
- Jee-Woong Park
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Korea
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28
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Lin Q, Jia K, Gou H, He H, Wen J, Shen H, Chen K, Wu Y, Lu B, Liao M, Han Y, Zhang J. A smartphone-assisted high-throughput integrated color-sensing platform for the rapid detection of Campylobacter coli. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Li Q, Xue H, Fei Y, Cao M, Xiong X, Xiong X, Yang Y, Wang L. Visual detection of rainbow trout ( Oncorhynchus mykiss) and Atlantic salmon ( Salmo salar) simultaneously by duplex loop-mediated isothermal amplification. FOOD CHEMISTRY. MOLECULAR SCIENCES 2022; 4:100107. [PMID: 35769395 PMCID: PMC9235052 DOI: 10.1016/j.fochms.2022.100107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is often confounded by the non-specific amplification arising from primer dimers, off-target priming, and other artifacts. Precipitation of the DNA produced during LAMP with the use of specific fluorescently labeled probe has proved the effectiveness in specific detection. Herein, two fluorophores (ROX and FAM) were attached to the primers S-LB-6 and R-FIP for Atlantic salmon and rainbow trout, respectively, which are self-quenched in unbound state and become de-quenched after binding to the dumbbell-shaped DNA specifically. The DNA precipitation and appearance of small sediment took 10 s of centrifugation at 1000 g, by adding polyethylenimine (PEI) 600. Each target species was specifically amplified with the predicted color of PEI-DNA sediment, namely red for Atlantic salmon, green for rainbow trout, and pale yellow for mixed species. The optimized duplex LAMP system has proved its specificity and can detect as little as 1 ng DNA in visual detection.
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Affiliation(s)
- Qiuping Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yanjin Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Min Cao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Libin Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Jiangsu Province 210037, China
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30
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Mannier C, Yoon JY. Progression of LAMP as a Result of the COVID-19 Pandemic: Is PCR Finally Rivaled? BIOSENSORS 2022; 12:492. [PMID: 35884295 PMCID: PMC9312731 DOI: 10.3390/bios12070492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 06/01/2023]
Abstract
Reflecting on the past three years and the coronavirus disease 19 (COVID-19) pandemic, varying global tactics offer insights into the most effective public-health responses. In the US, specifically, rapid and widespread testing was quickly prioritized to lower restrictions sooner. Essentially, only two types of COVID-19 diagnostic tests were publicly employed during the peak pandemic: the rapid antigen test and reverse transcription polymerase chain reaction (RT-PCR). However, neither test ideally suited the situation, as rapid antigen tests are far too inaccurate, and RT-PCR tests require skilled personnel and sophisticated equipment, leading to long wait times. Loop-mediated isothermal amplification (LAMP) is another exceptionally accurate nucleic acid amplification test (NAAT) that offers far quicker time to results. However, RT-LAMP COVID-19 tests have not been embraced as extensively as rapid antigen tests or RT-PCR. This review will investigate the performance of current RT-LAMP-based COVID-19 tests and summarize the reasons behind the hesitancy to embrace RT-LAMP instead of RT-PCR. We will also look at other LAMP platforms to explore possible improvements in the accuracy and portability of LAMP, which could be applied to COVID-19 diagnostics and future public-health outbreaks.
