1
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Song Z, Hu K, Rao J, Cheng B, Xu L, An R, Liang X. Unexpected Mechanism and Inhibition Effect for Nonspecific Amplification Involving Dynamic Binding of Primers with Background DNA. Anal Chem 2023; 95:16819-16829. [PMID: 37922263 DOI: 10.1021/acs.analchem.3c02274] [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: 11/05/2023]
Abstract
Nonspecific amplification is a serious issue in DNA detection as it can lead to false-positive results and reduce specificity. It is very important to well understand its mechanism through sequencing nonspecific products. Here, an approach is developed using a nanopore sequencing technique after acquiring the long repetitive sequence of DNA products from nonspecific amplification. Based on the sequencing results, a new mechanism of nonspecific amplification designated as dynamic mismatched primer binding (DMPB) with the background DNA (bgDNA) is proposed. Unexpectedly, our findings show that the primers (∼20 nt) can bind to bgDNA for primer extension when only 6-11 fully matched (9-14 mismatched) base pairs are formed. After the single-stranded DNAs (ssDNAs) attached to the first primer are produced, more interestingly, with the aid of DNA polymerase, the other primer can bind to these ssDNAs in the case that the fully matched base pairs formed between them are even shorter than 6 bp. As a result, perfect "seeds" for polymerase chain reaction with information on both primers are produced so that exponential nonspecific amplification can occur. The DMPB mechanism can explain nonspecific amplification in other approaches as well. Finally, a mini-hairpin DNA is used to effectively inhibit nonspecific amplification by preventing the formation of an unexpected primer-bgDNA complex.
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Affiliation(s)
- Ziting Song
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Kunling Hu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Jun Rao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Bingxiao Cheng
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Liyuan Xu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Ran An
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xingguo Liang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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2
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Velazquez-Salinas L, Ramirez-Medina E, Rai A, Pruitt S, Vuono EA, Espinoza N, Gladue DP, Borca MV. Development Real-Time PCR Assays to Genetically Differentiate Vaccinated Pigs From Infected Pigs With the Eurasian Strain of African Swine Fever Virus. Front Vet Sci 2021; 8:768869. [PMID: 34778441 PMCID: PMC8579032 DOI: 10.3389/fvets.2021.768869] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/27/2021] [Indexed: 01/26/2023] Open
Abstract
Currently, African swine fever virus (ASFV) represents one of the most important economic threats for the global pork industry. Recently, significant advances have been made in the development of potential vaccine candidates to protect pigs against this virus. We have previously developed attenuated vaccine candidates by deleting critical viral genes associated with virulence. Here, we present the development of the accompanying genetic tests to discriminate between infected and vaccinated animals (DIVA), a necessity during an ASFV vaccination campaign. We describe here the development of three independent real-time polymerase chain reaction (qPCR) assays that detect the presence of MGF-360-12L, UK, and I177L genes, which were previously deleted from the highly virulent Georgia strain of ASFV to produce the three recombinant live attenuated vaccine candidates. When compared with the diagnostic reference qPCR that detects the p72 gene, all assays demonstrated comparable levels of sensitivity, specificity, and efficiency of amplification to detect presence/absence of the ASFV Georgia 2007/1 strain (prototype virus of the Eurasian lineage) from a panel of blood samples from naïve, vaccinated, and infected pigs. Collectively, the results of this study demonstrate the potential of these real-time PCR assays to be used as genetic DIVA tests, supporting vaccination campaigns associated with the use of ASFV-ΔMGF, ASFV-G-Δ9GL/ΔUK, and ASFV-ΔI177L or cell culture adapted ASFV-ΔI177LΔLVR live attenuated vaccines in the field.
