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Qiao J, Zhao Z, Li Y, Lu M, Man S, Ye S, Zhang Q, Ma L. Recent advances of food safety detection by nucleic acid isothermal amplification integrated with CRISPR/Cas. Crit Rev Food Sci Nutr 2023:1-22. [PMID: 37691410 DOI: 10.1080/10408398.2023.2246558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Food safety problems have become one of the most important public health issues worldwide. Therefore, the development of rapid, effective and robust detection is of great importance. Amongst a range of methods, nucleic acid isothermal amplification (NAIA) plays a great role in food safety detection. However, the widespread application remains limited due to a few shortcomings. CRISPR/Cas system has emerged as a powerful tool in nucleic acid detection, which could be readily integrated with NAIA to improve the detection sensitivity, specificity, adaptability versatility and dependability. However, currently there was a lack of a comprehensive summary regarding the integration of NAIA and CRISPR/Cas in the field of food safety detection. In this review, the recent advances in food safety detection based on CRISPR/Cas-integrated NAIA were comprehensively reviewed. To begin with, the development of NAIA was summarized. Then, the types and working principles of CRISPR/Cas were introduced. The applications of the integration of NAIA and CRISPR/Cas for food safety were mainly introduced and objectively discussed. Lastly, current challenges and future opportunities were proposed. In summary, this technology is expected to become an important approach for food safety detection, leading to a safer and more reliable food industry.
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Affiliation(s)
- Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Minghui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Shengying Ye
- Pharmacy Department, The 983th Hospital of the Joint Logistics Support Force of the, Chinese People's Liberation Army, Tianjin, China
| | - Qiang Zhang
- Branch of Tianjin Third Central Hospital, Tianjin, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
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Glökler J, Lim TS, Ida J, Frohme M. Isothermal amplifications - a comprehensive review on current methods. Crit Rev Biochem Mol Biol 2021; 56:543-586. [PMID: 34263688 DOI: 10.1080/10409238.2021.1937927] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
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Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
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Wang L, Qi W, Liu Y, Essien D, Zhang Q, Lin J. Recent Advances on Bioaerosol Collection and Detection in Microfluidic Chips. Anal Chem 2021; 93:9013-9022. [PMID: 34160193 DOI: 10.1021/acs.analchem.1c00908] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioaerosols containing pathogenic microorganisms have posed a great threat to human and animal health. Effective monitoring of bioaerosols containing pathogenic viruses and bacteria is of great significance to prevent and control infectious diseases. This Feature summarizes recent advances on bioaerosol collection and detection based on microfluidic chips. Besides, the challenges and trends for bioaerosol collection and detection were also discussed.
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Affiliation(s)
- Lei Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.,Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada
| | - Wuzhen Qi
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Yuanjie Liu
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Desmond Essien
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada
| | - Qiang Zhang
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
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Katsarou K, Bardani E, Kallemi P, Kalantidis K. Viral Detection: Past, Present, and Future. Bioessays 2019; 41:e1900049. [PMID: 31441081 DOI: 10.1002/bies.201900049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/04/2019] [Indexed: 12/26/2022]
Abstract
Viruses are essentially composed of a nucleic acid (segmented or not, DNA, or RNA) and a protein coat. Despite their simplicity, these small pathogens are responsible for significant economic and humanitarian losses that have had dramatic consequences in the course of human history. Since their discovery, scientists have developed different strategies to efficiently detect viruses, using all possible viral features. Viruses shape, proteins, and nucleic acid are used in viral detection. In this review, the development of these techniques, especially for plant and mammalian viruses, their strengths and weaknesses as well as the latest cutting-edge technologies that may be playing important roles in the years to come are described.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, GR-70013, Greece.,Department of Biology, University of Crete, Heraklion, GR-70013, Greece
| | - Eirini Bardani
- Department of Biology, University of Crete, Heraklion, GR-70013, Greece
| | - Paraskevi Kallemi
- Department of Biology, University of Crete, Heraklion, GR-70013, Greece
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, GR-70013, Greece.,Department of Biology, University of Crete, Heraklion, GR-70013, Greece