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Affiliation(s)
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, the University of Arizona, Tucson, AZ 85721, USA;
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31
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Zhang X, Zhao Y, Ma C, Wu W, Dong M, You J, Liu J, Yun S. An Optimized Visual Loop Mediated Isothermal Amplification Assay for Efficient Detection of Minute Virus of Mice With Hydroxynaphthol Blue Dye. J Virol Methods 2022; 308:114575. [DOI: 10.1016/j.jviromet.2022.114575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/26/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022]
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32
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Zhao L, Zhao Z, E H, Yang X, Li X, Fan T, Zhang Y, Chen A, Zhao X, Zhou C. Rapid on-site identification of Lepiota brunneoincarnata-induced mushroom poisoning by simple DNA extraction and loop-mediated isothermal amplification strategy. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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33
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Cao Y, Ye C, Zhang C, Zhang G, Hu H, Zhang Z, Fang H, Zheng J, Liu H. Simultaneous detection of multiple foodborne bacteria by loop-mediated isothermal amplification on a microfluidic chip through colorimetric and fluorescent assay. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108694] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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34
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A microfluidic genoserotyping strategy for fast and objective identification of common Salmonella serotypes isolated from retail food samples in China. Anal Chim Acta 2022; 1201:339657. [DOI: 10.1016/j.aca.2022.339657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/14/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022]
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35
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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
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.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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36
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Suarez GD, Suarez DA, Kiu Tang YY, Zhang JX, Li J, Nagl S, Cheung PPH. Uncovering mechanisms of RT-LAMP colorimetric SARS-CoV-2 detection to improve assay reliability. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:378-382. [PMID: 35006230 DOI: 10.1039/d1ay01395e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Improved diagnostics are needed to manage the ongoing COVID-19 pandemic. In this study, we enhanced the color changes and sensitivity of colorimetric SARS-CoV-2 RT-LAMP assays based on triarylmethane dyes. We determined a mechanism for the color changes and obtained sensitivities of 10 RNA copies per microliter.
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Affiliation(s)
- Gianmarco D Suarez
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Quommni Technologies Limited, Hong Kong
| | | | | | - Jing-Xuan Zhang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jun Li
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Stefan Nagl
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Li Ka Shing Medical Sciences Building, Shatin, New Territories, Hong Kong
- Quommni Technologies Limited, Hong Kong
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37
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Mao R, Wang T, Zhao Y, Wu X, Zhang S, Cai T. Closed dumbbell mediated isothermal amplification of nucleic acids for DNA diagnostic assays. Talanta 2022; 240:123217. [PMID: 35033926 DOI: 10.1016/j.talanta.2022.123217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/05/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022]
Abstract
Nucleic acid amplification tests have been widely applied in clinical diagnostics, food safety monitoring, and molecular biology. As a well-established isothermal amplification method, Loop-mediated isothermal amplification (LAMP) has gained recognition. However, the need for specifically designed four to six primers and non-specific amplification pose challenges for further application of LAMP based detection methods. Here, a novel isothermal amplification method, termed closed dumbbell mediated isothermal amplification (CDA) of nucleic acids, was developed. The primers are easily designed by adding two different parts of middle sequence to the canonical PCR primers at 5'-ends. CDA method was demonstrated in detecting MERS-CoV orf1a gene and H1N1 gene fragments with merits of short core primer, simple primer design process and high amplification efficiency. In addition, CDA showed excellent amplification efficacy over LAMP and competitive annealing mediated isothermal amplification (CAMP) by slight modification of primers targeting at same sequence. Furthermore, real-time and HNB based colorimetric CDA detection of Shigella were developed for practical application, both exhibited 100% success. In all, the developed CDA method with high specificity, simplicity, efficiency and rapidity has shown its great potential for point of care nucleic acids diagnostic.
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Affiliation(s)
- Rui Mao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
| | - Tianzuo Wang
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Yue Zhao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Xinyao Wu
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Shun Zhang
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Ting Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
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Yost J, Gagnon Z. Faradaic-free electrokinetic nucleic acid amplification (E-NAAMP) using localized on-chip high frequency Joule heating. BIOMICROFLUIDICS 2022; 16:014101. [PMID: 35111277 PMCID: PMC8791667 DOI: 10.1063/5.0072198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
We present a novel Faradaic reaction-free nucleic acid amplification (NAA) method for use with microscale liquid samples. Unlike previous Joule heating methods where the electrodes produce electrolysis gaseous by-products and require both the electrodes be isolated from a sample and the venting of produced electrolysis gas, our electrokinetic Nucleic Acid Amplification (E-NAAMP) method alleviates these issues using a radio frequency (RF) alternating current electric field. In this approach, a pair of microscale thin film gold electrodes are placed directly in contact with a nucleic acid reaction mixture. A high frequency (10-40 MHz) RF potential is then applied across the electrode pair to induce a local Ohmic current within the sample and drive the sample temperature to increase by Joule heating. The temperature increase is sustainable in that it can be generated for several hours of constant use without generating any pH change to the buffer or any microscopically observable gaseous electrolysis by-products. Using this RF Joule heating approach, we demonstrate successful direct thermal amplification using two popular NAA biochemical reactions: loop-mediated isothermal amplification and polymerase chain reaction. Our results demonstrate that a simple microscale electrode structure can be used for thermal regulation for NAA reactions without observable electrolytic reactions, minimal enzyme activity loss and sustained (>50 h use per device) continuous operations without electrode delamination. As such, E-NAAMP offers substantial miniaturization of the heating elements for use in microfluidic or miniaturized NAA reaction systems.