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Affiliation(s)
- Lauro Velazquez-Salinas
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States.,Department of Anatomy and Physiology, Kansas State University, Manhattan, KS, United States
| | - Elizabeth Ramirez-Medina
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States
| | - Ayushi Rai
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
| | - Sarah Pruitt
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States
| | - Elizabeth A Vuono
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States.,Department of Pathobiology and Population Medicine, Mississippi State University, Mississippi, MS, United States
| | - Nallely Espinoza
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States
| | - Douglas P Gladue
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States
| | - Manuel V Borca
- Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, United States
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3
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Ansah F, Suurbaar J, Darko D, Anabire NG, Blankson SO, Domson BKS, Soulama A, Kpasra P, Chirawurah JD, Amenga-Etego L, Kanyong P, Awandare GA, Aniweh Y. Development of Cooperative Primer-Based Real-Time PCR Assays for the Detection of Plasmodium malariae and Plasmodium ovale. J Mol Diagn 2021; 23:1393-1403. [PMID: 34425259 PMCID: PMC8591562 DOI: 10.1016/j.jmoldx.2021.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/16/2021] [Accepted: 07/14/2021] [Indexed: 11/27/2022] Open
Abstract
Plasmodium malariae and Plasmodium ovale are increasingly gaining public health attention as the global transmission of falciparum malaria is decreasing. However, the absence of reliable Plasmodium species-specific detection tools has hampered accurate diagnosis of these minor Plasmodium species. In this study, SYBR Green-based real-time PCR assays were developed for the detection of P. malariae and P. ovale using cooperative primers that significantly limit the formation and propagation of primers-dimers. Both the P. malariae and P. ovale cooperative primer-based assays had at least 10-fold lower detection limit compared with the corresponding conventional primer-based assays. More important, the cooperative primer-based assays were evaluated in a cross-sectional study using 560 samples obtained from two health facilities in Ghana. The prevalence rates of P. malariae and P. ovale among the combined study population were 18.6% (104/560) and 5.5% (31/560), respectively. Among the Plasmodium-positive cases, P. malariae and P. ovale mono-infections were 3.6% (18/499) and 1.0% (5/499), respectively, with the remaining being co-infections with Plasmodium falciparum. The study demonstrates the public health importance of including detection tools with lower detection limits in routine diagnosis and surveillance of nonfalciparum species. This will be necessary for comprehensively assessing the effectiveness of malaria interventions and control measures aimed toward global malaria elimination.
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Affiliation(s)
- Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Jonathan Suurbaar
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Derrick Darko
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Nsoh G Anabire
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry and Molecular Medicine, School of Medicine, University for Development Studies, Tamale, Ghana
| | - Samuel O Blankson
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Bright K S Domson
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Alamissa Soulama
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Paulina Kpasra
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Jersley D Chirawurah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Prosper Kanyong
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Flexmedical Solutions Ltd., Eliburn Industrial Park, Livingston, United Kingdom
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.
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4
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SantaLucia J, Sozhamannan S, Gans JD, Koehler JW, Soong R, Lin NJ, Xie G, Olson V, Roth K, Beck L. Appendix Q: Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern In Silico Approaches. J AOAC Int 2021; 103:882-899. [PMID: 33241357 PMCID: PMC8370429 DOI: 10.1093/jaoacint/qsaa045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 11/13/2022]
Affiliation(s)
| | - Shanmuga Sozhamannan
- Logistics Management Institute supporting Defense Biological Product Assurance Office (DBPAO), Joint Project Leads (JPL) Chemical, Biological, Radiological, and Nuclear Defense (CBRND) Enabling Biotechnologies (EB)
| | | | - Jeffrey W Koehler
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID)
| | | | - Nancy J Lin
- National Institute of Standards and Technology (NIST)
| | - Gary Xie
- Los Alamos National Laboratory (LANL)
| | | | | | - Linda Beck
- Joint Research and Development, Inc. (JRAD) supporting Joint Program Executive Office (JPEO) JPL CBRND EB; Deputy Under Secretary of the Army, Test and Evaluation (DUSA TE)
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5
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Ganguli A, Mostafa A, Berger J, Lim J, Araud E, Baek J, Stewart de Ramirez SA, Baltaji A, Roth K, Aamir M, Aedma S, Mady M, Mahajan P, Sathe S, Johnson M, White K, Kumar J, Valera E, Bashir R. Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Ultrasensitive Detection of SARS-CoV-2 in Saliva and Viral Transport Medium Clinical Samples. Anal Chem 2021; 93:7797-7807. [PMID: 34033472 DOI: 10.1021/acs.analchem.0c05170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The COVID-19 pandemic has underscored the shortcomings in the deployment of state-of-the-art diagnostics platforms. Although several polymerase chain reaction (PCR)-based techniques have been rapidly developed to meet the growing testing needs, such techniques often need samples collected through a swab, the use of RNA extraction kits, and expensive thermocyclers in order to successfully perform the test. Isothermal amplification-based approaches have also been recently demonstrated for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by minimizing sample preparation while also reducing the instrumentation and reaction complexity. In addition, there are limited reports of saliva as the sample source, and some of these indicate inferior sensitivity when comparing reverse transcription loop-mediated isothermal amplification (RT-LAMP) with PCR-based techniques. In this paper, we demonstrate an improved sensitivity assay from saliva using a two-step RT-LAMP assay, where a short 10 min RT step is performed with only B3 and backward inner primers before the final reaction. We show that while the one-step RT-LAMP demonstrates satisfactory results, the optimized two-step approach allows detection of only few molecules per reaction and performs significantly better than the one-step RT-LAMP and conventional two-step RT-LAMP approaches with all primers included in the RT step. We show control measurements with RT-PCR, and importantly, we demonstrate RNA extraction-free RT-LAMP-based assays for detection of SARS-CoV-2 from viral transport media and saliva clinical samples.