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Jung C, Ellington AD. A primerless molecular diagnostic: phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP). Anal Bioanal Chem 2016; 408:8583-8591. [PMID: 27032410 DOI: 10.1007/s00216-016-9479-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 12/01/2022]
Abstract
There are various ways that priming can occur in nucleic acid amplification reactions. While most reactions rely on a primer to initiate amplification, a mechanism for DNA amplification has been developed in which hairpin sequences at the 3' terminus of a single-stranded oligonucleotide fold on themselves to initiate priming. Unfortunately, this method is less useful for diagnostic applications because the self-folding efficiency is low and only works over a narrow range of reaction temperatures. In order to adapt this strategy for analytical applications we have developed a variant that we term phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP). In PS-THSP a phosphorothioate (PS) modification is incorporated into the DNA backbone, leading to a reduction in the thermal stability of dsDNA and increased self-folding of terminal hairpins. By optimizing the number of PS linkages that are included in the initial template, we greatly increased self-folding efficiency and the range of reaction temperatures, ultimately achieving a detection limit of 1 pM. This improved method was readily adapted to the detection of single nucleotide polymorphisms and to the detection of non-nucleic acid analytes, such as alkaline phosphatase, which was quantitatively detected at a limit of 0.05 mU/mL, approximately 10-fold better than commercial assays. Graphical abstract Efficient self-folding by phosphorothioate (PS) modification.
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Affiliation(s)
- Cheulhee Jung
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway MBB 3.424, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway MBB 3.424, Austin, TX, 78712, USA.
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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7
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Levin RE. Recent Developments in Molecular Detection of Food-Borne Disease Bacteria and GMOs. FOOD BIOTECHNOL 2015. [DOI: 10.1080/08905436.2014.996896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R. Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Res 2014; 186:20-31. [DOI: 10.1016/j.virusres.2013.12.007] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/08/2013] [Accepted: 12/09/2013] [Indexed: 01/02/2023]
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Abstract
Effective prevention of HIV/AIDS requires early diagnosis, initiation of therapy, and regular plasma viral load monitoring of the infected individual. In addition, incidence estimation using accurate and sensitive assays is needed to facilitate HIV prevention efforts in the public health setting. Therefore, more affordable and accessible point-of-care (POC) technologies capable of providing early diagnosis, HIV viral load measurements, and CD4 counts in settings where HIV is most prevalent are needed to enable appropriate intervention strategies and ultimately stop transmission of the virus within these populations to achieve the future goal of an AIDS-free generation. This review discusses the available and emerging POC technologies for future application to these unmet public health needs.
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Mitsunaga S, Shimizu S, Okudaira Y, Oka A, Tanaka M, Kimura M, Kulski JK, Inoue I, Inoko H. Improved loop-mediated isothermal amplification for HLA-DRB1 genotyping using RecA and a restriction enzyme for enhanced amplification specificity. Immunogenetics 2013; 65:405-15. [PMID: 23474534 DOI: 10.1007/s00251-013-0690-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 02/15/2013] [Indexed: 12/12/2022]
Abstract
Our aim was to test and develop the use of loop-mediated isothermal amplification (LAMP) for HLA-DRB1 genotyping. Initially, we found that the conventional LAMP protocols produced non-specific and variable amplification results depending on the sample DNA conditions. Experiments with different concentrations of DNase in the reaction mixture with and without T4 DNA ligase-treated samples suggested that the strand displacement activity of DNA polymerase in LAMP, at least in part, started from randomly existing nicks because T4 DNA ligase treatment of sample DNA resulted in no amplification. Such non-specific amplification due to the randomly existing nicks was improved specifically by the addition of RecA of Escherichia coli and a restriction enzyme, for example, PvuII, to the reaction mixture. We applied the modified LAMP (mLAMP) (1) to detect specific HLA-DRB1 alleles by using only specific primers for amplification or (2) for genotyping in multiple samples with a multi-probe typing system. In the latter case, HLA-DRB1 genotyping was developed by combining the mLAMP with amplicon capture using polymorphic region-specific probes fixed onto the bottom of the wells of a 96-well plate and the captured amplicons visualized as a black spot at the bottom of the well. The multi-probe human leukocyte antigen (HLA) typing method and the specific HLA allele detection method could be applied for point-of-care testing due to no requirement for specific and expensive instruments.
