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Jang M, Kim S. Inhibition of Non-specific Amplification in Loop-Mediated Isothermal Amplification via Tetramethylammonium Chloride. BIOCHIP JOURNAL 2022; 16:326-333. [PMID: 35909465 PMCID: PMC9326409 DOI: 10.1007/s13206-022-00070-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 02/02/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) may be used in molecular and point-of-care diagnostics for pathogen detection. The amplification occurs under isothermal conditions using up to six primers. However, non-specific amplification is frequently observed in LAMP. Non-specific amplification has the potential to be triggered by forward and reverse internal primers. And the relatively low reaction temperature (55-65 °C) induces the secondary structure via primer-primer interactions. Primer redesign and probe design have been recommended to solve this problem. LAMP primers have strict conditions, such as Tm, GC contents, primer dimer, and distance between primers compared to conventional PCR primers. Probe design requires specialized knowledge to have high specificity for a target. In polymerase chain reaction (PCR), some chemicals or proteins are used for improving specificity and efficiency. Therefore, we hypothesized that additives can suppress the non-specific amplification. In this study, tetramethylammonium chloride (TMAC), formamide, dimethyl sulfoxide, Tween 20, and bovine serum albumin have been used as LAMP additives. In our study, TMAC was presented as a promising additive for suppressing non-specific amplification in LAMP. Supplementary Information The online version contains supplementary material available at 10.1007/s13206-022-00070-3.
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Affiliation(s)
- MinJu Jang
- grid.256155.00000 0004 0647 2973Department of Bionanotechnology, Gachon University, Seongnam, 13120 Republic of Korea
| | - Sanghyo Kim
- grid.256155.00000 0004 0647 2973Department of Bionanotechnology, Gachon University, Seongnam, 13120 Republic of Korea
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Jia Z, Ding M, Nakano M, Hong K, Huang R, Becker D, Glazebrook J, Katagiri F, Han X, Tsuda K. Letter to the Editor: DNA Purification-Free PCR from Plant Tissues. PLANT & CELL PHYSIOLOGY 2021; 62:1503-1505. [PMID: 34320213 DOI: 10.1093/pcp/pcab120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/02/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Zhengnan Jia
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Miaomiao Ding
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Masahito Nakano
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Kunqi Hong
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Ruidong Huang
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dieter Becker
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, Cologne 50829, Germany
| | - Jane Glazebrook
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, Twin-Cities, Saint Paul, MN 55455, USA
| | - Fumiaki Katagiri
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, Twin-Cities, Saint Paul, MN 55455, USA
| | - Xiaowei Han
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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Barazorda KA, Salas CJ, Braga G, Ricopa L, Ampuero JS, Siles C, Sanchez JF, Montano S, Lizewski SE, Joya CA, Bishop DK, Valdivia HO. Validation study of Boil & Spin Malachite Green Loop Mediated Isothermal Amplification (B&S MG-LAMP) versus microscopy for malaria detection in the Peruvian Amazon. PLoS One 2021; 16:e0258722. [PMID: 34695122 PMCID: PMC8544869 DOI: 10.1371/journal.pone.0258722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
Malaria elimination efforts in Peru have dramatically reduced the incidence of cases in the Amazon Basin. To achieve the elimination, the detection of asymptomatic and submicroscopic carriers becomes a priority. Therefore, efforts should focus on tests sensitive enough to detect low-density parasitemia, deployable to resource-limited areas and affordable for large screening purposes. In this study, we assessed the performance of the Malachite–Green LAMP (MG-LAMP) using heat-treated DNA extraction (Boil & Spin; B&S MG-LAMP) on 283 whole blood samples collected from 9 different sites in Loreto, Peru and compared its performance to expert and field microscopy. A real-time PCR assay was used to quantify the parasite density. In addition, we explored a modified version of the B&S MG-LAMP for detection of submicroscopic infection in 500 samples and compared the turnaround time and cost of the MG-LAMP with microscopy. Compared to expert microscopy, the genus B&S MG-LAMP had a sensitivity of 99.4% (95%CI: 96.9%– 100%) and specificity of 97.1% (95%CI: 91.9%– 99.4%). The P. vivax specific B&S MG-LAMP had a sensitivity of 99.4% (96.6%– 100%) and specificity of 99.2% (95.5%– 100%) and the P. falciparum assay had a sensitivity of 100% (95%CI: 78.2%– 100%) and specificity of 99.3% (95%CI: 97.3%– 99.8%). The modified genus B&S MG-LAMP assay detected eight submicroscopic malaria cases (1.6%) which the species-specific assays did not identify. The turnaround time of B&S MG-LAMP was faster than expert microscopy with as many as 60 samples being processed per day by field technicians with limited training and utilizing a simple heat-block. The modified B&S MG-LAMP offers a simple and sensitive molecular test of choice for the detection of submicroscopic infections that can be used for mass screening in resources limited facilities in endemic settings nearing elimination and where a deployable test is required.
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Affiliation(s)
| | - Carola J. Salas
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Greys Braga
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Leonila Ricopa
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Julia S. Ampuero
- Department of Virology and Emerging infections, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Crystyan Siles
- Department of Virology and Emerging infections, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Juan F. Sanchez
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Silvia Montano
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Stephen E. Lizewski
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Christie A. Joya
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Danett K. Bishop
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
| | - Hugo O. Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit N°6 (NAMRU-6), Lima, Peru
- * E-mail:
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