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Detection of low-abundance point mutations by competitive strand assisted endonuclease IV signal amplification system. Curr Med Sci 2017; 37:803-806. [PMID: 29058299 DOI: 10.1007/s11596-017-1808-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/11/2017] [Indexed: 10/18/2022]
Abstract
Genetic mutations are important molecular biomarkers for cancer diagnosis and surveillance. Therefore, the development of methods for mutation detection characterized with straightforward, highly specific and sensitive to low-level mutations within various sequence contexts is extremely needed. Although some of the currently available methods have shown very encouraging results, their discrimination efficiency is still very low. Herein, we demonstrate a fluorescent probe coupled with blocker and property of melting temperature discrimination, which is able to identify the presence of known or unknown single-base variations at abundances down to 0.1% within 20 min. The discrimination factors between the perfect-match target and single-base mismatched target are determined to be 10.15-38.48. The method is sequence independent, which assures a wide range of application. The new method would be an ideal choice for high-throughput in vitro diagnosis and precise clinical treatment.
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2
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Yu Y, Wan P, Cao Y, Zhang W, Chen J, Tan L, Wang Y, Sun Z, Zhang Q, Wan Y, Zhu Y, Liu F, Wu K, Liu Y, Wu J. Hepatitis B Virus e Antigen Activates the Suppressor of Cytokine Signaling 2 to Repress Interferon Action. Sci Rep 2017; 7:1729. [PMID: 28496097 PMCID: PMC5431827 DOI: 10.1038/s41598-017-01773-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/31/2017] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) infection causes acute hepatitis B (AHB), chronic hepatitis B (CHB), liver cirrhosis (LC), and eventually hepatocellular carcinoma (HCC). The presence of hepatitis B e antigen (HBeAg) in the serum generally indicates ongoing viral replication and disease progression. However, the mechanism by which HBeAg regulates HBV infection remains unclear. Interferons (IFNs) are pleiotropic cytokines that participate in host innate immunity. After binding to receptors, IFNs activate the JAK/STAT pathway to stimulate expression of IFN-stimulated genes (ISGs), leading to induction of antiviral responses. Here, we revealed that HBeAg represses IFN/JAK/STAT signaling to facilitate HBV replication. Initially, HBeAg stimulates the expression of suppressor of cytokine signaling 2 (SOCS2). Subsequently, SOCS2 impairs IFN/JAK/STAT signaling through reducing the stability of tyrosine kinase 2 (TYK2), downregulating the expression of type I and III IFN receptors, attenuating the phosphorylation and nucleus translocation of STAT1. Finally, SOCS2 inhibits the expression of ISGs, which leads to the repression of IFN action and facilitation of viral replication. These results demonstrate an important role of HBeAg in the regulation of IFN action, and provide a possible molecular mechanism by which HBV resists the IFN therapy and maintains persistent infection.
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Affiliation(s)
- Yi Yu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China.,Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Pin Wan
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Yanhua Cao
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Wei Zhang
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Junbo Chen
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Li Tan
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Yan Wang
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Zhichen Sun
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Qi Zhang
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Yushun Wan
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Ying Zhu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Fang Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Kailang Wu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China.
| | - Yingle Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China.
| | - Jianguo Wu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, 430071, China.
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Tu WH, Lv Y, Zhang YM, Hou W, Wang JY, Zhang YJ, Liu HY, Zhu HX, Qin YL, Mao RC, Zhang JM. Precore/basal core promoter mutants quantification throughout phases of hepatitis B virus infection by Simpleprobe. World J Gastroenterol 2015; 21:6639-6648. [PMID: 26074702 PMCID: PMC4458774 DOI: 10.3748/wjg.v21.i21.6639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 02/03/2015] [Accepted: 02/11/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate precore/basal core promoter (PC/BCP) mutants throughout hepatitis B virus (HBV) infection and to determine their relationship to hepatitis B early antigen (HBeAg) titers.
METHODS: We enrolled 191 patients in various stages of HBV infection at the Huashan Hospital and the Taizhou Municipal Hospital from 2010 to 2012. None of the patients received antiviral therapy. HBV DNA from serum, was quantified by real-time PCR. The HBV genotype was determined by direct sequencing of the S gene. We used the Simpleprobe ultrasensitive quantitative method to detect PC/BCP mutants in each patient. We compared the strain number, percentage, and the changes in PC/BCP mutants in different phases, and analyzed the relationship between PC/BCP mutants and HBeAg by multiple linear regression and logistic regression.