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Affiliation(s)
- Shigeki Mitsunaga
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan
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Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. LAB ON A CHIP 2012; 12:2469-86. [PMID: 22592150 DOI: 10.1039/c2lc40100b] [Citation(s) in RCA: 483] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.
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Affiliation(s)
- Pascal Craw
- Department of Electronic & Computer Engineering, School of Engineering & Design, Brunel University, London, UK.
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12
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De Boer SH, López MM. New grower-friendly methods for plant pathogen monitoring. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:197-218. [PMID: 22607454 DOI: 10.1146/annurev-phyto-081211-172942] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Accurate plant disease diagnoses and rapid detection and identification of plant pathogens are of utmost importance for controlling plant diseases and mitigating the economic losses they incur. Technological advances have increasingly simplified the tools available for the identification of pathogens to the extent that, in some cases, this can be done directly by growers and producers themselves. Commercially available immunoprinting kits and lateral flow devices (LFDs) for detection of selected plant pathogens are among the first tools of what can be considered grower-friendly pathogen monitoring methods. Research efforts, spurned on by point-of-care needs in the medical field, are paving the way for the further development of on-the-spot diagnostics and multiplex technologies in plant pathology. Grower-friendly methods need to be practical, robust, readily available, and cost-effective. Such methods are not restricted to on-the-spot testing but extend to laboratory services, which are sometimes more practicable for growers, extension agents, regulators, and other users of diagnostic tests.
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Affiliation(s)
- Solke H De Boer
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, PE, C1A 5T1 Canada.
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13
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Owens RA, Sano T, Duran-Vila N. Plant viroids: isolation, characterization/detection, and analysis. Methods Mol Biol 2012; 894:253-71. [PMID: 22678585 DOI: 10.1007/978-1-61779-882-5_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
When Diener discovered Potato spindle tuber viroid in 1971 (Diener, Virology 45:411-428, 1971), only a limited number of techniques were available for plant virus detection and purification. Biological assays using indicator hosts showing characteristic symptoms of infection and able to support high levels of viroid replication played a critical role in viroid detection and characterization. Polyacrylamide gel electrophoresis (PAGE) was the first molecular technique to be used for the rapid (2-3 days) identification of viroid-infected plants. Because it is the only diagnostic method that is sequence-independent, PAGE under denaturing conditions continues to play a key role in the identification of new viroids. Starting in the early 1980s, dot blot hybridization began to replace PAGE for routine viroid diagnosis. The first diagnostic protocols based on reverse transcription-polymerase chain reaction (RT-PCR) appeared approximately 10 years later, and much effort has subsequently been devoted to simplifying the sample preparation procedure and identifying group-specific primer pairs. This chapter describes four simple, easy-to-follow protocols-two involving PAGE and two others based on enzymatic amplification of viroid cDNAs-that currently play key roles in viroid discovery and characterization.
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Affiliation(s)
- Robert A Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD, USA.
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Ogino S, Munakata Y, Ohashi S, Fukui M, Sakamoto H, Sekiya Y, Noormohammadi AH, Morrow CJ. Genotyping of Japanese field isolates of Mycoplasma synoviae and rapid molecular differentiation from the MS-H vaccine strain. Avian Dis 2011; 55:187-94. [PMID: 21793432 DOI: 10.1637/9461-071310-reg.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mycoplasma synoviae is an important causative agent of avian mycoplasmosis. In the present study the conserved domain of the variable lipoprotein and hemagglutinin (vlhA) gene of M. synoviae was sequenced and analyzed for 19 field strains of M. synoviae isolated from chickens across Japan. This analysis revealed that there were at least nine genotypes of M. synoviae present in Japan. Furthermore, we found a single nucleotide polymorphism (SNP) within this region in all the Japanese isolates, and based on this finding, we established a PCR method with cycling probe technology to differentiate between these field isolates and the live M. synoviae vaccine strain Mycoplasma synoviae-H (MS-H).
