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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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2
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LIU Z, LIU T, TAO CA, CHEN X, HUANG J, WANG F, WANG J. Amplified Analysis of DNA or Proteins by TdT-generated DNAzyme. ANAL SCI 2020; 36:835-840. [DOI: 10.2116/analsci.19p387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhuoliang LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University
| | - Tianxiong LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Cheng-an TAO
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Xianzhe CHEN
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jian HUANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Fang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jianfang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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Gu L, Yan W, Wu H, Fan S, Ren W, Wang S, Lyu M, Liu J. Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum. Anal Chem 2019; 91:7887-7893. [DOI: 10.1021/acs.analchem.9b01707] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | - Wei Ren
- Key Laboratory of Marine Biology, Nanjing Agricultural University, Nanjing, Jiangsu 210000, P. R. China
| | | | | | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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5
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Peng H, Newbigging AM, Wang Z, Tao J, Deng W, Le XC, Zhang H. DNAzyme-Mediated Assays for Amplified Detection of Nucleic Acids and Proteins. Anal Chem 2017; 90:190-207. [DOI: 10.1021/acs.analchem.7b04926] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hanyong Peng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Ashley M. Newbigging
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Zhixin Wang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Wenchan Deng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
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Gomez A, Miller N, Smolina I. Visual detection of bacterial pathogens via PNA-based padlock probe assembly and isothermal amplification of DNAzymes. Anal Chem 2014; 86:11992-8. [PMID: 25415469 PMCID: PMC4270401 DOI: 10.1021/ac5018748] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/21/2014] [Indexed: 12/12/2022]
Abstract
We have developed a self-reporting isothermal system for visual bacterial pathogen detection with single base resolution. The new DNA diagnostic is based on combination of peptide nucleic acid (PNA) technology, rolling circle amplification (RCA) and DNAzymes. PNAs are used as exceedingly selective chemical tools that bind genomic DNA at a predetermined sequence under nondenaturing conditions. After assembly of the PNA-DNA construct a padlock probe is circularized on the free strand. The probe incorporates a G-quadruplex structure flanked by nicking enzyme recognition sites. The assembled circle serves as a template for a novel hybrid RCA strategy that allows for exponential amplification and production of short single-stranded DNA pieces. These DNA fragments fold into G-quadruplex structures and when complexed with hemin become functional DNAzymes. The catalytic activity of each DNAzyme unit leads to colorimetric detection and provides the second amplification step. The combination of PNA, RCA, and DNAzymes allows for sequence-specific and highly sensitive detection of bacteria with a colorimetric output observed with the naked eye. Herein, we apply this method for the discrimination of Escherichia coli, Salmonella typhimurium, and Clostridium difficile genomes.
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Affiliation(s)
- Anastasia Gomez
- Department
of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Nancy
S. Miller
- Department
of Pathology and Laboratory Medicine, Boston
Medical Center and Boston University School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Irina Smolina
- Department
of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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Bone SM, Todd AV. MNAzymes provide a universal mechanism for triggering DNAzyme synthesis cascades. Chem Commun (Camb) 2014; 50:13243-6. [DOI: 10.1039/c4cc05919k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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Bi S, Cui Y, Li L. Dumbbell probe-mediated cascade isothermal amplification: A novel strategy for label-free detection of microRNAs and its application to real sample assay. Anal Chim Acta 2013; 760:69-74. [DOI: 10.1016/j.aca.2012.11.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 09/23/2012] [Accepted: 11/01/2012] [Indexed: 12/26/2022]
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Bi S, Cui Y, Li L. Ultrasensitive detection of mRNA extracted from cancerous cells achieved by DNA rotaxane-based cross-rolling circle amplification. Analyst 2012; 138:197-203. [PMID: 23148205 DOI: 10.1039/c2an36118c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
An ultrasensitive and highly selective method for polymerase chain reaction-free (PCR-free) messenger RNA (mRNA) expression profiling is developed through a novel cross-rolling circle amplification (C-RCA) process based on DNA-rotaxane nanostructures. Two species of DNA pseudorotaxane (DPR) superstructures (DPR-I and DPR-II) are assembled by threading a linear DNA rod through a double-stranded DNA (dsDNA) ring containing two single-stranded gaps. In this assay, cDNA that is specific for β-actin (ACTB) mRNA is taken as a model analyte. Upon the introduction of the target cDNA, the cDNA and the biotin-modified primer are hybridized to the single-stranded regions of the DNA rod and the gap-ring, respectively. As a result, the DPR-I dethreads into free DNA macrocycle and a dumbbell-shaped DNA nanostructure. In the presence of DNA polymerase/dNTPs, two release-DNA on the DPR-I are replaced by polymerase with strand-displacement activity, which can act as the input of the DPR-II to trigger the dethreading of DPR-II and the RCA reaction, releasing another two specified release-DNA strands those in turn serve as the "mimic cDNA" for DPR-I. The C-RCA reaction then proceeds autonomously. To overcome the high background induced by hemin itself, the biotinylated rolling circle products are captured by streptavidin-coated MNPs, achieving a detection limit as low as 0.1 zmol cDNA. The assay also exhibits an excellent selectivity due to its unique DNA nanostructure fabricated through base pairing hybridization. The ACTB mRNA expression in mammary cancer cells (MCF-7) is successfully detected.
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Affiliation(s)
- Sai Bi
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China.
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11
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Wen Y, Xu Y, Mao X, Wei Y, Song H, Chen N, Huang Q, Fan C, Li D. DNAzyme-Based Rolling-Circle Amplification DNA Machine for Ultrasensitive Analysis of MicroRNA in Drosophila Larva. Anal Chem 2012; 84:7664-9. [DOI: 10.1021/ac300616z] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yanqin Wen
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yan Xu
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yingliang Wei
- Key Laboratory of Systems Biology,
CAS, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haiyun Song
- Key Laboratory of Systems Biology,
CAS, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nan Chen
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Di Li
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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