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Kowitdamrong E, Anoma S, Loykaew T, Hansasuta P, Bhattarakosol P. ƩS COVID-19 is a rapid high throughput and sensitive one-step quadruplex real-time RT-PCR assay. Sci Rep 2024; 14:20590. [PMID: 39232060 PMCID: PMC11374890 DOI: 10.1038/s41598-024-71705-8] [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: 06/18/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Real-time reverse transcription polymerase chain reaction (RT-PCR), a standard method recommended for the diagnosis of coronavirus disease 2019 (COVID-19) requires 2-4 h to get the result. Although antigen test kit (ATK) is used for COVID-19 screening within 15-30 min, the drawback is its limited sensitivity. Hence, a rapid one-step quadruplex real-time RT-PCR assay: termed ƩS COVID-19 targeting ORF1ab, ORF3a, and N genes of SARS-CoV-2; and Avocado sunblotch viroid (ASBVd) as an internal control was developed. Based on strategies including designing high melting temperature primers with short amplicons, applying a fast ramp rate, minimizing hold time, and reducing the range between denaturation and annealing/extension temperatures; the assay could be accomplished within 25 min. The limit of detection of ORF1ab, ORF3a, and N genes were 1.835, 1.310, and 1 copy/reaction, respectively. Validation was performed in 205 combined nasopharyngeal and oropharyngeal swabs. The sensitivity, specificity, positive predictive value, and negative predictive value were 92.8%, 100%, 100%, and 97.1%, respectively with 96.7% accuracy. Cohen's Kappa was 0.93. The newly developed rapid real-time RT-PCR assay was highly sensitive, specific, and fast, making it suitable for use as an alternative method to support laboratory diagnosis of COVID-19 in outpatient and emergency departments.
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Affiliation(s)
- Ekasit Kowitdamrong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Center of Excellence in Applied Medical Virology, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Sasiprapa Anoma
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Applied Medical Virology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thitiya Loykaew
- Department of Microbiology, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, 10330, Thailand
| | - Pokrath Hansasuta
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Parvapan Bhattarakosol
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Applied Medical Virology, Chulalongkorn University, Bangkok, 10330, Thailand
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2
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Wittwer CT. Rapid Cycle and Extreme Polymerase Chain Reaction. Methods Mol Biol 2023; 2621:257-266. [PMID: 37041449 DOI: 10.1007/978-1-0716-2950-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Rapid cycle polymerase chain reaction (PCR) amplifies DNA in 10-30 min, while extreme PCR is complete in less than 1 min. These methods do not sacrifice quality for speed; sensitivity, specificity, and yield are equivalent or better than conventional PCR. What is required (and not widely available) is rapid, accurate control of reaction temperature during cycling. Specificity improves with cycling speed, and efficiency can be maintained by increasing polymerase and primer concentrations. Speed is aided by simplicity, dyes that stain double-stranded DNA are less expensive than probes, and one of the simplest polymerases, the deletion mutant KlenTaq, is used throughout. Rapid amplification can be coupled with endpoint melting analysis to verify product identity. Instead of commercial master mixes, detailed formulations for reagents and master mixes compatible with rapid cycle and extreme PCR are described.
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3
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Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Int J Mol Sci 2022; 23:ijms23126373. [PMID: 35742812 PMCID: PMC9224347 DOI: 10.3390/ijms23126373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.
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4
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Yin H, Wu Z, Shi N, Qi Y, Jian X, Zhou L, Tong Y, Cheng Z, Zhao J, Mao H. Ultrafast multiplexed detection of SARS-CoV-2 RNA using a rapid droplet digital PCR system. Biosens Bioelectron 2021; 188:113282. [PMID: 34020234 PMCID: PMC8093165 DOI: 10.1016/j.bios.2021.113282] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/01/2021] [Accepted: 04/22/2021] [Indexed: 12/24/2022]
Abstract
We report the first combination of droplet digital and rapid PCR techniques for efficient, accurate, and quantitative detection of SARS-CoV-2 RNA. The presented rapid digital PCR system simultaneously detects two specific targets (ORF1ab and N genes) and one reference gene (RNase P) with a single PCR thermal cycling period around 7 s and the total running time less than 5 min. A clear positive signal could be identified within 115 s via the rapid digital RT-PCR, suggesting its efficiency for the end-point detection. In addition, benchmark tests with serial diluted reference samples of SARS-CoV-2 RNA reveal the excellent accuracy of our system (R2>0.99). More importantly, the rapid digital PCR system gives consistent and accurate detection of low-concentration reference samples, whereas qPCR yields Ct values with significant variations that could lead to false-negative results. Finally, we apply the rapid digital PCR system to analyze clinical samples with both positive and control cases, where results are consistent with qPCR test outcomes. By providing similar accuracy with qPCR while minimizing the detection time-consuming and the false-negative tendency, the presented rapid digital PCR system represents a promising improvement on the rapid diagnosis of COVID-19.
