1
|
Piri-Gharaghie T, Ghajari G, Lahijani NT, Pecho RDC, Hussam F, Castillo-Acobo RY, Aghassizadeh-Sherbaf M. Simultaneous and rapid detection of avian respiratory diseases of small poultry using multiplex reverse transcription-Polymerase Chain Reaction assay. Poult Sci 2023; 102:102852. [PMID: 37354617 PMCID: PMC10404739 DOI: 10.1016/j.psj.2023.102852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/26/2023] Open
Abstract
Major viral infections, such as Newcastle disease virus, infectious bronchitis virus, avian influenza virus, and infectious bursal disease virus, inflict significant injury to small poultry and tremendous economic damage to the poultry sector. This research aims to develop a multiplex reverse transcriptase polymerase chain reaction (m-RT-PCR) approach to simultaneously determine these important viral pathogens. The conserved segment of various viral genetic sequences was used to design and synthesize specific primers. Moreover, as positive controls, recombinant vectors were synthesized in this investigation. The d-optimal approach was used to improve PCR conditions in this investigation. Positive controls and clinical samples were used to assess the m-PCR assay's specificity, sensitivity, repeatability, and reproducibility. According to the sensitivity test findings, the m-PCR technique could generate the 8 target genes from viral genomes using 1 × 102. In addition, 8 viral pathogens were detected from the infected samples. The findings also suggest that live animal oral swabs were not significantly different from tissue sampling of a dead animal (P < 0.05), and this kit had a high sensitivity for analyzing both types of samples. The suggested m-PCR test may detect and evaluate viral infection in birds with excellent specificity, sensitivity, and throughput.
Collapse
Affiliation(s)
- Tohid Piri-Gharaghie
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran; Department of Biology, Faculty of Biological Sciences, East Tehran Branch, Islamic Azad University, Tehran, Iran.
| | - Ghazal Ghajari
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | | | - Fahdil Hussam
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | | | - Mona Aghassizadeh-Sherbaf
- Department of Biology, Faculty of Basic Sciences, Islamic Azad University, Tehran East Branch, Tehran, Iran
| |
Collapse
|
2
|
Polymerase chain reaction-based snake origin tracing in commercial venom crystals by targeting the mitochondrial D-loop. Toxicon 2022; 219:106933. [PMID: 36174762 DOI: 10.1016/j.toxicon.2022.106933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 12/10/2022]
Abstract
Snake venom is a valuable raw material for numerous therapeutic formulations because of its life-saving pharmacological potential. However, due to their high price, fake "snake venoms" have captured a significant portion of the global market, and there is currently no reliable reported DNA-based method available for quickly distinguishing between fakes and originals. Therefore, in this study, a set of newly designed snake-specific universal primers targeting mitochondrial D-loop fragments were employed to detect snake origins in commercial venom crystals by only simplex polymerase chain reaction analysis. Under the optimal thermal cycling conditions, only the 145-149 bp snake-specific mitochondrial D-loop fragments from pure and mixed backgrounds were amplified by the newly designed primers. Specificity was achieved by confirming no DNA amplification occurred in the DNA admixture of ten different chordates, and universality by individual DNA amplification of nine different snakes. The primers that efficiently amplified the minimum mitochondrial DNA contained in a total of 10-2 ng in a 10.0 μl reaction were also successfully able to detect the snake origin in commercial cobra venom crystals. These findings suggest that the newly designed primers can be used to differentiate the original and fake commercial snake venom crystals in order to achieve the highest standards of snake venom-based medications through amplifying the snake-specific mitochondrial D-loop fragments.
