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Real-time polymerase chain reaction

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Real-time polymerase chain reaction
In molecular biology, real-time polymerase chain reaction, also called quantitative real time polymerase chain reaction (Q-PCR/qPCR/qrt-PCR) or kinetic polymerase chain reaction (KPCR), is a laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a targeted DNA molecule. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The procedure follows the general principle of polymerase chain reaction; its key feature is that the amplified DNA is detected as the reaction progresses in real time, a new approach compared to standard PCR, where the product of the reaction is detected at its end. Two common methods for detection of products in real-time PCR are: (1) non-specific fluorescent dyes that intercalate with any double-stranded DNA, and (2) sequence-specific DNA probes consisting of oligonucleotides that are labeled with a fluorescent reporter which permits detection only after hybridization of the probe with its complementary DNA target. Frequently, real-time PCR is combined with reverse transcription to quantify messenger RNA and Non-coding RNA in cells or tissues. Abbreviations used for real-time PCR methods vary widely and include RTQ-PCR, Q-PCR or qPCR.[1] Real-time reverse-transcription PCR is often denoted as qRT-PCR,[2] RRT-PCR,[3] or RT-rt PCR.[4] The acronym RT-PCR commonly denotes reverse-transcription PCR and not real-time PCR, but not all authors adhere to this convention.[5]

Background
Cells in all organisms regulate gene expression and turnover of gene transcripts (messenger RNA, abbreviated to mRNA), and the number of copies of an mRNA transcript of a gene in a cell or tissue is determined by the rates of its expression and degradation. Northern blotting is often used to estimate the expression level of a gene by visualizing the abundance of its mRNA transcript in a sample. In this method, purified RNA is separated by agarose gel electrophoresis, transferred to a solid matrix (such as a nylon membrane), and probed with a specific DNA or RNA probe that is complementary to the gene of interest. Although this technique is still used to assess gene expression, it requires relatively large amounts of RNA and provides only qualitative or semiquantitative information of mRNA levels. In order to robustly detect and quantify gene expression from small amounts of RNA, amplification of the gene transcript is necessary. The polymerase chain reaction is a common method for amplifying DNA; for mRNA-based PCR the RNA sample is first reverse transcribed to cDNA with reverse transcriptase. Development of PCR technologies based on reverse transcription and fluorophores permits measurement of DNA amplification during PCR in real time, i.e., the amplified product is measured at each PCR cycle. The data thus generated can be analysed by computer software to calculate relative gene expression in several samples, or mRNA copy number. Real-time PCR can also be applied to the detection and quantification of DNA in samples to determine the presence and abundance of a particular DNA sequence in these samples.

Real-time PCR with double-stranded DNA-binding dyes as reporters
A DNA-binding dye binds to all double-stranded (ds)DNA in PCR, causing fluorescence of the dye. An increase in DNA product during PCR therefore leads to an increase in fluorescence intensity and is measured at each cycle, thus allowing DNA concentrations to be quantified. However, dsDNA dyes such as SYBR Green will bind to all dsDNA PCR products, including nonspecific PCR products (such as Primer dimer). This can potentially interfere with or prevent accurate quantification of the intended target sequence. 1. The reaction is prepared as usual, with the addition of fluorescent dsDNA dye.

