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Storms SM, Shisler J, Nguyen TH, Zuckermann FA, Lowe JF. Lateral flow paired with RT-LAMP: A speedy solution for Influenza A virus detection in swine. Vet Microbiol 2024; 296:110174. [PMID: 38981201 DOI: 10.1016/j.vetmic.2024.110174] [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: 02/16/2024] [Revised: 05/31/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024]
Abstract
Influenza A Virus in swine (IAV-S) is a zoonotic pathogen that is nearly ubiquitous in commercial swine in the USA. Swine possess sialic acid receptors that allow co-infection of human and avian viruses with the potential of pandemic reassortment. We aimed to develop a fast and robust testing method for IAV-S detection on swine farms. Two primers of the RT-LAMP assay were labeled for use in a lateral flow readout. A commercially available lateral flow kit was used to read the amplicon product. With a runtime of ∼ 45 minutes, the limit of detection for the assay is comparable with an RT-qPCR Cq less than 35, with a sensitivity of 83.5 % and a specificity of 89.6 %. This assay allows veterinarians and producers with limited access to diagnostic services to perform and detect Matrix gene amplification on-site with low equipment costs. The time from sample collection to detection is less than one hour, making this method an accessible, convenient, and affordable tool to prevent the spread of zoonotic disease.
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Affiliation(s)
- Suzanna M Storms
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, 2001 South Lincoln Ave, Urbana, IL 61802, USA.
| | - Joanna Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign. Chemical and Life Sciences Laboratory, B103 CLSL, MC-110, S Goodwin Ave, Urbana, IL 61801, USA.
| | - Thanh H Nguyen
- Department of Civil Engineering, University of Illinois at Urbana-Champaign, 205 N Mathews Ave, Urbana, IL 61801, USA.
| | - Federico A Zuckermann
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 South Lincoln Ave, Urbana, IL 61802, USA.
| | - James F Lowe
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, 2001 South Lincoln Ave, Urbana, IL 61802, USA.
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2
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Ming Z, Chen Q, Chen N, Lin M, Liu N, Hu J, Xiao X. Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection. Anal Chim Acta 2019; 1075:137-143. [PMID: 31196419 DOI: 10.1016/j.aca.2019.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 10/26/2022]
Abstract
Nucleic acid probes are very useful tools in biological and medical science. However, the essential sensing mechanism of nucleic acid probes was prone to the interference of surrounding sequences. Especially when the target sequences formed secondary structures such as hairpin or quadruplex, the nucleic acid probes were hindered from hybridizing with target strands, greatly disabled the function of probes. Herein, we have established an Open strand based strategy for eliminating the influence of secondary structures on the performance of nucleic acid probes. The strategy was general toward different lengths, secondary structures and sequences of the targeting strand, and we found that the improvement was higher when the secondary structure of the targeting strand was more complicated. Experiments on synthetic single stranded DNA and real clinical genomic DNA samples were conducted for low abundance mutation detection, and the limit of detection for TERT-C228T and BRCA2 rs80359065 mutations could be 0.02% and 0.05% respectively, demonstrating the clinical practicability of our proposed strategy in low abundance mutation detection.
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Affiliation(s)
- Zhihao Ming
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Qianzhi Chen
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Chen
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Meng Lin
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Liu
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Junbo Hu
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China.
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Houssin T, Cramer J, Grojsman R, Bellahsene L, Colas G, Moulet H, Minnella W, Pannetier C, Leberre M, Plecis A, Chen Y. Ultrafast, sensitive and large-volume on-chip real-time PCR for the molecular diagnosis of bacterial and viral infections. LAB ON A CHIP 2016; 16:1401-11. [PMID: 26952334 DOI: 10.1039/c5lc01459j] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
To control future infectious disease outbreaks, like the 2014 Ebola epidemic, it is necessary to develop ultrafast molecular assays enabling rapid and sensitive diagnoses. To that end, several ultrafast real-time PCR systems have been previously developed, but they present issues that hinder their wide adoption, notably regarding their sensitivity and detection volume. An ultrafast, sensitive and large-volume real-time PCR system based on microfluidic thermalization is presented herein. The method is based on the circulation of pre-heated liquids in a microfluidic chip that thermalize the PCR chamber by diffusion and ultrafast flow switches. The system can achieve up to 30 real-time PCR cycles in around 2 minutes, which makes it the fastest PCR thermalization system for regular sample volume to the best of our knowledge. After biochemical optimization, anthrax and Ebola simulating agents could be respectively detected by a real-time PCR in 7 minutes and a reverse transcription real-time PCR in 7.5 minutes. These detections are respectively 6.4 and 7.2 times faster than with an off-the-shelf apparatus, while conserving real-time PCR sample volume, efficiency, selectivity and sensitivity. The high-speed thermalization also enabled us to perform sharp melting curve analyses in only 20 s and to discriminate amplicons of different lengths by rapid real-time PCR. This real-time PCR microfluidic thermalization system is cost-effective, versatile and can be then further developed for point-of-care, multiplexed, ultrafast and highly sensitive molecular diagnoses of bacterial and viral diseases.
