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Wu Y, Chang Y, Sun Y, Wang Y, Li K, Lu Z, Liu Q, Wang F, Wei L. A multi-AS-PCR-coupled CRISPR/Cas12a assay for the detection of ten single-base mutations. Anal Chim Acta 2024; 1320:343027. [PMID: 39142774 DOI: 10.1016/j.aca.2024.343027] [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: 05/05/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 08/16/2024]
Abstract
Single-nucleotide polymorphism (SNP) detection is critical for diagnosing diseases, and the development of rapid and accurate diagnostic tools is essential for treatment and prevention. Allele-specific polymerase chain reaction (AS-PCR) is widely used for detecting SNPs with multiplexing capabilities, while CRISPR-based technologies provide high sensitivity and specificity in targeting mutation sites through specific guide RNAs (gRNAs). In this study, we have integrated the high sensitivity and specificity of CRISPR technology with the multiplexing capabilities of AS-PCR, achieving the simultaneous detection of ten single-base mutations. As for Multi-AS-PCR, our research identified that competitive inhibition of primers targeting the same loci, coupled with divergent amplification efficiencies of these primers, could result in diminished amplification efficiency. Consequently, we adjusted and optimized primer combinations and ratios to enhance the amplification efficacy of Multi-AS-PCR. Finally, we successfully developed a novel nested Multi-AS-PCR-Cas12a method for multiplex SNPs detection. To evaluate the clinical utility of this method in a real-world setting, we applied it to diagnose rifampicin-resistant tuberculosis (TB). The limit of detection (LoD) for the nested Multi-AS-PCR-Cas12a was 102 aM, achieving sensitivity, specificity, positive predictive value, and negative predictive value of 100 %, 93.33 %, 90.00 %, and 100 %, respectively, compared to sequencing. In summary, by employing an innovative design that incorporates a universal reverse primer alongside ten distinct forward allele-specific primers, the nested Multi-AS-PCR-Cas12a technique facilitates the parallel detection of ten rpoB gene SNPs. This method also holds broad potential for the detection of drug-resistant gene mutations in infectious diseases and tumors, as well as for the screening of specific genetic disorders.
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Affiliation(s)
- Yaozhou Wu
- First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, PR China; Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China
| | - Yanbin Chang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China
| | - Yingying Sun
- First School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750000, PR China
| | - Yulin Wang
- School of Public Health, Gansu University of Chinese Medicine, Lanzhou, 730000, PR China
| | - Keke Li
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China
| | - Zhangping Lu
- School of Public Health, Gansu University of Chinese Medicine, Lanzhou, 730000, PR China
| | - Qianqian Liu
- First School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750000, PR China
| | - Fang Wang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China.
| | - Lianhua Wei
- First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, PR China; Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China.
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Zhang Z, Guan L, Yao J, Li L, Liu C, Guo Y, Xie G. RART-LAMP: One-Step Extraction-Free Method for Genotyping within 40 min. Anal Chem 2023; 95:12487-12496. [PMID: 37534990 DOI: 10.1021/acs.analchem.3c02232] [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: 08/04/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a commonly used alternative to PCR for point-of-care detection of nucleic acids due to its rapidity, sensitivity, specificity, and simpler instrumentation. While dual-labeled TaqMan probes are widely used in PCR for single-nucleotide polymorphism (SNP) genotyping, real-time LAMP primarily relies on turbidimetry or intercalator fluorescence measurements, which can be non-specific and generate false-positive results. In this study, we propose a closed-tube, dual-labeled RNA-modified probes and RNase H II-assisted real-time LAMP (RART-LAMP) method for SNP genotyping. Our findings indicate that (1) fluorescence signals were predominantly derived from probe hydrolysis rather than hybridization, (2) temperature-controlled hybridization between the probe and template ensured the specificity of SNP analysis, and (3) RNase H II hydrolysis between the target containing SNP sites and probes did not exhibit sequence specificity. Our RART-LAMP approach demonstrated excellent performance in genotyping C677T clinical samples, including gDNA extracted from blood, saliva, and swabs. More importantly, saliva and swab samples could be directly analyzed without any pretreatment, indicating promising prospects for nucleic acid analysis at the point of care in resource-limited settings.