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Affiliation(s)
- Hao Yin
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenhua Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Nan Shi
- Expec-Advanced Research Center, Saudi Aramco, Dhahran, 34464, Saudi Arabia
| | - Yong Qi
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, Jiangsu, 210000, China
| | - Xiaoyu Jian
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Lin Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100049, China
| | - Zule Cheng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Kim J, Gang J. Double‐Stranded
DNA
‐Templated Copper Nanoclusters for Detection of
DNA
Polymerase Activity. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jungeun Kim
- Department of Nano Chemistry Gachon University Sungnam South Korea
| | - Jongback Gang
- Department of Nano Chemistry Gachon University Sungnam South Korea
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6
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Progress in molecular detection with high-speed nucleic acids thermocyclers. J Pharm Biomed Anal 2020; 190:113489. [DOI: 10.1016/j.jpba.2020.113489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022]
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Rejali NA, Zuiter AM, Quackenbush JF, Wittwer CT. Reverse transcriptase kinetics for one-step RT-PCR. Anal Biochem 2020; 601:113768. [PMID: 32416095 DOI: 10.1016/j.ab.2020.113768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 01/09/2023]
Abstract
Understanding reverse transcriptase (RT) activity is critical for designing fast one-step RT-PCRs. We report a stopped-flow assay that monitors SYBR Green I fluorescence to investigate RT activity in PCR conditions. We studied the influence of PCR conditions on RT activity and assessed the accuracy of cDNA synthesis predictions for one-step RT-PCR. Nucleotide incorporation increased from 26 to 89 s-1 between 1.5 and 6 mM MgCl2 but was largely unaffected by changes in KCl. Conversely, increasing KCl from 15 to 75 mM increased apparent rate constants for RT-oligonucleotide binding (0.010-0.026 nM-1 s-1) and unbinding (0.2-1.5 s-1). All rate constants increased between 22 and 42 °C. When evaluated by PCR quantification cycle, cDNA predictions differed from experiments using RNase H+ RT (average 1.7 cycles) and RNase H- (average 4.5 cycles). Decreasing H+ RT concentrations 10 to 104-fold from manufacturer recommendations improved cDNA predictions (average 0.8 cycles) and increased RT-PCR assay efficiency. RT activity assays and models can be used to aid assay design and improve the speed of RT-PCRs. RT type and concentration must be selected to promote rapid cDNA synthesis but minimize nonspecific amplification. We demonstrate 2-min one-step RT-PCR of a Zika virus target using reduced RT concentrations and extreme PCR.
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Affiliation(s)
- Nick A Rejali
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - Aisha M Zuiter
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - John F Quackenbush
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA.
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8
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The kinetic requirements of extreme qPCR. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100081. [PMID: 31285997 PMCID: PMC6591793 DOI: 10.1016/j.bdq.2019.100081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 01/02/2023]
Abstract
The kinetic requirements of quantitative PCR were experimentally dissected into the stages of DNA denaturation, primer annealing, and polymerase extension. The temperature/time conditions for 2 stages were kept optimal, while the other was limited until the amplification efficiency decreased as measured by an increase in quantification cycle (Cq). Extension was studied in a commercial capillary LightCycler®. Using a rapid deletion mutant of Taq (KlenTaq™), about 1 s was required for every 70 bp of product length. To study annealing and denaturation times of <1 s, a custom “extreme” PCR instrument with 3 temperatures was used along with increased primer and polymerase concentrations. Actual sample temperatures and times were measured rather than programmed or predicted. For denaturation, 200–500 ms above the denaturation threshold was necessary for maximal efficiency. For annealing, 300-1000 ms below the annealing threshold was required. Temperature thresholds were set at 98% primer annealing or PCR product denaturation as determined experimentally by melting curves. Progressing from rapid cycle PCR to extreme PCR decreased cycling times by 10–60 fold. If temperatures are controlled accurately and flexibility in reagents is allowed, PCR of short products can be performed in less than 15 s. We also put PCR in context to other emerging methods and consider its relevance to the evolution of molecular diagnostics.