Collapse
|
3
|
Li J, Li J, Wei Y, Xu S, Xiong S, Li D, Wang S, Liang A. Application of family-specific primers in multiplex real-time PCR for meat categories screening. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
4
|
Alcántara R, Peñaranda K, Mendoza-Rojas G, Nakamoto JA, Dueñas E, Alvarez D, Adaui V, Milón P. UnCovid: A versatile, low-cost, and open-source protocol for SARS-CoV-2 RNA detection. STAR Protoc 2021; 2:100878. [PMID: 34604812 PMCID: PMC8463329 DOI: 10.1016/j.xpro.2021.100878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Here, we describe a detailed step-by-step protocol to detect SARS-CoV-2 RNA using RT-PCR-mediated amplification and CRISPR/Cas-based visualization. The optimized assay uses basic molecular biology equipment such as conventional thermocyclers and transilluminators for qualitative detection. Alternatively, a fluorescence plate reader can be used for quantitative measurements. The protocol detects two regions of the SARS-CoV-2 genome in addition to the human RNaseP sample control. Aiming to reach remote regions, this work was developed to use the portable molecular workstation from BentoLab. For complete details on the use and execution of this protocol, please refer to Alcántara et al., 2021.
Collapse
Affiliation(s)
- Roberto Alcántara
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Katherin Peñaranda
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Gabriel Mendoza-Rojas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Jose A. Nakamoto
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Eva Dueñas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Daniela Alvarez
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Vanessa Adaui
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Pohl Milón
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| |
Collapse
|
5
|
Villanueva-Segura K, Ponce-Garcia G, Lopez-Monroy B, Mora-Jasso E, Perales L, Gonzalez-Santillan FJ, Ontiveros-Zapata K, Davila-Barboza JA, Flores AE. Multiplex PCR for simultaneous genotyping of kdr mutations V410L, V1016I and F1534C in Aedes aegypti (L.). Parasit Vectors 2020; 13:325. [PMID: 32586378 PMCID: PMC7318494 DOI: 10.1186/s13071-020-04193-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 06/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Knockdown resistance (kdr) is the main mechanism that confers resistance to pyrethroids and DDT. This is a product of non-synonymous mutations in the voltage-gated sodium channel (vgsc) gene, and these mutations produce a change of a single amino acid which reduces the affinity of the target site for the insecticide molecule. In Mexico, V410L, V1016I and F1534C mutations are common in pyrethroid-resistant Aedes aegypti (L.) populations. METHODS A multiplex PCR was developed to detect the V410L, V1016I and F1534C mutations in Ae. aegypti. The validation of the technique was carried out by DNA sequencing using field populations previously characterized for the three mutations through allele-specific PCR (AS-PCR) and with different levels of genotypic frequencies. RESULTS The standardized protocol for multiplex end-point PCR was highly effective in detecting 15 genotypes considering the three mutations V410L, V1106I and F1534C, in 12 field populations of Ae. aegypti from Mexico. A complete concordance with AS-PCR and DNA sequencing was found for the simultaneous detection of the three kdr mutations. CONCLUSIONS Our diagnostic method is highly effective for the simultaneous detection of V410L, V1016I and F1534C, when they co-occur. This technique represents a viable alternative to complement and strengthen current monitoring and resistance management strategies against Ae. aegypti.
Collapse
Affiliation(s)
- Karina Villanueva-Segura
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Gustavo Ponce-Garcia
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Beatriz Lopez-Monroy
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Esteban Mora-Jasso
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Lucia Perales
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Francisco J Gonzalez-Santillan
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Kevin Ontiveros-Zapata
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Jesus A Davila-Barboza
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Adriana E Flores
- Universidad Autonoma de Nuevo Leon (UANL), Av, Universidad s/n Cd. Universitaria, 66455, San Nicolas de los Garza, N.L., Mexico.