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Affiliation(s)
- Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Luhao Guan
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Medicine, Luzhou Traditional Chinese Medicine Hospital, Luzhou 646000, China
| | - Juan Yao
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Lijia Li
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Chunfang Liu
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Yongcan Guo
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
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Song S, Ji F, Zeng Q, Ding X, Lin J, Wang X, Xu Y, Deng R, Li J. Rapid and Sensitive Detection of Fungicide-Resistant Crop Fungal Pathogens Using an Isothermal Amplification Refractory Mutation System. Anal Chem 2023; 95:4966-4973. [PMID: 36890667 DOI: 10.1021/acs.analchem.2c05115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Fungicide abuse leads to the emergence of fungicide-resistant fungal pathogens, thus posing a threat to agriculture and food safety. Here, we developed an isothermal amplification refractory mutation system (termed iARMS) allowing us to resolve genetic mutations, enabling rapid, sensitive, and potentially field-applicable detection of fungicide-resistant crop fungal pathogens. iARMS yielded a limit of detection of 25 aM via a cascade signal amplification strategy of recombinase polymerase amplification (RPA) and Cas12a-mediated collateral cleavage at 37 °C within 40 min. Specificity for fungicide-resistant Puccinia striiformis (P. striiformis) detection was guaranteed by RPA primers and the flexible sequence of gRNA. The iARMS assay allowed us to detect as low as 0.1% cyp51-mutated P. striiformis that showed resistance to the demethylase inhibitor (DMI), which was 50 times more sensitive than the sequencing techniques. Thus, it is promising for the discovery of rare fungicide-resistant isolates. We applied iARMS to investigate the emergence of fungicide-resistant P. striiformis in western China and found that its proportion was over 50% in Qinghai, Sichuan, and Xinjiang Province. iARMS can serve as a molecular diagnostic tool for crop diseases and facilitate precision plant disease management.
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Affiliation(s)
- Sishuo Song
- College of Life Sciences, Institute of Biomedical Engineering, Qingdao University, Qingdao, Shandong 266071 China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Fan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Xiaoteng Ding
- College of Life Sciences, Institute of Biomedical Engineering, Qingdao University, Qingdao, Shandong 266071 China
| | - Jiahao Lin
- College of Life Sciences, Institute of Biomedical Engineering, Qingdao University, Qingdao, Shandong 266071 China
| | - Xinsheng Wang
- College of Life Sciences, Institute of Biomedical Engineering, Qingdao University, Qingdao, Shandong 266071 China
| | - Yuanhong Xu
- College of Life Sciences, Institute of Biomedical Engineering, Qingdao University, Qingdao, Shandong 266071 China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
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Rubio-Monterde A, Quesada-González D, Merkoçi A. Toward Integrated Molecular Lateral Flow Diagnostic Tests Using Advanced Micro- and Nanotechnology. Anal Chem 2023; 95:468-489. [PMID: 36413136 DOI: 10.1021/acs.analchem.2c04529] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ana Rubio-Monterde
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain
| | | | - Arben Merkoçi
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain.,The Barcelona Institute of Science and Technology (BIST), Campus UAB, 08036 Bellaterra, Barcelona Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
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Zhang J, Hui H, Xu W, Hua K, Cui Y, Liu X. A label-free strategy for visual genotyping based on phosphate induced coloration reaction. RSC Adv 2022; 12:22091-22096. [PMID: 36043069 PMCID: PMC9364437 DOI: 10.1039/d2ra03989c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/29/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic variation plays a crucial role in disease occurrence and development. However, current genotyping strategies not only require a long turnaround time for DNA purification, but also depend on sophisticated apparatus and complex data interpretation, which seriously limits their application in point of care diagnostic test scenarios. In this study, by integrating phosphate induced coloration reaction and loop-mediated isothermal amplification, a rapid and portable strategy for straightforward genotyping has been established to cater to the demand of precision medicine. By employing phosphate ions produced during the amplification as a signal generator, not only can the genotyping result be interpreted with only naked eye from a low-cost label-free strip, but also the amplification efficiency is increased to facilitate genotyping with a robust biological specimen ignoring DNA polymerase inhibitors. Moreover, the introduction of alkaline lysis for DNA release allows whole blood to be identified accurately avoiding DNA purification. As a proof of concept, the insertion/deletion polymorphisms of the angiotensin-converting enzyme, a crucial factor associated with cardiovascular and cerebrovascular diseases, has been selected as a model to evaluate the performance of this method. Accurate results can be obtained from as low as 1 ng genomic DNA within 30 min. For clinical specimen detection, a concordance rate up to 100% has been found compared with PCR-based electrophoresis. Thus, this novel strategy may serve as a promising tool for straightforward genotyping to provide timely diagnostic information, especially in resource-poor medical institutions. Phosphate induced coloration reaction facilitates visual genotyping and the target variant can be accurately identified within 30 min from blood directly.![]()
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Affiliation(s)
- Jiaxing Zhang
- College of Life Sciences, Northwest University Xi'an 710069 China .,Department of Immunology, The Fourth Military Medical University Xi'an 710032 China
| | - Hui Hui
- Shannxi Provincial Cancer Hospital Xi'an 710061 China
| | - Wei Xu
- College of Life Sciences, Northwest University Xi'an 710069 China
| | - Kai Hua
- College of Life Sciences, Northwest University Xi'an 710069 China
| | - Yali Cui
- College of Life Sciences, Northwest University Xi'an 710069 China
| | - Xiaonan Liu
- College of Life Sciences, Northwest University Xi'an 710069 China
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