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Affiliation(s)
- Jarad Yost
- Department of Chemical Engineering, Texas A&M University, 201 Jack E. Brown Building, College Station, Texas 77843, USA
| | - Zachary Gagnon
- Department of Chemical Engineering, Texas A&M University, 201 Jack E. Brown Building, College Station, Texas 77843, USA
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Nguyen VD, Van Nguyen H, Seo JW, Lee SH, Seo TS. Prediction of acute rejection in kidney transplanted patients based on the point-of-care isothermal molecular diagnostics platform. Biosens Bioelectron 2021; 199:113877. [PMID: 34920227 DOI: 10.1016/j.bios.2021.113877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/19/2022]
Abstract
In this study, we proposed an advanced point-of-care molecular diagnostic technology to evaluate the acute rejection (AR) in kidney transplanted patients. On the contrary to the conventional PCR method, we developed a colorimetric loop mediated isothermal amplification (LAMP) for quantitative analysis of the six biomarkers related to AR (CD3ϵ, IP-10, Tim-3-HAVCR2, CXCL9, PSMB9, C1QB) with a reference gene (18S rRNA). Using urinary cDNA samples of transplanted patients, it turned out that three biomarkers among six, namely IP-10, Tim-3-HAVCR2 and C1QB, have significant discrepancy in quantity between the stable graft (STA) patient and the AR patient. The AR prediction model using these three biomarkers was established, which could estimate the immune-rejection in the patients with 93.3% of accuracy. For the point-of-care (POC) molecular diagnostics for the AR evaluation, we constructed a centrifugal microfluidic platform, in which the RNA extraction from the clinical urinary samples, the quantitative reverse-transcription (RT)-LAMP reaction, and the data analysis based on the AR prediction model could be performed in a serial order. Ten blind clinical samples were analyzed on the POC genetic analyzer, showing 100% match with the validated qPCR data. Thus, the proposed advanced molecular diagnostic platform enables us to perform the timely treatment for the transplanted patients who are suffering from the allograft failure and side effects such as infection and malignancy.
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Affiliation(s)
- Van Dan Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, South Korea
| | - Hau Van Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, South Korea
| | - Jung Woo Seo
- Core Research Laboratory, Medical Science Institute, Kyung Hee University Hospital at Gangdong, Seoul, 05278, South Korea
| | - Sang Ho Lee
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, 02447, South Korea
| | - Tae Seok Seo
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, South Korea.