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Affiliation(s)
- Timothée Houssin
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France. and École Normale Supérieure-PSL Research University, 24 rue Lhomond, 75005, Paris, France.
| | - Jérémy Cramer
- École Normale Supérieure-PSL Research University, 24 rue Lhomond, 75005, Paris, France. and Cherry Biotech, Université de Rennes 1, Campus Santé, Bât8, Et2, 2 Av. du Pr. Léon Bernard, CS 34317, 35043 Rennes Cedex, France.
| | - Rébecca Grojsman
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France.
| | - Lyes Bellahsene
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France.
| | - Guillaume Colas
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France.
| | - Hélène Moulet
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France.
| | - Walter Minnella
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France.
| | | | - Maël Leberre
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France.
| | - Adrien Plecis
- Elvesys - Innovation Center, 83 avenue Philippe Auguste, 75011, Paris, France.
| | - Yong Chen
- École Normale Supérieure-PSL Research University, 24 rue Lhomond, 75005, Paris, France.
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Murray JL, Hu P, Shafer DA. Seven novel probe systems for real-time PCR provide absolute single-base discrimination, higher signaling, and generic components. J Mol Diagn 2015; 16:627-38. [PMID: 25307756 DOI: 10.1016/j.jmoldx.2014.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/14/2014] [Accepted: 06/11/2014] [Indexed: 12/19/2022] Open
Abstract
We have developed novel probe systems for real-time PCR that provide higher specificity, greater sensitivity, and lower cost relative to dual-labeled probes. The seven DNA Detection Switch (DDS)-probe systems reported here employ two interacting polynucleotide components: a fluorescently labeled probe and a quencher antiprobe. High-fidelity detection is achieved with three DDS designs: two internal probes (internal DDS and Flip probes) and a primer probe (ZIPR probe), wherein each probe is combined with a carefully engineered, slightly mismatched, error-checking antiprobe. The antiprobe blocks off-target detection over a wide range of temperatures and facilitates multiplexing. Other designs (Universal probe, Half-Universal probe, and MacMan probe) use generic components that enable low-cost detection. Finally, single-molecule G-Force probes employ guanine-mediated fluorescent quenching by forming a hairpin between adjacent C-rich and G-rich sequences. Examples provided show how these probe technologies discriminate drug-resistant Mycobacterium tuberculosis mutants, Escherichia coli O157:H7, oncogenic EGFR deletion mutations, hepatitis B virus, influenza A/B strains, and single-nucleotide polymorphisms in the human VKORC1 gene.
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Affiliation(s)
| | - Peixu Hu
- GeneTAG Technology, Inc., Atlanta, Georgia; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - David A Shafer
- GeneTAG Technology, Inc., Atlanta, Georgia; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia.
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Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta 2014; 439:231-50. [PMID: 25451956 DOI: 10.1016/j.cca.2014.10.017] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/28/2022]
Abstract
Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.
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Affiliation(s)
- E Navarro
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - G Serrano-Heras
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - M J Castaño
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - J Solera
- Internal Medicine Department, General University Hospital, Hermanos Falcó 37, 02006 Albacete, Spain.
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Zhang J, Nie H, Wu Z, Yang Z, Zhang L, Xu X, Huang S. Self-catalytic growth of unmodified gold nanoparticles as conductive bridges mediated gap-electrical signal transduction for DNA hybridization detection. Anal Chem 2013; 86:1178-85. [PMID: 24313362 DOI: 10.1021/ac4032675] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simple and sensitive gap-electrical biosensor based on self-catalytic growth of unmodified gold nanoparticles (AuNPs) as conductive bridges has been developed for amplifying DNA hybridization events. In this strategy, the signal amplification degree of such conductive bridges is closely related to the variation of the glucose oxidase (GOx)-like catalytic activity of AuNPs upon interaction with single- and double-stranded DNA (ssDNA and dsDNA), respectively. In the presence of target DNA, the obtained dsDNA product cannot adsorb onto the surface of AuNPs due to electrostatic interaction, which makes the unmodified AuNPs exhibit excellent GOx-like catalytic activity. Such catalytic activity can enlarge the diameters of AuNPs in the glucose and HAuCl4 solution and result in a connection between most of the AuNPs and a conductive gold film formation with a dramatically increased conductance. For the control sample, the catalytic activity sites of AuNPs are fully blocked by ssDNA due to the noncovalent interaction between nucleotide bases and AuNPs. Thus, the growth of the assembled AuNPs will not happen and the conductance between microelectrodes will be not changed. Under the optimal experimental conditions, the developed strategy exhibited a sensitive response to target DNA with a high signal-to-noise ratio. Moreover, this strategy was also demonstrated to provide excellent differentiation ability for single-nucleotide polymorphism. Such performances indicated the great potential of this label-free electrical strategy for clinical diagnostics and genetic analysis under real biological sample separation.