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Affiliation(s)
- Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jongwon Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Elbashir Araud
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Janice Baek
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Sarah A Stewart de Ramirez
- Emergency Medicine, University of Illinois College of Medicine at Peoria & OSF Healthcare, Peoria, Illinois 61603-3200, United States
| | - Ali Baltaji
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Kelly Roth
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Muhammad Aamir
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Surya Aedma
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mohamed Mady
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Pranav Mahajan
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Sanjivani Sathe
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mark Johnson
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Karen White
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - James Kumar
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
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6
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. The influence of quality of primers on the formation of primer dimers in PCR. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1251-1269. [PMID: 32799617 DOI: 10.1080/15257770.2020.1803354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Polymerase chain reaction (PCR) is the most commonly used method for nucleic acids amplification. PCR performance depends on several causes, among which the quality of primers is one of the main determinants affecting specificity, sensitivity and reliability of the reaction. Here, we report on the results of the detailed study devoted to the dimerization of the primers during PCR. The course and specificity of the reaction were studied on the model DNA templates as well as genomic DNA using primers that form amplifiable heterodimeric structures with different thermodynamic stability. It was confirmed that more than two 3'-overlapping nucleotides cause a considerable accumulation of primer dimers. It turned out that the presence of any DNA promotes the formation of dimers even for primers, which do not tend to nonspecific amplification in the absence of DNA. It was shown that dimerization could not be eliminated by commonly used techniques. Even the use of hot-start DNA polymerases does not prevent PD formation if primers with stable 3'-overlapping are employed. Despite several advantages of PCR with abutting primers, their close disposition has no benefits regarding the formation of PD if low-quality primers are utilized.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
| | - Aizilya A Galimova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
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7
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Yang Z, Le JT, Hutter D, Bradley KM, Overton BR, McLendon C, Benner SA. Eliminating primer dimers and improving SNP detection using self-avoiding molecular recognition systems. Biol Methods Protoc 2020; 5:bpaa004. [PMID: 32395633 PMCID: PMC7200914 DOI: 10.1093/biomethods/bpaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/25/2023] Open
Abstract
Despite its widespread value to molecular biology, the polymerase chain reaction (PCR) encounters modes that unproductively consume PCR resources and prevent clean signals, especially when high sensitivity, high SNP discrimination, and high multiplexing are sought. Here, we show how "self-avoiding molecular recognition systems" (SAMRS) manage such difficulties. SAMRS nucleobases pair with complementary nucleotides with strengths comparable to the A:T pair, but do not pair with other SAMRS nucleobases. This should allow primers holding SAMRS components to avoid primer-primer interactions, preventing primer dimers, allowing more sensitive SNP detection, and supporting higher levels of multiplex PCR. The experiments here examine the PCR performances of primers containing different numbers of SAMRS components placed strategically at different positions, and put these performances in the context of estimates of SAMRS:standard pairing strengths. The impact of these variables on primer dimer formation, the overall efficiency and sensitivity of SAMRS-based PCR, and the value of SAMRS primers when detecting single nucleotide polymorphisms (SNPs) are also evaluated. With appropriately chosen polymerases, SNP discrimination can be greater than the conventional allele-specific PCR, with the further benefit of avoiding primer dimer artifacts. General rules guiding the design of SAMRS-modified primers are offered to support medical research and clinical diagnostics products.