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40
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Natsuhara D, Saito R, Aonuma H, Sakurai T, Okamoto S, Nagai M, Kanuka H, Shibata T. A method of sequential liquid dispensing for the multiplexed genetic diagnosis of viral infections in a microfluidic device. LAB ON A CHIP 2021; 21:4779-4790. [PMID: 34812455 DOI: 10.1039/d1lc00829c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this study, we introduce polydimethylsiloxane (PDMS)-based microfluidic devices capable of sequential dispensing of samples into multiple reaction microchambers in a single operation to provide a fast and easy sample-to-answer platform for multiplexed genetic diagnosis of multiple viral infectious diseases. This approach utilizes the loop-mediated isothermal amplification (LAMP) method to amplify and detect specific nucleic acid (DNA/RNA) targets. We present a microfluidic flow control theory for sequential liquid dispensing phenomena, which provides design guidelines for device optimization. The device specifications, such as the possible dispensing number and maximal allowable flow rate, can be theoretically designed by optimizing the geometric dimensions of the microchannels and a pair of passive stop valves integrated into each microchamber together with the water contact angles of the materials used to fabricate the microfluidic devices. In addition, a passive stop valve with a vertical-type phaseguide structure was designed to improve device performance. We could simultaneously diagnose coronavirus disease 2019 (COVID-19) and other infectious diseases, such as severe acute respiratory syndrome (SARS), seasonal influenza A, and pandemic influenza A (H1N1) 2009. The colorimetric reverse transcription LAMP (RT-LAMP) assay suggests that the four viral infectious diseases can be detected within 30 min using a hue-based quantitative analysis, and the naked eye using our microfluidic devices.
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Affiliation(s)
- Daigo Natsuhara
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8560, Japan.
| | - Ryogo Saito
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8560, Japan.
| | - Hiroka Aonuma
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Tatsuya Sakurai
- Laboratory Animal Facilities, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Shunya Okamoto
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8560, Japan.
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8560, Japan.
| | - Hirotaka Kanuka
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
- Laboratory Animal Facilities, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Takayuki Shibata
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8560, Japan.
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Zhou Y, Wu Y, Ding L, Huang X, Xiong Y. Point-of-care COVID-19 diagnostics powered by lateral flow assay. Trends Analyt Chem 2021; 145:116452. [PMID: 34629572 PMCID: PMC8487324 DOI: 10.1016/j.trac.2021.116452] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Since its first discovery in December 2019, the global coronavirus disease 2019 (COVID-19) pandemic caused by the novel coronavirus (SARS-CoV-2) has been posing a serious threat to human life and health. Diagnostic testing is critical for the control and management of the COVID-19 pandemic. In particular, diagnostic testing at the point of care (POC) has been widely accepted as part of the post restriction COVID-19 control strategy. Lateral flow assay (LFA) is a popular POC diagnostic platform that plays an important role in controlling the COVID-19 pandemic in industrialized countries and resource-limited settings. Numerous pioneering studies on the design and development of diverse LFA-based diagnostic technologies for the rapid diagnosis of COVID-19 have been done and reported by researchers. Hundreds of LFA-based diagnostic prototypes have sprung up, some of which have been developed into commercial test kits for the rapid diagnosis of COVID-19. In this review, we summarize the crucial role of rapid diagnostic tests using LFA in targeting SARS-CoV-2-specific RNA, antibodies, antigens, and whole virus. Then, we discuss the design principle and working mechanisms of these available LFA methods, emphasizing their clinical diagnostic efficiency. Ultimately, we elaborate the challenges of current LFA diagnostics for COVID-19 and highlight the need for continuous improvement in rapid diagnostic tests.