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Affiliation(s)
- Jing Zhang
- Nanomaterials and Chemistry Key Laboratory, College of Chemistry and Chemical Engineering, Wenzhou University , Wenzhou, Zhejiang 325027, People's Republic of China
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Kutyavin IV. Use of extremely short Förster resonance energy transfer probes in real-time polymerase chain reaction. Nucleic Acids Res 2013; 41:e191. [PMID: 24013564 PMCID: PMC3814350 DOI: 10.1093/nar/gkt782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Described in the article is a new approach for the sequence-specific detection of nucleic acids in real-time polymerase chain reaction (PCR) using fluorescently labeled oligonucleotide probes. The method is based on the production of PCR amplicons, which fold into dumbbell-like secondary structures carrying a specially designed ‘probe-luring’ sequence at their 5′ ends. Hybridization of this sequence to a complementary ‘anchoring’ tail introduced at the 3′ end of a fluorescent probe enables the probe to bind to its target during PCR, and the subsequent probe cleavage results in the florescence signal. As it has been shown in the study, this amplicon-endorsed and guided formation of the probe-target duplex allows the use of extremely short oligonucleotide probes, up to tetranucleotides in length. In particular, the short length of the fluorescent probes makes possible the development of a ‘universal’ probe inventory that is relatively small in size but represents all possible sequence variations. The unparalleled cost-effectiveness of the inventory approach is discussed. Despite the short length of the probes, this new method, named Angler real-time PCR, remains highly sequence specific, and the results of the study indicate that it can be effectively used for quantitative PCR and the detection of polymorphic variations.
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Yu D, Chen Y, Wu S, Wang B, Tang YW, Li L. Simultaneous detection and differentiation of human papillomavirus genotypes 6, 11, 16 and 18 by AllGlo quadruplex quantitative PCR. PLoS One 2012; 7:e48972. [PMID: 23152833 PMCID: PMC3494670 DOI: 10.1371/journal.pone.0048972] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 10/03/2012] [Indexed: 12/12/2022] Open
Abstract
Background Human papillomaviruses (HPV) are classified into high-risk HPV and low-risk HPV. The most common high-risk HPV types in cervical cancer are HPV 16 and 18, and the most common low-risk types causing genital warts are HPV 6 and HPV 11. In this study, applying novel AllGlo fluorescent probes, we established a quadruplex quantitative PCR method to simultaneously detect and differentiate HPV 6, 11, 16 and 18 in a single tube. Methods The specificity, the sensitivity, the detection limit, the reproducibility and the standard curve of this method were examined. Finally, clinical samples that had been tested previously by TaqMan PCR and HPV GenoArray (GA) test were used to verify the accuracy and sensitivity of the method. Results The assay has a sensitivity of 101 to 102 copies/test and a linear detection range from 101 to 108 copies/test. The mean amplification efficiencies for HPV 6, 11, 16, and 18 were 0.97, 1.10, 0.93 and 1.20, respectively, and the mean correlation coefficient (r2) of each standard curve was above 0.99 for plasmid templates ranging from 103 to 107 copies/test. There was 100% agreement between the AllGlo quadruplex quantitative PCR, HPV GA test and TaqMan uniplex qPCR methods. Conclusions AllGlo quadruplex quantitative PCR in a single tube has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, and a wide linear range of detection. The convenient single tube format makes this assay a powerful tool for the studies of mixed infections by multiple pathogens, viral typing and viral load quantification.