RESULTS: Patients with HBV infection (n = 191) were assigned to groups by phase: Immune tolerance (IT) = 55, Immune clearance (IC) = 67, Low-replicative (LR) = 49, and HBeAg-negative hepatitis (ENH) = 20. Of the patients (male, 112; female, 79) enrolled, 122 were HBeAg-positive and 69 were HBeAg-negative. The median age was 33 years (range: 18-78 years). PC and BCP mutation detection rates were 84.82% (162/191) and 96.86% (185/191), respectively. In five HBeAg-negative cases, we detected double mutation G1896A/G1899A. The logarithm value of PC mutant quantities (log10 PC) significantly differed in IT, IC, and LR phases, as well as in the ENH phase (F = 49.350, P < 0.001). The logarithm value of BCP mutant quantities (log10 BCP) also differed during the four phases (F = 25.530, P < 0.001). Log10 PC and log10 BCP values were high in the IT and IC phases, decreased in the LR phase, and increased in the ENH phase, although the absolute value at this point remained lower than that in the IT and IC phases. PC mutant quantity per total viral load (PC%) and BCP mutant quantity per total viral load (BCP%) differed between phases (F = 20.040, P < 0.001; F = 10.830, P < 0.001), with PC% and BCP% gradually increasing in successive phases. HBeAg titers negatively correlated with PC% (Spearman’s rho = -0.354, P < 0.001) and BCP% (Spearman’s rho = -0.395, P < 0.001). The negative correlation between PC% and HBeAg status was significant (B = -5.281, P = 0.001), but there was no such correlation between BCP% and HBeAg status (B = -0.523, P = 0.552).
CONCLUSION: PC/BCP mutants become predominant in a dynamic and continuous process. Log10 PC, log10 BCP, PC% and BCP% might be combined to evaluate disease progression. PC% determines HBeAg status.
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Lu R, Shao J, Zhou M, Zhang H, Wu Y. Accurate Detection of Hepatitis B Virus G1896A Mutant by Developed Taqman-ARMS Followed a Strict Control System. J Clin Lab Anal 2015; 30:315-8. [PMID: 25968238 DOI: 10.1002/jcla.21857] [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: 02/12/2014] [Accepted: 04/07/2015] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) G1896A mutation was associated with HBeAg seronegativity and hepatitis B related acute-on-chronic liver failure. In this study, we developed Taqman amplification refractory mutation system (Taqman-ARMS) and established a strict control system to detect HBV G1896A mutant. METHODS HBV viral DNA was isolated from 60 patient serum samples, and full-length HBV genome was cloned. Then, Taqman-ARMS was used to detect HBV G1896A mutant. RESULTS The assay has the sensitivity of 1E+3 IU/ml G1896A template, and 0.1% weak population virus with G1896A could be found in mixtures. Total of all 60 clinical samples random collected were detected by Taqman-ARMS, the results were consistent with those by DNA sequencing. CONCLUSION The proposed Taqman-ARMS real-time PCR method for the detection of G1896A mutation of HBV was rapid, simple, sensitive, specific, and applicable in the clinical setting.