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Affiliation(s)
- Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jennifer T Le
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
| | - Daniel Hutter
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Benjamin R Overton
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
| | - Chris McLendon
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
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8
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PRIMEval: Optimization and screening of multiplex oligonucleotide assays. Sci Rep 2019; 9:19286. [PMID: 31848453 PMCID: PMC6917790 DOI: 10.1038/s41598-019-55883-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/03/2019] [Indexed: 11/08/2022] Open
Abstract
The development of multiplex polymerase chain reaction and microarray assays is challenging due to primer dimer formation, unspecific hybridization events, the generation of unspecific by-products, primer depletion, and thus lower amplification efficiencies. We have developed a software workflow with three underlying algorithms that differ in their use case and specificity, allowing the complete in silico evaluation of such assays on user-derived data sets. We experimentally evaluated the method for the prediction of oligonucleotide hybridization events including resulting products and probes, self-dimers, cross-dimers and hairpins at different experimental conditions. The developed method allows explaining the observed artefacts through in silico WGS data and thermodynamic predictions. PRIMEval is available publicly at https://primeval.ait.ac.at.
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9
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Wagner S, Roberson D, Boland J, Yeager M, Cullen M, Mirabello L, Dunn ST, Walker J, Zuna R, Schiffman M, Wentzensen N. Development of the TypeSeq Assay for Detection of 51 Human Papillomavirus Genotypes by Next-Generation Sequencing. J Clin Microbiol 2019; 57:e01794-18. [PMID: 30814267 PMCID: PMC6498001 DOI: 10.1128/jcm.01794-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/20/2019] [Indexed: 01/11/2023] Open
Abstract
We have developed a new human papillomavirus (HPV) genotyping assay for detection of 51 HPV genotypes by next-generation sequencing (NGS). The TypeSeq assay consists of 3 PCR steps that equalize viral load and each type's amplicon copies prior to genotyping by NGS, thereby maximizing multiple-type sensitivity with minimal sequencing reads. The analytical sensitivity of the TypeSeq assay is 10 copies per reaction for 49 of the 51 types, including 13 high-risk (HR) types. We tested 863 clinical cervical specimens previously evaluated with the Roche Linear Array HPV genotyping test (LA). TypeSeq achieved 94.4% positive agreement with LA for detection of any HR type. Positive agreement was 91.4% and 85.5% for HPV16 and HPV18, respectively. Low-risk (LR) types ranged from 40.0% positive agreement (HPV83) to 90.9% (HPV69). Our unique approach to HPV amplification achieved a multiple-type sensitivity comparable to that of LA, with 83.9% and 84.2% of specimens positive for multiple HPV types by TypeSeq or LA, respectively. A total of 48.2% of specimens showed perfect agreement for all 37 types common to both assays. The simplicity of our open-source TypeSeq assay allows for high-throughput yet scalable processing, with a single technician able to process up to 768 specimens within 3 days. By leveraging NGS sample multiplexing capabilities, the per-sample labor requirements are greatly reduced compared to those of traditional genotyping methods. These features and the broad spectrum of detectable types make TypeSeq highly suitable for a wide range of applications.
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Affiliation(s)
- Sarah Wagner
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Joseph Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - S Terence Dunn
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Joan Walker
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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10
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Johnston AD, Lu J, Ru KL, Korbie D, Trau M. PrimerROC: accurate condition-independent dimer prediction using ROC analysis. Sci Rep 2019; 9:209. [PMID: 30659212 PMCID: PMC6338771 DOI: 10.1038/s41598-018-36612-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 11/23/2018] [Indexed: 12/01/2022] Open
Abstract
To-date systematic testing and comparison of the accuracy of available primer-dimer prediction software has never been conducted, due in part to a lack of tools able to measure the efficacy of Gibbs free energy (ΔG) calculations at predicting dimer formation in PCR. To address this we have developed a novel online tool called PrimerROC (www.primer-dimer.com/roc/), which uses epidemiologically-based Receiver Operating Characteristic (ROC) curves to assess dimer prediction accuracy. Moreover, by integrating PrimerROC with our PrimerDimer prediction software we can determine a ΔG-based dimer-free threshold above which dimer formation is predicted unlikely to occur. Notably, PrimerROC determines this cut-off without any additional information such as salt concentration or annealing temperature, meaning that our PrimerROC method is an assay and condition independent prediction tool. To demonstrate the broad utility of PrimerROC we assessed the performance of seven publically available primer design and dimer analysis tools using a dataset of over 300 primer pairs. We found that our PrimerROC/PrimerDimer software consistently outperforms these other tools and can achieve predictive accuracies greater than 92%. To illustrate its predictive power this method was used in multiplex PCR design to successfully generate four resequencing assays containing up to 126 primers with no observable primer-primer amplification artefacts.