Ct. and once the polymerase reaches the probe.e. e. breakdown of the probe by the 5' to 3' exonuclease activity of the Taq polymerase breaks the reporter-quencher proximity and thus allows unquenched emission of fluorescence. the levels of fluorescence are measured with a detector. Like other real-time PCR methods. which can be detected after excitation with a laser. and enables quantification even in the presence of non-specific DNA amplification. As the reaction commences. Fluorescent probes can be used in multiplex assays—for detection of several genes in the same reaction—based on specific probes with different-coloured labels. A threshold for detection of fluorescence above background is determined. fluorescent reporter probes do not prevent the inhibitory effect of the primer dimers. which may depress accumulation of the desired products in the reaction. The PCR is prepared as usual (see PCR). the dye only fluoresces when bound to the dsDNA (i. 2 Fluorescent reporter probe method Fluorescent reporter probes detect only the DNA containing the probe sequence. allowing only relative comparisons between different tissues or experimental conditions. 1.g. during the annealing stage of the PCR both probe and primers anneal to the DNA target. 3. and the reporter probe is added. and its geometric increase corresponding to exponential increase of the product is used to determine the threshold cycle (CT) in each reaction. the PCR product)... The close proximity of the reporter to the quencher prevents detection of its fluorescence. To ensure accuracy in the quantification. its 5'-3'-exonuclease degrades the probe. The reaction is run in a Real-time PCR instrument.Real-time polymerase chain reaction 2. Quantification Quantifying gene expression by traditional methods presents several problems.e. The method relies on a DNA-based probe with a fluorescent reporter at one end and a quencher of fluorescence at the opposite end of the probe. Relative concentrations of DNA present during the exponential phase of the reaction are determined by plotting fluorescence against cycle number on a logarithmic scale (so an exponentially increasing quantity will give a straight line). physically separating the fluorescent reporter from the quencher. 4. An increase in the product targeted by the reporter probe at each PCR cycle therefore causes a proportional increase in fluorescence due to the breakdown of the probe and release of the reporter. The specificity of fluorescent reporter probes also prevents interference of measurements caused by primer dimers. use of the reporter probe significantly increases specificity. Firstly. the amount of product reaches a plateau determined more by the amount of primers in the reaction mix than by the input template/sample. over the 20-40 cycles of a typical PCR. Fluorescence is detected and measured in the real-time PCR thermocycler. As described above. Also. and after each cycle. provided that all targeted genes are amplified with similar efficiency. This can correct possible differences in RNA quantity or quality across experimental samples. a comparison of a measured DNA/RNA sample to a standard dilution will only give a fraction or ratio of the sample relative to the standard. The cycle at which the fluorescence from a sample crosses the threshold is called the cycle threshold. detection of mRNA on a Northern blot or PCR products on a gel or Southern blot is time-consuming and does not allow precise quantification. therefore. With reference to a standard dilution. However. a sample whose Ct is 3 . The quantity of DNA theoretically doubles every cycle during the exponential phase and relative amounts of DNA can be calculated. 2. resulting in an increase in fluorescence. which are undesirable potential by-products in PCR. it is usually necessary to normalize expression of a target gene to a stably expressed gene (see below). the values obtained do not have absolute units associated with them (i. mRNA copies/cell). the dsDNA concentration in the PCR can be determined. Polymerisation of a new DNA strand is initiated from the primers.

provided that the expression of the reference (housekeeping) gene used in the normalization is very similar across all the samples. As mentioned above. real-time PCR is mainly used to provide quantitative measurements of gene transcription. (2009).67 times more template). Methods Mol Biol 436: 19–26. Heilmann J. "Relative quantification of mRNA levels in Jurkat T cells with RT-real time-PCR (RT-rt-PCR): new possibilities for the screening of anti-inflammatory and cytotoxic compounds". doi:10. one has to calculate the reaction efficiency first. and often challenging. the measured amount of RNA from the gene of interest is divided by the amount of RNA from a housekeeping gene measured in the same sample to normalize for possible variation in the amount and quality of RNA between different samples. Methods such as MAK2[8] have been shown to have equal or better quantitative performance to standard curve methods. PMID 18474036. Amounts of RNA or DNA are then determined by comparing the results to a standard curve produced by real-time PCR of serial dilutions (e. infectious diseases. Absolute quantification gives the exact number of target DNA molecules by comparison with DNA standards. doi:10. for example. by using this as the base and the cycle difference Ct as the exponent. cancer and genetic abnormalities. References [1] VanGuilder HD. These mechanism based methods use knowledge about the polymerase amplification process to generate estimates of the original sample concentration. Real-time PCR can be used to quantify nucleic acids by two methods: relative quantification and absolute quantification. Vrana KE. in diagnostic tests. PMID 12240952. Biotechniques 44 (5): 619–626. Sticher O. Kirstin Edwards. Thus. "Development and evaluation of different normalization strategies for gene expression studies in Candida albicans biofilms by real-time PCR". PMC 2518243. "Type A influenza virus detection and quantitation by real-time RT-PCR".[10] and is deployed as a tool to detect newly emerging diseases.[11] In research settings. Saunders N. Güttinger M. [5] edited by Julie Logan. 1:64) of a known amount of RNA or DNA. Caister Academic Press.061143. The technology may be used in determining how the genetic expression of a particular gene changes over time. Logan J. Plant Cell 20 (7): 1736–1737.1007/978-1-59745-279-3_4. Scheible WR (2008). Relative quantification is based on internal reference genes to determine fold-differences in expression of the target gene. "Eleven Golden Rules of Quantitative RT-PCR". Since all sets of primers don't work equally well. if efficiency was 98%. Real-Time PCR: Current Technology and Applications. 1:16. This normalization permits accurate comparison of expression of the gene of interest between different samples. PMID 18664613.g.2144/000112776. [6] Nailis H. and have the advantage that they do not require a standard curve for quantification. doi:10. [4] Gertsch J. progression of cell differentiation. ISBN 978-1-904455-39-4. "Twenty-five years of quantitative PCR for gene expression analysis". doi:10. BMC Mol Biol. and Nick Saunders. to accurately quantify gene expression.1023/A:1019818814336.Real-time polymerase chain reaction cycles earlier than another's has 23 = 8 times more template. Nelis HJ (2006). Freeman WM (2008). because only very few genes show equal levels of expression across a range of different conditions or tissues. the precise difference in starting template can be calculated (in previous example. 1:4. The introduction of real-time PCR assays to the clinical microbiology laboratory has significantly improved the diagnosis of infectious diseases. Coenye T.1105/tpc. Pharm Res 19: 1236–1243. such as flu. 7: 25. It is commonly used for both diagnostic and basic research.1186/1471-2199-7-25. undiluted. then the sample would have 2(3 * 98%) = (298%)3 = 7. Edwards K.[9] 3 Applications of real-time polymerase chain reaction There are numerous applications for real-time polymerase chain reaction in the laboratory.[6] [7] Mechanism based qPCR quantification methods have also been suggested. ed. PMC 1557526. such as in the response of tissue and cell cultures to an administration of a pharmacological agent. (2002). Diagnostic real-time PCR is applied to rapidly detect nucleic acids that are diagnostic of. Van Nieuwerburgh F. Choosing a reference gene fulfilling this criterion is therefore of high importance. [2] Udvardi MK. [3] Spackman E. doi:10. .108. Suarez DL (2008). PMID 18370037. Deforce D. or in response to changes in environmental conditions. Czechowski T.