| |
Collapse
|
6
|
Yao M, Zhang X, Gao Y, Song S, Xu D, Yan L. Development and application of multiplex PCR method for simultaneous detection of seven viruses in ducks. BMC Vet Res 2019; 15:103. [PMID: 30935399 PMCID: PMC6444421 DOI: 10.1186/s12917-019-1820-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/25/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Major viruses, including duck-origin avian influenza virus, duck-origin Newcastle disease virus, novel duck parvovirus, duck hepatitis A virus, duck Tembusu virus, fowl adenovirus, and duck enteritis virus, pose great harm to ducks and cause enormous economic losses to duck industry. This study aims to establish a multiplex polymerase chain reaction (m-PCR) method for simultaneous detection of these seven viruses. RESULTS Specific primers were designed and synthesized according to the conserved region of seven viral gene sequences. Then, seven recombinant plasmids, as the positive controls, were reconstructed in this study. Within the study, D-optimal design was adopted to optimize PCR parameters. The optimum parameters for m-PCR were annealing temperature at 57 °C, Mg2+ concentration at 4 mM, Taq DNA polymerase concentration at 0.05 U/μL, and dNTP concentration at 0.32 mM. With these optimal parameters, the m-PCR method produced neither cross-reactions among these seven viruses nor nonspecific reactions with other common waterfowl pathogens. The detection limit of m-PCR for each virus was 1 × 104 viral DNA copies/μL. In addition, the m-PCR method could detect a combination of several random viruses in co-infection analysis. Finally, the m-PCR method was successfully applied to clinical samples, and the detection results were consistent with uniplex PCR. CONCLUSION Given its rapidity, specificity, sensitivity, and convenience, the established m-PCR method is feasible for simultaneous detection of seven duck-infecting viruses and can be applied to clinical diagnosis of viral infection in ducks.
Collapse
Affiliation(s)
- Ming Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiyu Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunfei Gao
- Nanjing Tianbang Bio-Industry co., LTD, Nanjing, 211102, China
| | - Suquan Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danning Xu
- Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Zhongkai University of Agricultural and Engineering, Guangzhou, 510225, China.
| | - Liping Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China. .,Jiangsu Detection Center of Terrestrial Wildlife Disease, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
7
|
Marques CA, Tiengwe C, Lemgruber L, Damasceno JD, Scott A, Paape D, Marcello L, McCulloch R. Diverged composition and regulation of the Trypanosoma brucei origin recognition complex that mediates DNA replication initiation. Nucleic Acids Res 2016; 44:4763-84. [PMID: 26951375 PMCID: PMC4889932 DOI: 10.1093/nar/gkw147] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/01/2016] [Indexed: 01/14/2023] Open
Abstract
Initiation of DNA replication depends upon recognition of genomic sites, termed origins, by AAA+ ATPases. In prokaryotes a single factor binds each origin, whereas in eukaryotes this role is played by a six-protein origin recognition complex (ORC). Why eukaryotes evolved a multisubunit initiator, and the roles of each component, remains unclear. In Trypanosoma brucei, an ancient unicellular eukaryote, only one ORC-related initiator, TbORC1/CDC6, has been identified by sequence homology. Here we show that three TbORC1/CDC6-interacting factors also act in T. brucei nuclear DNA replication and demonstrate that TbORC1/CDC6 interacts in a high molecular complex in which a diverged Orc4 homologue and one replicative helicase subunit can also be found. Analysing the subcellular localization of four TbORC1/CDC6-interacting factors during the cell cycle reveals that one factor, TbORC1B, is not a static constituent of ORC but displays S-phase restricted nuclear localization and expression, suggesting it positively regulates replication. This work shows that ORC architecture and regulation are diverged features of DNA replication initiation in T. brucei, providing new insight into this key stage of eukaryotic genome copying.
Collapse
Affiliation(s)
- Catarina A Marques
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Calvin Tiengwe
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Leandro Lemgruber
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Jeziel D Damasceno
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Alan Scott
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Daniel Paape
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Lucio Marcello
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| |
Collapse
|
8
|
Kimura Y, Soma T, Kasahara N, Delobel D, Hanami T, Tanaka Y, de Hoon MJL, Hayashizaki Y, Usui K, Harbers M. Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays. PLoS One 2016; 11:e0146950. [PMID: 26863543 PMCID: PMC4749234 DOI: 10.1371/journal.pone.0146950] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 12/22/2015] [Indexed: 01/13/2023] Open
Abstract
Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.