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9
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Cai Q, Fauvart M, Wiederkehr RS, Jones B, Cools P, Goos P, Vaneechoutte M, Stakenborg T. Ultra-fast, sensitive and quantitative on-chip detection of group B streptococci in clinical samples. Talanta 2018; 192:220-225. [PMID: 30348381 DOI: 10.1016/j.talanta.2018.09.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/04/2018] [Accepted: 09/11/2018] [Indexed: 12/29/2022]
Abstract
PCR enables sensitive and specific detection of infectious disease agents, but application in point-of-care diagnostic testing remains scarce. A compact tool that runs PCR assays in less than a few minutes and that relies on mass-producible, disposable reactors could revolutionize while-you-wait molecular testing. We here exploit well-established semiconductor manufacturing processes to produce silicon ultra-fast quantitative PCR (UF-qPCR) chips that can run PCR protocols with limited assay optimization. A total of 110 clinical samples were analyzed for the detection of group B streptococci using both a validated benchtop and an on-chip qPCR assay. For the on-chip assay, the total reaction time was reduced after optimization to less than 5 min. The standard curve, spanning a concentration range of 5 log units, yielded a PCR efficiency of 94%. The sensitivity obtained was 96% (96/100; CI: 90-98%) and the specificity 70% (7/10; CI: 40-90%). We show that if melting analyses would be integrated, the obtained sensitivity would drop slightly to 93% (CI: 86-96%), while the specificity would increase to 100% (CI: 72% - 100%). In comparison to the benchtop reference qPCR assay performed on a LightCycler©96, the on-chip assay demonstrated a highly significant qualitative (Spearman's rank correlation) and quantitative (linear regression) correlation. Using a mass-producible qPCR chip and limited assay optimization, we were able to develop a validated qPCR protocol that can be carried out in less than five minutes. The analytical performance of the microchip-based UF-qPCR system was shown to match that of a benchtop assay. This is the first report to provide UF-qPCR validation using clinical samples. We demonstrate that qPCR-based while-you-wait testing is feasible without jeopardizing assay performance.
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Affiliation(s)
- Qing Cai
- Imec, Kapeldreef 75, B-3001 Leuven, Belgium
| | | | | | | | - Piet Cools
- Laboratory for Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Heymanslaan 10 185, Entrance 38 (MRB2), 9000 Gent, Belgium
| | - Peter Goos
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven Kasteelpark Arenberg 30 - bus 2456, 3001 Leuven, Belgium; Department of Engineering Management, University of Antwerp, 2000 Antwerpen, Belgium
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Heymanslaan 10 185, Entrance 38 (MRB2), 9000 Gent, Belgium
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10
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Andini N, Hu A, Zhou L, Cogill S, Wang TH, Wittwer CT, Yang S. A "Culture" Shift: Broad Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing Directly from Whole Blood. Clin Chem 2018; 64:1453-1462. [PMID: 30087140 DOI: 10.1373/clinchem.2018.290189] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND The time required for bloodstream pathogen detection, identification (ID), and antimicrobial susceptibility testing (AST) does not satisfy the acute needs of disease management. Conventional methods take up to 3 days for ID and AST. Molecular diagnostics have reduced times for ID, but their promise to supplant culture is unmet because AST times remain slow. We developed a combined quantitative PCR (qPCR)-based ID+AST assay with sequential detection, ID, and AST of leading nosocomial bacterial pathogens. METHODS ID+AST was performed on whole blood samples by (a) removing blood cells, (b) brief bacterial enrichment, (c) bacterial detection and ID, and (d) species-specific antimicrobial treatment. Broad-spectrum qPCR of the internal transcribed spacer between the 16S and 23S was amplified for detection. High-resolution melting identified the species with a curve classifier. AST was enabled by Ct differences between treated and untreated samples. RESULTS A detection limit of 1 CFU/mL was achieved for Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. All species were accurately identified by unique melting curves. Antimicrobial minimum inhibitory concentrations were identified with Ct differences of ≥1 cycle. Using an RNA target allowed reduction of AST incubation time from 60 min to 5 min. Rapid-cycle amplification reduced qPCR times by 83% to 30 min. CONCLUSIONS Combined, sequential ID+AST protocols allow rapid and reliable detection, ID, and AST for the diagnosis of bloodstream infections, enabling conversion of empiric to targeted therapy by the second dose of antimicrobials.