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Affiliation(s)
- Andrew D Johnston
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, 4072, QLD, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Jennifer Lu
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, 4072, QLD, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Ke-Lin Ru
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, 4072, QLD, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Darren Korbie
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, 4072, QLD, Australia. .,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, QLD, Australia.
| | - Matt Trau
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, 4072, QLD, Australia. .,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, QLD, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, QLD, Australia.
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11
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Pel J, Leung A, Choi WWY, Despotovic M, Ung WL, Shibahara G, Gelinas L, Marziali A. Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers. PLoS One 2018; 13:e0208283. [PMID: 30517195 PMCID: PMC6281261 DOI: 10.1371/journal.pone.0208283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/14/2018] [Indexed: 11/18/2022] Open
Abstract
Targeted Next Generation Sequencing (NGS) is being adopted increasingly broadly in many research, commercial and clinical settings. Currently used target capture methods, however, typically require complex and lengthy (sometimes multi-day) workflows that complicates their use in certain applications. In addition, small panels for high sequencing depth applications such as liquid biopsy typically have low on-target rates, resulting in unnecessarily high sequencing cost. We have developed a novel targeted sequencing library preparation method, named Linked Target Capture (LTC), which replaces typical multi-day target capture workflows with a single-day, combined ‘target-capture-PCR’ workflow. This approach uses physically linked capture probes and PCR primers and is expected to work with panel sizes from 100 bp to >10 Mbp. It reduces the time and complexity of the capture workflow, eliminates long hybridization and wash steps and enables rapid library construction and target capture. High on-target read fractions are achievable due to repeated sequence selection in the target-capture-PCR step, thus lowering sequencing cost. We have demonstrated this technology on sample types including cell-free DNA (cfDNA) and formalin-fixed, paraffin-embedded (FFPE) derived DNA, capturing a 35-gene pan-cancer panel, and therein detecting single nucleotide variants, copy number variants, insertions, deletions and gene fusions. With the integration of unique molecular identifiers (UMIs), variants as low as 0.25% abundance were detected, limited by input mass and sequencing depth. Additionally, sequencing libraries were prepared in less than eight hours from extracted DNA to loaded sequencer, demonstrating that LTC holds promise as a broadly applicable tool for rapid, cost-effective and high performance targeted sequencing.
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Affiliation(s)
- Joel Pel
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | - Amy Leung
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | | | | | - W. Lloyd Ung
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | | | - Laura Gelinas
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | - Andre Marziali
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
- University of British Columbia, Department of Physics and Astronomy, Vancouver, British Columbia, Canada
- * E-mail:
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12
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Jiang W, Yue S, He S, Chen C, Liu S, Jiang H, Tong H, Liu X, Wang J, Zhang F, Sun H, Li M, Wang C. New design of probe and central-homo primer pairs to improve TaqMan™ PCR accuracy for HBV detection. J Virol Methods 2018; 254:25-30. [PMID: 29407210 DOI: 10.1016/j.jviromet.2018.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 01/03/2023]
Abstract
Quantitative PCR (qPCR) assay using TaqMan™ probe was widely used in the detection of different nucleic acids. However, this technology has several drawbacks, including false negative results caused by primer-dimer (PD) and false positive issues due to primer-probe aggregations. Here, we designed a modified TaqMan™-Molecular Beacon probe by adding an antisense base and a new type of primer pair named central-homo primer pairs bearing 5-10 bases homologous sequence on the 3' end. Using the HBV qPCR assay as a proof of concept, the new design significantly improved the accuracy of the TaqMan™ qPCR assay for HBV detection. Application of the central-homo primer pair led to significantly delayed Ct values by 5-10 cycles compared with conventional primer design. The modified probe containing an antisense base did not produce any detectable signal in repeating primer-probe aggregation experiments. Furthermore, the use of the central-homo primer pair and the non-competitive internal control could solve the false negative problem caused by PD formation. We validated this customized duplex qPCR system using 208 clinical samples collected from patients in clinic showing accuracy was higher than that of the conventional qPCR method.
