Abstract
Quantitative real-time polymerase chain reaction is a technique for simultaneous amplification and product quantification of a target DNA as the process takes place in real time in a “closed-tube” system. Although this technique can provide an absolute quantification of the initial template copy number, quantification relative to a control sample or second sequence is typically adequate. The quantification process employs melting curve analysis and/or fluorescent detection systems and can provide amplification and genoty** in a relatively short time. Here we describe the properties and uses of various fluorescent detection systems used for quantification.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bustin SA, Benes V, Garson JA et al (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55(4):611–622
Nolan T, Hands RE, Bustin SA (2006) Quantification of mRNA using real-time RT-PCR. Nat Protoc 1(3):1559–1582
Burns MJ, Nixon GJ, Foy CA et al (2005) Standardisation of data from real-time quantitative PCR methods – evaluation of outliers and comparison of calibration curves. BMC Biotechnol 5:31
Huggett J, Dheda K, Bustin S et al (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6(4):279–284
Ririe KM, Rasmussen RP, Wittwer CT (1997) Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 245(2):154–160
Reed GH, Wittwer CT (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 50(10):1748–1754
Pryor RJ, Wittwer CT (2006) Real-time polymerase chain reaction and melting curve analysis. Methods Mol Biol 336:19–32
Mitsuhashi M (1996) Technical report: part 2. Basic requirements for designing optimal PCR primers. J Clin Lab Anal 10(5):285–293
Haas SA, Hild M, Wright AP et al (2003) Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res 31(19):5576–5581
Sugimoto N, Nakano S, Yoneyama M et al (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24(22):4501–4505
Rychlik W, Spencer WJ, Rhoads RE (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res 18(21):6409–6412
Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37(2):226–231
Mount DW (2007) Using the basic local alignment search tool (BLAST). CSH Protocol. pdb top17
Sherry ST, Ward MH, Kholodov M et al (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29(1):308–311
Giglio S, Monis PT, Saint CP (2003) Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR. Nucleic Acids Res 31(22): e136
Bengtsson M, Karlsson HJ, Westman G et al (2003) A new minor groove binding asymmetric cyanine reporter dye for real-time PCR. Nucleic Acids Res 31(8):e45
Morrison TB, Weis JJ, Wittwer CT (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechniques 24(6):954–958
Ram S, Singh RL, Shanker R (2008) In silico comparison of real-time PCR probes for detection of pathogens. In Silico Biol 8(3–4):251–259
Simon A, Labalette P, Ordinaire I et al (2004) Use of fluorescence resonance energy transfer hybridization probes to evaluate quantitative real-time PCR for diagnosis of ocular toxoplasmosis. J Clin Microbiol 42(8):3681–3685
Johansson MK (2006) Choosing reporter-quencher pairs for efficient quenching through formation of intramolecular dimers. Methods Mol Biol 335:17–29
Wittwer CT, Herrmann MG, Moss AA et al (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 22(1):130–131
Kostrikis LG, Tyagi S, Mhlanga MM et al (1998) Spectral genoty** of human alleles. Science 279(5354):1228–1229
Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14(3):303–308
Fang X, Li JJ, Perlette J, Tan W et al (2002) Molecular beacons: novel fluorescent probes. Anal Chem 72(23):747A–753A
Lyon E, Wittwer CT (2009) LightCycler technology in molecular diagnostics. J Mol Diagn 11(2):93–101
Wittwer CT, Ririe KM, Andrew RV et al (1997) The LightCycler: a microvolume multisample fluorimeter with rapid temperature control. Biotechniques 22(1):176–181
Vu HL, Troubetzkoy S, Nguyen HH et al (2000) A method for quantification of absolute amounts of nucleic acids by (RT)-PCR and a new mathematical model for data analysis. Nucleic Acids Res 28(7):E18
Regier N, Frey B (2010) Experimental comparison of relative RT-qPCR quantification approaches for gene expression studies in poplar. BMC Mol Biol 11:57
Bustin SA, Mueller R (2005) Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin Sci 109(4):365–379
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Singh, C., Roy-Chowdhuri, S. (2016). Quantitative Real-Time PCR: Recent Advances. In: Luthra, R., Singh, R., Patel, K. (eds) Clinical Applications of PCR. Methods in Molecular Biology, vol 1392. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3360-0_15
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3360-0_15
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3358-7
Online ISBN: 978-1-4939-3360-0
eBook Packages: Springer Protocols