Collapse
Affiliation(s)
- Yasumasa Kimura
- K.K. DNAFORM, 75–1, Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0046, Japan
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Takahiro Soma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Naoko Kasahara
- RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Diane Delobel
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Takeshi Hanami
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Yuki Tanaka
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Michiel J. L. de Hoon
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine & Diagnosis Innovation Program, 2–1 Hirosawa, Wako-shi, Saitama, 351–0198, Japan
| | - Kengo Usui
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
- RIKEN Preventive Medicine & Diagnosis Innovation Program, 2–1 Hirosawa, Wako-shi, Saitama, 351–0198, Japan
| | - Matthias Harbers
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| |
Collapse
|
9
|
Marques CA, Dickens NJ, Paape D, Campbell SJ, McCulloch R. Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe. Genome Biol 2015; 16:230. [PMID: 26481451 PMCID: PMC4612428 DOI: 10.1186/s13059-015-0788-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/21/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania. RESULTS Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins. CONCLUSIONS The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.
Collapse
Affiliation(s)
- Catarina A Marques
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Nicholas J Dickens
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Daniel Paape
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Samantha J Campbell
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
| |
Collapse
|
10
|
Daher RK, Stewart G, Boissinot M, Boudreau DK, Bergeron MG. Influence of sequence mismatches on the specificity of recombinase polymerase amplification technology. Mol Cell Probes 2014; 29:116-21. [PMID: 25481659 DOI: 10.1016/j.mcp.2014.11.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 11/28/2022]
Abstract
Recombinase polymerase amplification (RPA) technology relies on three major proteins, recombinase proteins, single-strand binding proteins, and polymerases, to specifically amplify nucleic acid sequences in an isothermal format. The performance of RPA with respect to sequence mismatches of closely-related non-target molecules is not well documented and the influence of the number and distribution of mismatches in DNA sequences on RPA amplification reaction is not well understood. We investigated the specificity of RPA by testing closely-related species bearing naturally occurring mismatches for the tuf gene sequence of Pseudomonas aeruginosa and/or Mycobacterium tuberculosis and for the cfb gene sequence of Streptococcus agalactiae. In addition, the impact of the number and distribution of mismatches on RPA efficiency was assessed by synthetically generating 14 types of mismatched forward primers for detecting five bacterial species of high diagnostic relevance such as Clostridium difficile, Staphylococcus aureus, S. agalactiae, P. aeruginosa, and M. tuberculosis as well as Bacillus atropheus subsp. globigii for which we use the spores as internal control in diagnostic assays. A total of 87 mismatched primers were tested in this study. We observed that target specific RPA primers with mismatches (n > 1) at their 3'extrimity hampered RPA reaction. In addition, 3 mismatches covering both extremities and the center of the primer sequence negatively affected RPA yield. We demonstrated that the specificity of RPA was multifactorial. Therefore its application in clinical settings must be selected and validated a priori. We recommend that the selection of a target gene must consider the presence of closely-related non-target genes. It is advisable to choose target regions with a high number of mismatches (≥36%, relative to the size of amplicon) with respect to closely-related species and the best case scenario would be by choosing a unique target gene.
Collapse
Affiliation(s)
- Rana K Daher
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), CHUL, 2705, Boul. Laurier, RC 709, Québec, Québec, G1V 4G2, Canada; Département de microbiologie-immunologie, faculté de médecine, Université Laval, 1045 Avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Gale Stewart
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), CHUL, 2705, Boul. Laurier, RC 709, Québec, Québec, G1V 4G2, Canada
| | - Maurice Boissinot
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), CHUL, 2705, Boul. Laurier, RC 709, Québec, Québec, G1V 4G2, Canada
| | - Dominique K Boudreau
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), CHUL, 2705, Boul. Laurier, RC 709, Québec, Québec, G1V 4G2, Canada
| | - Michel G Bergeron
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), CHUL, 2705, Boul. Laurier, RC 709, Québec, Québec, G1V 4G2, Canada.
| |
Collapse
|
11
|
Poritz MA, Ririe KM. Getting things backwards to prevent primer dimers. J Mol Diagn 2014; 16:159-62. [PMID: 24457120 DOI: 10.1016/j.jmoldx.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 12/30/2013] [Accepted: 01/09/2014] [Indexed: 02/04/2023] Open
Abstract
This Commentary highlights the article by Satterfield that describes a new class of primer technology-cooperative primers, which prevent primer-dimer amplification.
Collapse
|