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Affiliation(s)
- Renfei Lu
- Department of Laboratory, The Third People's Hospital of Nantong, Nantong, Jiangsu, P. R., China
| | - Jianguo Shao
- Department of Laboratory, The Third People's Hospital of Nantong, Nantong, Jiangsu, P. R., China
| | - Min Zhou
- Nantong Center for Disease Control and Prevention, Nantong, Jiangsu, P. R., China
| | - Hongping Zhang
- Nantong Center for Disease Control and Prevention, Nantong, Jiangsu, P. R., China
| | - Yueping Wu
- Department of Laboratory, The Third People's Hospital of Nantong, Nantong, Jiangsu, P. R., China
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Hardikar W, Schwarz KB. Treatment options for chronic hepatitis B and C infection in children. Expert Rev Anti Infect Ther 2014; 4:583-91. [PMID: 17009938 DOI: 10.1586/14787210.4.4.583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There has been a dramatic increase in treatment options for both chronic hepatitis B (CHB) and chronic hepatitis C (CHC) infection in adults over the past 5-10 years, resulting in standardized regimes for initial treatment, relapsers and even infection in the setting of recurrence post-liver transplantation. These regimes have resulted in the halting of the disease progression, reduction in the risk of hepatocellular carcinoma and removal of these infections as a contraindication for liver transplantation. However, treatment in children must be considered carefully in the context of the natural history of these infections and host factors, particularly the immunological mileu, which may affect response to therapy. The as yet unknown long-term effects of medications must also be balanced with the probability of significant life-long morbidity or mortality from chronic hepatitis and its complications. Furthermore, the development of drug resistance, particularly in the case of CHB, has significant implications for the pediatric patient who may exhaust effective therapeutic options at a relatively young age. For these reasons, initiation of therapy must be based on sound criteria. Based on the current data, we recommend that therapy should be offered to children with CHB who have an elevation in alanine aminotransferase (>2-3 x upper limit of normal) for more than 6 months. Therapy with interferon-alpha should be offered in the majority of cases with the aim of immune clearance as measured by early antigen seroconversion. By contrast, treatment indication for CHC in children remains controversial. If used, combination therapy with pegylated interferon and ribavirin is likely to produce the highest rates of sustained viral response.
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Affiliation(s)
- Winita Hardikar
- Royal Children's Hospital, Department of Gastroenterology and Nutrition, Melbourne, Australia.
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6
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Combination of a modified block PCR and endonuclease IV-based signal amplification system for ultra-sensitive detection of low-abundance point mutations. Methods 2013; 64:255-9. [DOI: 10.1016/j.ymeth.2013.06.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/19/2013] [Accepted: 06/21/2013] [Indexed: 11/22/2022] Open
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Abstract
Real-time PCR or quantitative PCR (QPCR) is a powerful technique that allows measurement of PCR product while the amplification reaction proceeds. It incorporates the fluorescent element into conventional PCR as the calculation standard to provide a quantitative result. In this sense, fluorescent chemistry is the key component in QPCR. Till now, two types of fluorescent chemistries have been adopted in the QPCR systems: one is nonspecific probe and the other is specific. As a brilliant invention by Kramer et al. in 1996, molecular beacon is naturally suited as the reporting element in real-time PCR and has been adapted for many molecular biology applications. In this chapter, we briefly introduce the working principle of QPCR and overview different fluorescent chemistries, and then we focus on the applications of molecular beacons-like gene expression study, single-nucleotide polymorphisms and mutation detection, and pathogenic detection.
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Affiliation(s)
- Chaoyong James Yang
- Department of Chemical Biology College of Chemistry and Chemical Xiamen University, Xiamen, Fujian China, People's Republic
| | - Weihong Tan
- Department of Biomedical Engineering and Department of Chemistry Hunan University, Changsha, China, People's Republic
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8
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Han SX, Jia X, Ma JL, Zhu Q. Molecular beacons: a novel optical diagnostic tool. Arch Immunol Ther Exp (Warsz) 2013; 61:139-48. [PMID: 23292078 PMCID: PMC7079750 DOI: 10.1007/s00005-012-0209-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/20/2012] [Indexed: 12/31/2022]
Abstract
As a result of the efforts of the Human Genome Project and the rise in demand for molecular diagnostic assays, the development and optimization of novel hybridization probes have focused on speed, reliability, and accuracy in the identification of nucleic acids. Molecular beacons (MBs) are single-stranded, fluorophore-labeled nucleic acid probes that are capable of generating a fluorescent signal in the presence of target, but are dark in the absence of target. Because of the high specificity and sensitivity characteristics, MBs have been used in variety of fields. In this review, MBs are introduced and discussed as diagnostic tools in four sections: several technologies of MBs will be illustrated primarily; the limitation of MBs next; the third part is new fashions of MBs; and the last one is to present the application of MBs in disease diagnosis.