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Affiliation(s)
- Shoji Ogino
- Central Research Laboratories, Nippon Zenyaku Kogyo Co., Ltd., Asaka-machi, Koriyama-shi, Fukushima 963-0196, Japan.
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Asiello PJ, Baeumner AJ. Miniaturized isothermal nucleic acid amplification, a review. LAB ON A CHIP 2011; 11:1420-30. [PMID: 21387067 DOI: 10.1039/c0lc00666a] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.
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Affiliation(s)
- Peter J Asiello
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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Jung C, Chung JW, Kim UO, Kim MH, Park HG. Isothermal target and signaling probe amplification method, based on a combination of an isothermal chain amplification technique and a fluorescence resonance energy transfer cycling probe technology. Anal Chem 2010; 82:5937-43. [PMID: 20575518 DOI: 10.1021/ac100606m] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An iTPA (isothermal target and signaling probe amplification) method for the quantitative detection of nucleic acids, based on a combination of novel ICA (isothermal chain amplification) and fluorescence resonance energy transfer cycling probe technology (FRET CPT), is described. In the new ICA method, which relies on the strand displacement activity of DNA polymerase and the RNA degrading activity of RNase H, two displacement events occur in the presence of four specially designed primers. This phenomenon leads to powerful amplification of target DNA. Since the amplification is initiated only after hybridization of the four primers, the ICA method leads to high specificity for the target sequence. As part of the new ICA method, iTPA is achieved by incorporating FRET CPT to generate multiple fluorescence signals from a single target molecule. Using the resulting dual target and signaling probe amplification system, even a single copy level of a target gene can be successfully detected and quantified under isothermal conditions.
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Affiliation(s)
- Cheulhee Jung
- Department of Chemical and Biomolecular Engineering, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
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Garafutdinov RR, Nikonorov IM, Chemeris DA, Postrigan' BN, Chubukova OV, Talipov RF, Vakhitov VA, Chemeris AV. [New approaches to the real-time detection of nucleotide mismatches by means of chimeric hybridization probes]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009; 35:665-73. [PMID: 19915645 DOI: 10.1134/s1068162009050100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
New approaches to the detection of impaired nucleotides based on the allele specific ligation of a "C probe" followed by rolling circle amplification have been developed. The detection of amplification products was realized by using enzymatic and deoxyribozyme digestion of fluorescently-labeled DNA-RNA-DNA chimeric oligonucleotide structures in cycling probe technology (CPT) in real-time mode.
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Affiliation(s)
- R R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia.
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Use of chimeric DNA-RNA primers in quantitative PCR for detection of Ehrlichia canis and Babesia canis. Appl Environ Microbiol 2009; 75:6393-8. [PMID: 19633128 DOI: 10.1128/aem.00720-09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To overcome the problem of nonspecific by-products in quantitative PCR (qPCR) assays, we constructed DNA-RNA chimeric primers and evaluated their use in the detection and quantification of the Ehrlichia canis 16S rRNA, Babesia canis Hsp70, and canine beta-actin genes. Several RNA bases were incorporated into specific positions in the DNA primers, while no RNA stretches were allowed. qPCR reactions were carried out without preamplification steps. This resulted in decreased formation of undesirable by-products and a 10-fold increase in assay sensitivity.
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Semi-automated bacterial spore detection system with micro-fluidic chips for aerosol collection, spore treatment and ICAN DNA detection. Biosens Bioelectron 2009; 24:3299-305. [DOI: 10.1016/j.bios.2009.04.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 03/27/2009] [Accepted: 04/17/2009] [Indexed: 11/18/2022]
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Mukai H, Takeda O, Usui K, Asada K, Kato I. SNP typing of aldehyde dehydrogenase2 gene with Cycleave ICAN. Mol Cell Probes 2008; 22:333-7. [DOI: 10.1016/j.mcp.2008.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 07/31/2008] [Accepted: 07/31/2008] [Indexed: 11/17/2022]
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