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Affiliation(s)
- Wencan Jiang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Suwen Yue
- Beijing Tag Array Molecular Test Co., Ltd, Beijing 100085, People's Republic of China
| | - Shang He
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Chen Chen
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Shanshan Liu
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Hong Jiang
- Beijing Tag Array Molecular Test Co., Ltd, Beijing 100085, People's Republic of China
| | - Hongli Tong
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Xiaoting Liu
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Jianan Wang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Fan Zhang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Huizhen Sun
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Mianyang Li
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China.
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13
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Luo K, Wang Q, Qiu Q, Li X, Jia X, Chen X, Zhang Z, Zheng G, He Z. Simultaneous amplification of exons 18 to 21 of the EGFR gene using 5' tailed primers and a two-stage protocol. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:1-19. [PMID: 29337648 DOI: 10.1080/15257770.2017.1375517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Reduction of non-specific amplification and achievement of efficient amplification of multiple gene fragments under the same reaction condition is the basic goal of PCR diagnosis; however, this is often difficult. This study was conducted to establish a highly specific and effective amplification of the epidermal growth factor receptor (EGFR) gene's exons, 18-21, simultaneously. METHODS The 5'-tailed primers were synthesized by adding 10 to 20 bp of a non-specific sequence to the 5'-terminus of sequence-specific primers (tailless primers). The two-stage protocol consisted of 5-10 cycles of a conventional 3-step cycling, which was then followed by 30-35 cycles of two-step cycling. The exons 18-21 of EGFR gene were amplified in 28 non-small cell lung cancer (NSCLC) patients using an optimized PCR that combined 5' tailed primers with a two-stage protocol. RESULTS The 5' tailed primers exhibited a wider range of suitable annealing temperatures, similar range of primer concentration, similar sensitivity, specificity, and reproducibility, as well as a reduced, non-specific amplification compared with the corresponding tailless primers. The amplification of exons 18-21 of EGFR gene in NSCLC patients revealed that a combination of 5' tailed primers with two-stage protocol (optimized PCR) had a similar PCR success rate (P = 0.873) but had significantly reduced non-specific amplification (P <0.001) compared to conventional PCR. CONCLUSION 5' tailed primers exhibited a wider range of suitable annealing temperatures and improved specificity compared with conventional PCR primers. An optimized PCR was established with 5' tailed primers and a two-stage protocol to amplify exons 18-21 of the EGFR gene in NSCLC patients.
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Affiliation(s)
- Kai Luo
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Qian Wang
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Qinwei Qiu
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Xiemengdan Li
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Xiaoting Jia
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Xiaoliang Chen
- b Cancer Research Institute , Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Zhijie Zhang
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Guopei Zheng
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
| | - Zhiming He
- a Cancer Research Institute , Affiliated Cancer Hospital of Guangzhou Medical University , Guangzhu , Guangdong , P.R. China
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Schoenbrunner NJ, Gupta AP, Young KKY, Will SG. Covalent modification of primers improves PCR amplification specificity and yield. Biol Methods Protoc 2017; 2:bpx011. [PMID: 32161793 PMCID: PMC6994073 DOI: 10.1093/biomethods/bpx011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/31/2017] [Accepted: 11/09/2017] [Indexed: 01/01/2023] Open
Abstract
We report a method for covalent modification of primers that enhances the specificity of PCR and increases the yield of specific amplification products at the end of PCR. The introduction of thermally stable covalent modifications, such as alkyl groups to the exocyclic amines of deoxyadenosine or cytosine residues at the 3'-ends of primers results in enhanced specificity of reactions. This higher specificity can result in greater sensitivity of detection by reducing competition with non-productive reactions. The reduction in the amplification of unintended byproducts is most apparent when both primers are modified at their respective 3'-ends. The T Ms of such modified primers are only slightly affected by the inclusion of these modifiers. The principal mode of action is believed to be driven by the poor enzyme extension of substrates with closely juxtaposed bulky alkyl groups, such as would result from the replication of primer dimer artifact.