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Affiliation(s)
- Su-Xia Han
- Department of Oncology, The First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi 710061, People's Republic of China
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9
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Toh ST, Jin Y, Liu L, Wang J, Babrzadeh F, Gharizadeh B, Ronaghi M, Toh HC, Chow PKH, Chung AYF, Ooi LLPJ, Lee CGL. Deep sequencing of the hepatitis B virus in hepatocellular carcinoma patients reveals enriched integration events, structural alterations and sequence variations. Carcinogenesis 2012; 34:787-98. [PMID: 23276797 DOI: 10.1093/carcin/bgs406] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is epidemiologically associated with hepatocellular carcinoma (HCC), but its role in HCC remains poorly understood due to technological limitations. In this study, we systematically characterize HBV in HCC patients. HBV sequences were enriched from 48 HCC patients using an oligo-bead-based strategy, pooled together and sequenced using the FLX-Genome-Sequencer. In the tumors, preferential integration of HBV into promoters of genes (P < 0.001) and significant enrichment of integration into chromosome 10 (P < 0.01) were observed. Integration into chromosome 10 was significantly associated with poorly differentiated tumors (P < 0.05). Notably, in the tumors, recurrent integration into the promoter of the human telomerase reverse transcriptase (TERT) gene was found to correlate with increased TERT expression. The preferred region within the HBV genome involved in integration and viral structural alteration is at the 3'-end of hepatitis B virus X protein (HBx), where viral replication/transcription initiates. Upon integration, the 3'-end of the HBx is often deleted. HBx-human chimeric transcripts, the most common type of chimeric transcripts, can be expressed as chimeric proteins. Sequence variation resulting in non-conservative amino acid substitutions are commonly observed in HBV genome. This study highlights HBV as highly mutable in HCC patients with preferential regions within the host and virus genome for HBV integration/structural alterations.
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Affiliation(s)
- Soo Ting Toh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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10
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Gold-nanobeacons for real-time monitoring of RNA synthesis. Biosens Bioelectron 2012; 36:161-7. [DOI: 10.1016/j.bios.2012.04.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/20/2012] [Accepted: 04/09/2012] [Indexed: 12/20/2022]
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Zhang J, Xu WJ, Wang Q, Zhang Y, Shi M. Prevalence of the precore G1896A mutation in Chinese patients with e antigen negative hepatitis B virus infection and its relationship to pre-S1 antigen. Braz J Microbiol 2009; 40:965-71. [PMID: 24031448 PMCID: PMC3768560 DOI: 10.1590/s1517-838220090004000031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 11/06/2008] [Accepted: 05/15/2009] [Indexed: 12/29/2022] Open
Abstract
This study investigated the prevalence of the precore G1896A mutation in Chinese patients with hepatitis B e antigen (HBeAg) negative HBV infection and its relation to serum HBV pre-S1 antigen. The overall prevalence of the precore G1896A mutation was 72.6% in HBeAg-negative Chinese patients with detectable serum HBV DNA. The prevalence of the precore G1896A is significantly higher in Chinese HBeAg-negative patients with chronic hepatitis B than that in inactive HBV carriers with detectable serum HBV DNA. Serum pre-S1 and the precore G1896A mutation were simultaneously detected in most of Chinese HBeAg-negative patients.
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Affiliation(s)
- Jing Zhang
- Department of Clinical Laboratory, Dalian Central Hospital, Dalian 116033 , Liaoning Province , China
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12
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Ginya H, Asahina J, Nakao R, Tamada Y, Takahashi M, Yohda M, Yatsuhashi H. Semi-quantitative discrimination of HBV mutants using allele-specific oligonucleotide hybridization with Handy Bio-Strand. J Biosci Bioeng 2009; 109:94-100. [PMID: 20129090 DOI: 10.1016/j.jbiosc.2009.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 06/17/2009] [Accepted: 06/27/2009] [Indexed: 11/15/2022]
Abstract
The analysis of hepatitis B virus (HBV) mutations is important for understanding HBV progression and for deciding on appropriate clinical treatments. However, it is difficult to determine the quantitative abundance of various mutants in heterogeneous mixtures by conventional methods such as direct sequencing or the TaqMan assay. In this study, we investigated the possibility of using both allele-specific oligonucleotide hybridization (ASOH) and allele-specific oligonucleotide competitive hybridization (ASOCH) with the Handy Bio-Strand system for the quantitative identification of three well-defined HBV variants: the basal core promoter (BCP) mutations (nt1762 and nt1764), the pre-core (PC) mutation (nt1896), and variance at nt1858. Using standardized mixtures of wild-type and mutant DNA, optimal hybridization conditions for ASOH and ASOCH were determined. Next, the performance of these methods was evaluated using actual serum DNAs from HBV patients. Excellent reproducibility was obtained both in the analysis of internal positive controls and in the semi-quantitative categorization of heterogeneous viral mixtures into five abundance groups (0%, 25%, 50%, 75%, and 100% mutant virus). Combined with real-time PCR to determine the HBV viral load, this hybridization method offers a new tool with applications both in HBV clinical research and treatment.