gov/ bbs/ topics/ NEWS/ 2009/ NEW02002. • openwetware (http://openwetware. doi:10. G. Paul JH.2006. University of South Carolina.info/) all about real-time qPCR and qRT-PCR • realtimepcr. Tabita FR (2002) Real-time PCR quantification of rbcL (ribulose-1. Protoc. P.dk (http://realtimepcr.com) .info (http://www.jim. April 27. Fockler. [10] Sails AD (2009).1016/j.. [11] FDA Authorizes Emergency Use of Influenza Medicines.sc.. External links • Real-time PCR literature (http://www. fda. September 5.01. • Higuchi. 354 (1-2): 34–9.". R. Caister Academic Press. doi:10. ISBN 978-1-904455-39-4. PMID 20109462.org/wiki/Q-PCR) . John Kenneth and TB Trials Study Group. Immunol Methods. 1 (3): 1559–1582. Environ. Walsh. PMID 20814578. I. FDA News. PLOS One 5 (8): e12355. Caister Academic Press. G.236.5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes.gene-quantification. [8] Boggy G. [7] Nolan T. "A Mechanistic Model of PCR for Accurate Quantification of Quantitative PCR Data"." Biotechnology 10:413–417. "Comparison of different standards for real-time PCR-based absolute quantification". Bustin SA (2006).med..Current literature • Real Time PCR Tutorial (http://pathmicro. doi:10. Microbiol. R.T. 2006 • www. Diagnostic Test in Response to Swine Flu Outbreak in Humans. M. • Mackay.Real-time polymerase chain reaction PMID 16889665.1038/nprot. Nat. (1992).2010. S. ISBN 978-1-904455-39-4." Caister Academic Press. 2009. Dollinger.htm) by Dr Margaret Hunt.pone.edu/pcr/realtime-home. R. Hands RE. "Simultaneous amplification and detection of specific DNA sequences. "Applications in Clinical Microbiology". Dollinger.. • Logan J. (2007).. [9] S. "Real-Time PCR in Microbiology. "Kinetic PCR: Real time monitoring of DNA amplification reactions. Dhanasekaran. (http:/ / www. Appl. Denmark. PMID 17406449.dk) Real time PCR experiences from researchers from the university of Copenhagen. html) 4 Further reading • Higuchi. and Watson. Edwards K.gene-quantification.004.1371/journal.rt-pcr." Biotechnology 11:1026–1030. (2010 Mar). Real-Time PCR: Current Technology and Applications.. Real-Time PCR: Current Technology and Applications. R. and Griffith. Saunders N (editors) (2009).com/rtmic) • Wawrik B. Woolf PJ (2010). (1993). "Quantification of mRNA using real-time RT-PCR.horizonpress.0012355. PMC 2930010. 68:3771-3779. C. ISBN 978-1-904455-18-9 (http://www. Mark Doherty.

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