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Affiliation(s)
- Daojun Yu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Clinical Laboratories, Hangzhou First People’s Hospital, Hangzhou, China
| | - Yu Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shenghai Wu
- Department of Clinical Laboratories, Hangzhou First People’s Hospital, Hangzhou, China
| | - Baohong Wang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi-Wei Tang
- Clinical Microbiology Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Lanjuan Li
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- * E-mail:
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10
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Liu M, Yuan M, Lou X, Mao H, Zheng D, Zou R, Zou N, Tang X, Zhao J. Label-free optical detection of single-base mismatches by the combination of nuclease and gold nanoparticles. Biosens Bioelectron 2011; 26:4294-300. [DOI: 10.1016/j.bios.2011.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 04/07/2011] [Accepted: 04/07/2011] [Indexed: 11/16/2022]
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12
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Xie P, Sayers JR. A model for transition of 5'-nuclease domain of DNA polymerase I from inert to active modes. PLoS One 2011; 6:e16213. [PMID: 21264264 PMCID: PMC3021548 DOI: 10.1371/journal.pone.0016213] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 12/15/2010] [Indexed: 12/27/2022] Open
Abstract
Bacteria contain DNA polymerase I (PolI), a single polypeptide chain consisting of ∼930 residues, possessing DNA-dependent DNA polymerase, 3′-5′ proofreading and 5′-3′ exonuclease (also known as flap endonuclease) activities. PolI is particularly important in the processing of Okazaki fragments generated during lagging strand replication and must ultimately produce a double-stranded substrate with a nick suitable for DNA ligase to seal. PolI's activities must be highly coordinated both temporally and spatially otherwise uncontrolled 5′-nuclease activity could attack a nick and produce extended gaps leading to potentially lethal double-strand breaks. To investigate the mechanism of how PolI efficiently produces these nicks, we present theoretical studies on the dynamics of two possible scenarios or models. In one the flap DNA substrate can transit from the polymerase active site to the 5′-nuclease active site, with the relative position of the two active sites being kept fixed; while the other is that the 5′-nuclease domain can transit from the inactive mode, with the 5′-nuclease active site distant from the cleavage site on the DNA substrate, to the active mode, where the active site and substrate cleavage site are juxtaposed. The theoretical results based on the former scenario are inconsistent with the available experimental data that indicated that the majority of 5′-nucleolytic processing events are carried out by the same PolI molecule that has just extended the upstream primer terminus. By contrast, the theoretical results on the latter model, which is constructed based on available structural studies, are consistent with the experimental data. We thus conclude that the latter model rather than the former one is reasonable to describe the cooperation of the PolI's polymerase and 5′-3′ exonuclease activities. Moreover, predicted results for the latter model are presented.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Jon R. Sayers
- Department of Infection and Immunity, Krebs Institute, University of Sheffield Medical School, Sheffield, United Kingdom
- * E-mail:
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Pajič T. Factor V Leiden and FII 20210 testing in thromboembolic disorders. Clin Chem Lab Med 2010; 48 Suppl 1:S79-87. [PMID: 21091236 DOI: 10.1515/cclm.2010.372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Factor V Leiden and prothrombin (F2) c.20210G>A mutation detection are very important in order to define the increased relative risk for venous thromboembolism in selected patients. Use of DNA-based methods to detect both mutations has become widely available in clinical diagnostic laboratories, including fluorescence-based quantitative real-time PCR (qPCR). The latter is a rapid, simple, robust and reliable method to identify genotypes of interest. There are several chemistries used for qPCR; this article describes their principles and applicability for Factor V Leiden and prothrombin (F2) c.20210G>A mutation detection.
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Affiliation(s)
- Tadej Pajič
- Department of Haematology, Division of Internal Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
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Kutyavin IV. Use of base modifications in primers and amplicons to improve nucleic acids detection in the real-time snake polymerase chain reaction. Assay Drug Dev Technol 2010; 9:58-68. [PMID: 21050073 DOI: 10.1089/adt.2010.0303] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The addition of relatively short flap sequence at the 5'-end of one of the polymerase chain reaction (PCR) primers considerably improves performance of real-time assays based on 5'-nuclease activity. This new technology, called Snake, was shown to supersede the conventional methods like TaqMan, Molecular Beacons, and Scorpions in the signal productivity and discrimination of target polymorphic variations as small as single nucleotides. The present article describes a number of reaction conditions and methods that allow further improvement of the assay performance. One of the identified approaches is the use of duplex-destabilizing modifications such as deoxyinosine and deoxyuridine in the design of the Snake primers. This approach was shown to solve the most serious problem associated with the antisense amplicon folding and cleavage. As a result, the method permits the use of relatively long-in this study-14-mer flap sequences. Investigation also revealed that only the 5'-segment of the flap requires the deoxyinosine/deoxyuridine destabilization, whereas the 3'-segment is preferably left unmodified or even stabilized using 2-amino deoxyadenosine d(2-amA) and 5-propynyl deoxyuridine d(5-PrU) modifications. The base-modification technique is especially effective when applied in combination with asymmetric three-step PCR. The most valuable discovery of the present study is the effective application of modified deoxynucleoside 5'-triphosphates d(2-amA)TP and d(5-PrU)TP in Snake PCR. This method made possible the use of very short 6-8-mer 5'-flap sequences in Snake primers.
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Affiliation(s)
- Igor V Kutyavin
- Perpetual Genomics, 18943 203rd Ave. NE, Woodinville, WA 98077, USA.
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