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Affiliation(s)
- Nadya Andini
- Department of Emergency Medicine, Stanford University, Stanford, CA
| | - Anne Hu
- Department of Emergency Medicine, Stanford University, Stanford, CA
| | - Luming Zhou
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Steven Cogill
- Department of Emergency Medicine, Stanford University, Stanford, CA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD
| | - Carl T Wittwer
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, CA;
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11
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Rejali NA, Moric E, Wittwer CT. The Effect of Single Mismatches on Primer Extension. Clin Chem 2018; 64:801-809. [PMID: 29444902 DOI: 10.1373/clinchem.2017.282285] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/26/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Allele-specific PCR is an important diagnostic tool that identifies single-nucleotide variants by preferential amplification of a particular allele, using primers that are mismatched to all but one allele variant. METHODS We applied a fluorescent stopped-flow polymerase assay to measure extension rates from oligonucleotide hairpins to simulate primer-template pairs. Under PCR-applicable conditions, reaction rates were recorded in nucleotides per second per polymerase (nt/s/poly). The effects of temperature, potassium chloride, mismatch type, and position were studied with primarily a deletion mutant of Thermus aquaticus (Taq) DNA polymerase and 135 oligonucleotide sequences. RESULTS Rates at 65 °C were between 205 ± 11 and 177 ± 8 nt/s/poly for matched templates and between 4.55 ± 0.21 and 0.008 ± 0.005 nt/s/poly for 3'-mismatched templates. Although extension rates progressively increased with mismatches further away from the 3' end, rates were still reduced by as much as 84% with a C · C mismatch 6 bases from the 3' end. The optimal extension temperature for matched sequences was 70 °C, shifting to 55-60 °C for 3' mismatches. KCl inhibited mismatch extension. The Michaelis constant (Km) was increased and the apparent unimolecular rate constant (kcat) decreased for 3' mismatches relative to matched templates. CONCLUSIONS Although primer extension of mismatches depends on mismatch type and position, variation also depends on local sequence, KCl concentration, and the type of polymerase. Introduction of 3' mismatches reduces the optimal temperature for extension, suggesting higher annealing temperatures for better allele discrimination. Quantitative descriptions of expected specificity in allele-specific PCR provide additional design direction and suggest when other methods (e.g., high-resolution melting analysis) may be a better choice.
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Affiliation(s)
- Nick A Rejali
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Endi Moric
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT.
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12
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DNA synthesis from diphosphate substrates by DNA polymerases. Proc Natl Acad Sci U S A 2018; 115:980-985. [PMID: 29339523 DOI: 10.1073/pnas.1712193115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The activity of DNA polymerase underlies numerous biotechnologies, cell division, and therapeutics, yet the enzyme remains incompletely understood. We demonstrate that both thermostable and mesophilic DNA polymerases readily utilize deoxyribonucleoside diphosphates (dNDPs) for DNA synthesis and inorganic phosphate for the reverse reaction, that is, phosphorolysis of DNA. For Taq DNA polymerase, the KMs of the dNDP and phosphate substrates are ∼20 and 200 times higher than for dNTP and pyrophosphate, respectively. DNA synthesis from dNDPs is about 17 times slower than from dNTPs, and DNA phosphorolysis about 200 times less efficient than pyrophosphorolysis. Such parameters allow DNA replication without requiring coupled metabolism to sequester the phosphate products, which consequently do not pose a threat to genome stability. This mechanism contrasts with DNA synthesis from dNTPs, which yield high-energy pyrophosphates that have to be hydrolyzed to phosphates to prevent the reverse reaction. Because the last common ancestor was likely a thermophile, dNDPs are plausible substrates for genome replication on early Earth and may represent metabolic intermediates later replaced by the higher-energy triphosphates.