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Affiliation(s)
- Yaofeng Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Yuhao Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Lu Ding
- Hypertension Research Institute of Jiangxi Province, Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
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Rivoarilala LO, Victor J, Crucitti T, Collard JM. LAMP assays for the simple and rapid detection of clinically important urinary pathogens including the detection of resistance to 3rd generation cephalosporins. BMC Infect Dis 2021; 21:1037. [PMID: 34615472 PMCID: PMC8495977 DOI: 10.1186/s12879-021-06720-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Background Timely and accurate identification of uropathogens and determination of their antimicrobial susceptibility is paramount to the management of urinary tract infections (UTIs). The main objective of this study was to develop an assay using LAMP (Loop mediated isothermal amplification) technology for simple, rapid and sensitive detection of the most common bacteria responsible for UTIs, as well as for the detection of the most prevalent genes (encoding cefotaximases from CTX-M group 1) responsible for resistance to 3rd generation of cephalosporins. Method We designed primers targeting Proteus mirabilis, while those targeting Escherichia coli, Klebsiella pneumoniae and Enterococcus faecalis and the CTX-M group 1 resistance gene were benchmarked from previous studies. The amplification reaction was carried out in a warm water bath for 60 min at 63 ± 0.5 °C. The amplicons were revealed by staining with Sybr Green I. Specificity and sensitivity were determined using reference DNA extracts spiked in sterile urine samples. The analytical performance of the assays was evaluated directly on pellets of urine samples from patients suspected of UTI and compared with culture. Results We found a high specificity (100%) for LAMP assays targeting the selected bacteria (P. mirabilis, E. coli, K. pneumoniae, E. faecalis) and the CTX-M group 1 when using DNA extracts spiked in urine samples. The sensitivities of the assays were around 1.5 103 Colony Forming Units (CFU) /mL corresponding to the cut-off value used to define bacteriuria or UTIs in patients with symptoms. Out of 161 urine samples tested, using culture as gold standard, we found a sensitivity of the LAMP techniques ranging from 96 to 100% and specificity from 95 to 100%. Conclusion We showed that the LAMP assays were simple and fast. The tests showed high sensitivity and specificity using a simple procedure for DNA extraction. In addition, the assays could be performed without the need of an expensive device such as a thermal cycler. These LAMP assays could be useful as an alternative or a complementary tool to culture reducing the time to diagnosis and guiding for more effective treatment of UTIs but also as a powerful diagnostic tool in resource-limited countries where culture is not available in primary health care structures. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06720-5.
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Affiliation(s)
| | | | - Tania Crucitti
- Experimental Bacteriology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean Marc Collard
- Experimental Bacteriology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Experimental Bacteriology Laboratory, Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai/Chinese Academy of Sciences, Shanghai, People's Republic of China
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Shi Y, Xu M, Duan X, Li S, Ding JW, Chen L. WarmStart colorimetric loop-mediated isothermal amplification for the one-tube, contamination-free and visualization detection of Shigella flexneri. Int J Infect Dis 2021; 112:55-62. [PMID: 34517048 DOI: 10.1016/j.ijid.2021.09.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 09/06/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Shigella flexneri (S. flexneri) is prevalent worldwide and the most common Shigella in many countries, causing highly contagious diarrhea, which seriously threatens public health. This study aimed to develop a colorimetric loop-mediated isothermal amplification (LAMP) for the rapid, accurate, and visualization detection of S. flexneri. METHODS According to the screened specific genes of S. flexneri, three groups of LAMP primers were designed and evaluated, and the colorimetric LAMP reaction volume was optimized. The specificity of the colorimetric LAMP was validated by 20 S. flexneri and 96 non-S. flexneri clinical isolates. In addition, the sensitivity of the developed assay was evaluated by the serial 10-fold dilutions of plasmid DNA. RESULTS A colorimetric LAMP assay was developed based on the specific S. flexneri hypothetical protein gene (Accession: AE014073 Region: 4170556.4171068). The colorimetric LAMP method had good specificity for detecting S. flexneri and enabled detection of S. flexneri within 30 minutes, with a plasmid detection limit of 7*10° copies/μL. The results of amplification could be easily identified by color. CONCLUSIONS This colorimetric LAMP assay could be used for rapid and accurate diagnosis of S. flexneri infection, especially in remote hospitals and laboratories with under-equipped medical facilities, and in situations where an urgent diagnosis is needed.
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Affiliation(s)
- Yaoqiang Shi
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Min Xu
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Xiaoqiong Duan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Jia-Wei Ding
- Clinical Laboratory Department, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
| | - Limin Chen
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China; Toronto General Research Institute, University of Toronto, Toronto, ON, Canada.