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Affiliation(s)
- Harumi Ginya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka-cho, Koganei, Japan.
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Zhao J, He D, He H, Li L, Zhang LL, Wang XY. Primary Application Study in Early Diagnosis of Bladder Cancer by Survivin Molecular Beacons. Urology 2007; 70:60-4. [PMID: 17656209 DOI: 10.1016/j.urology.2007.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 02/09/2007] [Accepted: 03/07/2007] [Indexed: 01/14/2023]
Abstract
OBJECTIVES To develop a sensitive method for the detection of bladder cancer cells in the urine castoff cells of patients with bladder cancer, we examined the feasibility of using molecular beacon (MB) probes specific for tumor-specific survivin mRNA. METHODS MBs are single-stranded oligonucleotide hybridization probes that form a stem-and-loop structure and have high sensitivity and specificity. Western blot analysis showed that a high level of survivin gene expression is detected in human bladder cancer 5637 and J82 cell lines but not in normal human prostate fibroblast cells. These cell lines were incubated with survivin MBs, and the fluorescence intensity was examined in those cells using a fluorescence microscope. RESULTS We found that survivin MBs could detect expression of the survivin gene and generated fluorescent signals in the cancer cells. However, the fluorescence signal was not detected in the normal prostate fibroblast cells. The green fluorescent signal was present in the exfoliated cells of patients with bladder cancer but not in the healthy adult after incubating with survivin MBs. CONCLUSIONS Our results have demonstrated that the survivin MB is a specific and sensitive molecular probe for detecting bladder cancer cells and urine castoff cells of patients with bladder cancer. It has great potential for the development of a clinical diagnostic procedure for the early detection of bladder cancer and follow-up after surgery.
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Affiliation(s)
- Jun Zhao
- Department of Urology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi, People's Republic of China
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Li X, Huang Y, Guan Y, Zhao M, Li Y. A novel one cycle allele specific primer extension--molecular beacon displacement method for DNA point mutation detection with improved specificity. Anal Chim Acta 2006; 584:12-8. [PMID: 17386579 DOI: 10.1016/j.aca.2006.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Revised: 10/19/2006] [Accepted: 11/06/2006] [Indexed: 01/08/2023]
Abstract
We report here a new method for the real-time detection of DNA point mutations with molecular beacon as the fluorescence tracer and 3' (exo-) Bst DNA polymerase large fragment as the polymerase. The method is based on the mechanism of allele specific primer extension-strand displacement (ASPE-SD). To improve the specificity of the method only one cycle of the allele specific polymerase chain reaction (PCR) was used that could largely eliminate the non-specific reactions between the primers and template of the "wrong" genotype. At first, the primer and molecular beacon both hybridize to the DNA template, and the molecular beacon emits intensive fluorescence. The role of 3' exonuclease excision of Bst DNA polymerase large fragment is utilized for primer extension. When 3'-termini matches its corresponding template, the primer would efficiently extend and replace the molecular beacon that would simultaneously return to its closed form leading to the quenching of the fluorescence. However, when 3'-termini of the primer mismatches its corresponding template primer extension and molecular beacon displacement would not happen and fluorescence of the hybridized molecular beacon holds the line without fluorescence quenching. This approach was fully demonstrated in synthetic template systems and applied to detect point mutation at codon 259, a possible point mutation site in exon 7 of p53 gene, obtained from human genomic DNA samples with unambiguous differentiation power.
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Affiliation(s)
- Xiaomin Li
- The Key Laboratory of Bioorganic Chemistry & Molecular Engineering and the Research Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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16
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Watzinger F, Ebner K, Lion T. Detection and monitoring of virus infections by real-time PCR. Mol Aspects Med 2006. [PMID: 16481036 DOI: 10.1016/j.mam.2005.12.00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.
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Affiliation(s)
- F Watzinger
- Children's Cancer Research Institute, St. Anna Kinderspital, A-1090 Vienna, Austria
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17
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Abstract
The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.
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Affiliation(s)
| | | | - T. Lion
- Corresponding author. Tel.: +43 1 40470 489; fax: +43 1 40470 437.
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