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13
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qPCR primer design revisited. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 14:19-28. [PMID: 29201647 PMCID: PMC5702850 DOI: 10.1016/j.bdq.2017.11.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 11/08/2017] [Accepted: 11/12/2017] [Indexed: 01/04/2023]
Abstract
Primers are arguably the single most critical components of any PCR assay, as their properties control the exquisite specificity and sensitivity that make this method uniquely powerful. Consequently, poor design combined with failure to optimise reaction conditions is likely to result in reduced technical precision and false positive or negative detection of amplification targets. Despite the framework provided by the MIQE guidelines and the accessibility of wide-ranging support from peer-reviewed publications, books and online sources as well as commercial companies, the design of many published assays continues to be less than optimal: primers often lack intended specificity, can form dimers, compete with template secondary structures at the primer binding sites or hybridise only within a narrow temperature range. We present an overview of the main steps in the primer design workflow, with data that illustrate some of the unexpected variability that often occurs when theory is translated into practice. We also strongly urge researchers to report as much information about their assays as possible in their publications.
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14
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Nikoomanzar A, Dunn MR, Chaput JC. Evaluating the Rate and Substrate Specificity of Laboratory Evolved XNA Polymerases. Anal Chem 2017; 89:12622-12625. [DOI: 10.1021/acs.analchem.7b03807] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ali Nikoomanzar
- Departments of Pharmaceutical Sciences,
Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - Matthew R. Dunn
- Departments of Pharmaceutical Sciences,
Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - John C. Chaput
- Departments of Pharmaceutical Sciences,
Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
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15
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Bustin SA. How to speed up the polymerase chain reaction. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 12:10-14. [PMID: 28702368 PMCID: PMC5496742 DOI: 10.1016/j.bdq.2017.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 11/25/2022]
Abstract
Reducing the time taken to run qPCR assays on today’s qPCR cyclers is rather straightforward and requires no specialised reagents or instruments. As the first article in a new series of short technical reports, I demonstrate that it is possible to reduce significantly both denaturation temperatures and cycling times, whilst retaining sensitivity and specificity of the original qPCR conditions.
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Affiliation(s)
- Stephen A Bustin
- Faculty of Medical Science, Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford CM1 1SQ, UK
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16
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Development of an on-site rapid real-time polymerase chain reaction system and the characterization of suitable DNA polymerases for TaqMan probe technology. Anal Bioanal Chem 2016; 408:5641-9. [DOI: 10.1007/s00216-016-9668-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/16/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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17
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Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces. Sci Rep 2015; 5:12066. [PMID: 26174478 PMCID: PMC4502528 DOI: 10.1038/srep12066] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022] Open
Abstract
The engineering of high-performance enzymes for future sequencing and PCR technologies as well as the development of many anticancer drugs requires a detailed analysis of DNA/RNA synthesis processes. However, due to the complex molecular interplay involved, real-time methodologies have not been available to obtain comprehensive information on both binding parameters and enzymatic activities. Here we introduce a chip-based method to investigate polymerases and their interactions with nucleic acids, which employs an electrical actuation of DNA templates on microelectrodes. Two measurement modes track both the dynamics of the induced switching process and the DNA extension simultaneously to quantitate binding kinetics, dissociation constants and thermodynamic energies. The high sensitivity of the method reveals previously unidentified tight binding states for Taq and Pol I (KF) DNA polymerases. Furthermore, the incorporation of label-free nucleotides can be followed in real-time and changes in the DNA polymerase conformation (finger closing) during enzymatic activity are observable.
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18
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Clark KD, Yamsek MM, Nacham O, Anderson JL. Magnetic ionic liquids as PCR-compatible solvents for DNA extraction from biological samples. Chem Commun (Camb) 2015; 51:16771-3. [DOI: 10.1039/c5cc07253k] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel strategy for the rapid detection of bacterial plasmid DNA preconcentrated by hydrophobic magnetic ionic liquids (MILs) is described.