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44
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Karami A, Hasani M, Azizi Jalilian F, Ezati R. Hairpin-Spherical Nucleic Acids for Diagnosing COVID-19: a Simple Method to Generalize the Conventional PCR for Molecular Assays. Anal Chem 2021; 93:9250-9257. [PMID: 34156834 PMCID: PMC8247783 DOI: 10.1021/acs.analchem.1c01515] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic revealed during the first global wave of this infectious disease that mass diagnostic testing was necessary to more rapidly detect infection in patients and control the pandemic. Therefore, extra research efforts to develop reliable and more accessible techniques for disease diagnosis are of supreme importance. Here, a target-responsive assembly of gold nanoparticle-core hairpin-spherical nucleic acids (AuNP-core H-SNAs) was implemented to modify the conventional polymerase chain reaction (PCR) assay for the "naked-eye" colorimetric detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Two hairpin DNA ligands are designed based on the two highly conserved regions within N and E genes of SARS-CoV-2 RNA by positioning two short palindromic arms (stem) on either side of a recognition sequence (loop). In the presence of a sequence-specific probe (activator), hairpin DNAs anchored to the surface of AuNPs unfold and expose the palindromic ends to the DNA-directed assembly of AuNPs. The sequence of the activator probes was chosen to be identical to the TaqMan probe in a real-time reverse transcription PCR (RT-PCR) assay for specifically targeting the N and E genes of SARS-CoV-2 RNA. They may either be degraded by the 5'-exonuclease activity of DNA polymerase during PCR cycles or stay intact depending on the presence or absence of the target template in the sample, respectively. Post-addition of H-SNA solutions to the final PCR products of some preconfirmed clinical samples for COVID-19 generated naked-eye-observable red and blue colors for positive and negative cases, respectively, with similar sensitivity to that of the real-time RT-PCR method.
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Affiliation(s)
- Abbas Karami
- Faculty
of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran
| | - Masoumeh Hasani
- Faculty
of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran
| | - Farid Azizi Jalilian
- Department
of Medical Virology, Faculty of Medicine, Hamedan University of Medical Sciences, Hamedan 6517619654, Iran
| | - Razieh Ezati
- Department
of Molecular Diagnosis, Farzan Molecular
and Pathobiology Laboratory, Hamedan 6515638377, Iran
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Layne T, Jackson K, Scott A, Tanner NA, Piland A, Haverstick DM, Landers JP. Optimization of novel loop-mediated isothermal amplification with colorimetric image analysis for forensic body fluid identification. J Forensic Sci 2021; 66:1033-1041. [PMID: 33559876 DOI: 10.1111/1556-4029.14682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Accurate presumptive and confirmatory test use for forensic body fluid identification is essential for gaining contextual information for crime scene investigators. Loop-mediated isothermal amplification (LAMP) is an ideal method for forensic body fluid identification because it is highly specific and generates multi-sized amplicon DNA, and successful amplification results can be read out colorimetrically. Here, we show preliminary data on a LAMP method that rapidly identifies body fluids including venous blood, semen, and saliva, based on colorimetric response and image analysis. The method is designed for easy implementation into forensic casework protocols with minimal disruption to DNA analysis. LAMP naturally increases target specificity due to the use of multiple primers for one target and mRNA targets were used for tissue and human specificity. With colorimetric detection as an inherent part of LAMP, samples that are positive or negative for any of the body fluids are readily identified by image capture and analysis, thus eliminating subjectivity. Results show by using the 3D-printed imaging system specific color ranges can be set for easy determination of body fluids. The resulting color change can be seen in <30 min using a universal temperature and primer concentration for all body fluids. This simple method and imaging system allow for minimal hands-on time with objective image analysis and presents a pathway for creating a new potential method for forensic body fluid identification.
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Affiliation(s)
- Tiffany Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Kimberly Jackson
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Anchi Scott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | - Annie Piland
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Doris M Haverstick
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.,Departments of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, USA
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Liu M, Li CC, Luo X, Ma F, Zhang CY. 5-Hydroxymethylcytosine Glucosylation-Triggered Helicase-Dependent Amplification-Based Fluorescent Biosensor for Sensitive Detection of β-Glucosyltransferase with Zero Background Signal. Anal Chem 2020; 92:16307-16313. [DOI: 10.1021/acs.analchem.0c04382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Chen-chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
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