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Affiliation(s)
| | | | | | - Stephen G Will
- Research Department, Roche Molecular Systems, Inc., 4300 Hacienda Drive, Pleasanton, CA 94588, USA
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Anglès d'Auriac MB. COMplementary Primer ASymmetric PCR (COMPAS-PCR) Applied to the Identification of Salmo salar, Salmo trutta and Their Hybrids. PLoS One 2016; 11:e0165468. [PMID: 27783658 PMCID: PMC5082663 DOI: 10.1371/journal.pone.0165468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/12/2016] [Indexed: 12/26/2022] Open
Abstract
Avoiding complementarity between primers when designing a PCR assay constitutes a central rule strongly anchored in the mind of the molecular scientist. 3'-complementarity will extend the primers during PCR elongation using one another as template, consequently disabling further possible involvement in traditional target amplification. However, a 5'-complementarity will leave the primers unchanged during PCR cycles, albeit sequestered to one another, therefore also suppressing target amplification. We show that 5'-complementarity between primers may be exploited in a new PCR method called COMplementary-Primer-Asymmetric (COMPAS)-PCR, using asymmetric primer concentrations to achieve target PCR amplification. Moreover, such a design may paradoxically reduce spurious non-target amplification by actively sequestering the limiting primer. The general principles were demonstrated using 5S rDNA direct repeats as target sequences to design a species-specific assay for identifying Salmo salar and Salmo trutta using almost fully complementary primers overlapping the same target sequence. Specificity was enhanced by using 3'-penultimate point mutations and the assay was further developed to enable identification of S. salar x S. trutta hybrids by High Resolution Melt analysis in a 35 min one-tube assay. This small paradigm shift, using highly complementary primers for PCR, should help develop robust assays that previously would not be considered.
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Dellett M, Simpson DA. Considerations for optimization of microRNA PCR assays for molecular diagnosis. Expert Rev Mol Diagn 2016; 16:407-14. [PMID: 26854938 DOI: 10.1586/14737159.2016.1152184] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The remarkable stability of microRNAs in biofluids underlies their potential as biomarkers, but their small size presents challenges for detection by RT-qPCR. The heterogeneity of microRNAs, with each one comprising a series of variants or 'isomiRs', adds additional complexity. Presented here are the key considerations for use of RT-qPCR to measure microRNAs and their isomiRs, with a focus on plasma. Modified nucleotides can be incorporated into primer sequences to enhance affinity and provide increased specificity and sensitivity for RT-qPCR assays. Approaches based upon polyA tailing and use of a common oligo(dT)-based reverse transcription oligonucleotide will detect most isomiRs. Conversely, stem-loop RT oligonucleotides and sequence specific probes can enable detection of specific isomiRs of interest. Next generation sequencing of all the products of a microRNA RT-PCR reaction is a promising new approach for both microRNA quantification and characterization.
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Affiliation(s)
- Margaret Dellett
- a Centre for Experimental Medicine , Queen's University Belfast , Belfast , Northern Ireland , UK
| | - David Arthur Simpson
- a Centre for Experimental Medicine , Queen's University Belfast , Belfast , Northern Ireland , UK
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Drábek J. Surmounting a PCR challenge using a Contradictory matrix from the Theory of Inventive Problem Solving (TRIZ). SPRINGERPLUS 2016; 5:56. [PMID: 26835236 PMCID: PMC4720617 DOI: 10.1186/s40064-015-1577-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 12/01/2015] [Indexed: 11/21/2022]
Abstract
In this paper I tested whether Contradictory Matrix with 40 Inventive Principles, the simplest instrument from the Theory of Inventive Problem Solving (TRIZ), is a useful approach to a real-life PCR scenario. The PCR challenge consisted of standardization of fluorescence melting curve measurements in Competitive Amplification of Differentially Melting Amplicons (CADMA) PCR for multiple targets. Here I describe my way of using the TRIZ Matrix to generate seven alternative solutions from which I can choose the successful solution, consisting of repeated cycles of amplification and melting in a single PCR run.
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Affiliation(s)
- Jiří Drábek
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University, Teaching Hospital Olomouc, Hněvotínská 5, 779 00 Olomouc, The Czech Republic
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