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Affiliation(s)
| | - Melissa M. Yamsek
- Department of Chemistry and Biochemistry
- University of Toledo
- Toledo
- USA
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Abstract
BACKGROUND PCR is a key technology in molecular biology and diagnostics that typically amplifies and quantifies specific DNA fragments in about an hour. However, the kinetic limits of PCR are unknown. METHODS We developed prototype instruments to temperature cycle 1- to 5-μL samples in 0.4-2.0 s at annealing/extension temperatures of 62 °C-76 °C and denaturation temperatures of 85 °C-92 °C. Primer and polymerase concentrations were increased 10- to 20-fold above typical concentrations to match the kinetics of primer annealing and polymerase extension to the faster temperature cycling. We assessed analytical specificity and yield on agarose gels and by high-resolution melting analysis. Amplification efficiency and analytical sensitivity were demonstrated by real-time optical monitoring. RESULTS Using single-copy genes from human genomic DNA, we amplified 45- to 102-bp targets in 15-60 s. Agarose gels showed bright single bands at the expected size, and high-resolution melting curves revealed single products without using any "hot start" technique. Amplification efficiencies were 91.7%-95.8% by use of 0.8- to 1.9-s cycles with single-molecule sensitivity. A 60-bp genomic target was amplified in 14.7 s by use of 35 cycles. CONCLUSIONS The time required for PCR is inversely related to the concentration of critical reactants. By increasing primer and polymerase concentrations 10- to 20-fold with temperature cycles of 0.4-2.0 s, efficient (>90%), specific, high-yield PCR from human DNA is possible in <15 s. Extreme PCR demonstrates the feasibility of while-you-wait testing for infectious disease, forensics, and any application where immediate results may be critical.
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Affiliation(s)
- Jared S Farrar
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT; Current affiliation: MD-PhD Program, Virginia Commonwealth University, Richmond, VA
| | - Carl T Wittwer
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT;
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20
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The influence of nucleotide sequence and temperature on the activity of thermostable DNA polymerases. J Mol Diagn 2014; 16:305-13. [PMID: 24607271 DOI: 10.1016/j.jmoldx.2014.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 11/23/2022] Open
Abstract
Extension rates of a thermostable, deletion-mutant polymerase were measured from 50°C to 90°C using a fluorescence activity assay adapted for real-time PCR instruments. Substrates with a common hairpin (6-base loop and a 14-bp stem) were synthesized with different 10-base homopolymer tails. Rates for A, C, G, T, and 7-deaza-G incorporation at 75°C were 81, 150, 214, 46, and 120 seconds(-1). Rates for U were half as fast as T and did not increase with increasing concentration. Hairpin substrates with 25-base tails from 0% to 100% GC content had maximal extension rates near 60% GC and were predicted from the template sequence and mononucleotide incorporation rates to within 30% for most sequences. Addition of dimethyl sulfoxide at 7.5% increased rates to within 1% to 17% of prediction for templates with 40% to 90% GC. When secondary structure was designed into the template region, extension rates decreased. Oligonucleotide probes reduced extension rates by 65% (5'-3' exo-) and 70% (5'-3' exo+). When using a separate primer and a linear template to form a polymerase substrate, rates were dependent on both the primer melting temperature (Tm) and the annealing/extension temperature. Maximum rates were observed from Tm to Tm - 5°C with little extension by Tm + 5°C. Defining the influence of sequence and temperature on polymerase extension will enable more rapid and efficient PCR.
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21
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Montgomery JL, Wittwer CT. Influence of PCR reagents on DNA polymerase extension rates measured on real-time PCR instruments. Clin Chem 2013; 60:334-40. [PMID: 24081987 DOI: 10.1373/clinchem.2013.212829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Radioactive DNA polymerase activity methods are cumbersome and do not provide initial extension rates. A simple extension rate assay would enable study of basic assumptions about PCR and define the limits of rapid PCR. METHODS A continuous assay that monitors DNA polymerase extension using noncovalent DNA dyes on common real-time PCR instruments was developed. Extension rates were measured in nucleotides per second per molecule of polymerase. To initiate the reaction, a nucleotide analog was heat activated at 95 °C for 5 min, the temperature decreased to 75 °C, and fluorescence monitored until substrate exhaustion in 30-90 min. RESULTS The assay was linear with time for over 40% of the reaction and for polymerase concentrations over a 100-fold range (1-100 pmol/L). Extension rates decreased continuously with increasing monovalent cation concentrations (lithium, sodium, potassium, cesium, and ammonium). Melting-temperature depressors had variable effects. DMSO increased rates up to 33%, whereas glycerol had little effect. Betaine, formamide, and 1,2-propanediol decreased rates with increasing concentrations. Four common noncovalent DNA dyes inhibited polymerase extension. Heat-activated nucleotide analogs were 92% activated after 5 min, and hot start DNA polymerases were 73%-90% activated after 20 min. CONCLUSIONS Simple DNA extension rate assays can be performed on real-time PCR instruments. Activity is decreased by monovalent cations, DNA dyes, and most melting temperature depressors. Rational inclusion of PCR components on the basis of their effects on polymerase extension is likely to be useful in PCR, particularly rapid-cycle or fast PCR.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
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