Competitive PCR for precise nucleic acid quantification

Nature Protocols

Volumn 2, Issue 9, 2007, Pages 2092-2104

  Zentilin, Lorena ^a   Giacca, Mauro ^a  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID; OLIGONUCLEOTIDE; PRIMER DNA; VASCULOTROPIN A;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; GENE TARGETING; INTERMETHOD COMPARISON; MOUSE; NONHUMAN; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; ADENO ASSOCIATED VIRUS; ANIMAL; GENE VECTOR; GENETIC TRANSDUCTION; GENETICS; METHODOLOGY; MOLECULAR CLONING;

ANIMALS; CLONING, MOLECULAR; DEPENDOVIRUS; DNA; DNA PRIMERS; GENETIC VECTORS; MICE; POLYMERASE CHAIN REACTION; TRANSDUCTION, GENETIC; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 38049094365     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2007.299     Document Type: Article

References (37)

1. Arrigo, S.J., Weitsman, S., Rosenblatt, J.D. & Chen, I.S. Analysis of rev gene function on human immunodeficiency virus type 1 replication in Lymphoid cells by using a quantitative polymerase chain reaction method. J. Virol. 63, 4875-4881 (1989).
2. Chelly, J., Concordet, J.P., Kaplan, J.C. & Kahn, A. Illegitimate transcription: Transcription of any gene in any cell type. Proc. Natl. Acad. Sci. USA 86, 2617-2621 (1989).
3. Oka, S. et al. Quantitative analysis of human immunodeficiency virus type-1 DNA in asymptomatic carriers using the polymerase chain reaction. Biochem. Biophys. Res. Commun. 167, 1-8 (1990).
4. Simmonds, P. et al. Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear ceLls and at low copy numbers. J. Virol. 64, 864-872 (1990).
5. Livak, K.J., Flood, S.J., Marmaro, J., Giusti, W. & Deetz, K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 4, 357-362 (1995).
6. Gilliland, G., Perrin, S., Blanchard, K. & Bunn, H.F. Analysis of cytokine mRNA and DNA: Detection and quantitation by competitive polymerase chain reaction. Proc. Natl. Acad. Sci. USA 87, 2725-2729 (1990).
7. Siebert, P.D. & Larrick, J.W. Competitive PCR. Nature 359, 557-558 (1992).
8. Becker-Andre, M. & Hahlbrock, K. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucleic Acids Res. 17, 9437-9446 (1989).
9. Diviacco, S. et al. A novel procedure for quantitative polymerase chain reaction by coamplification of competitive templates. Gene 122, 313-320 (1992).
10. Celi, F.S., Zenilman, M.E. & Shuldiner, A.R. A rapid and versatile method to synthesize internal standards for competitive PCR. Nucleic Acids Res. 21, 1047 (1993).
11. Henco, K. & Heibey, M. Quantitative PCR: The determination of template copy numbers by temperature gradient get electrophoresis (TGGE). Nucleic Acids Res. 18, 6733-6734 (1990).
12. Tani, H. et al. Quantitative method for specific nucleic acid sequences using competitive polymerase chain reaction with an alternately binding probe. Anal. Chem. 79, 974-979 (2007).
13. Giacca, M. et al. Fine mapping of a replication origin of human DNA. Proc Natl. Acad Sci. USA 91, 7119-7123 (1994).
14. Sestini, R. et al. Measuring c-erbB-2 oncogene amplification in fresh and paraffin-embedded tumors by competitive polymerase chain reaction. Clin. Chem. 40, 630-636 (1994).
15. Kato, K. et al. Cancer gene expression database (CGED): A database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res. 33, D533-D536 (2005).
16. Lusic, M., Marcella, A., Cereseto, & & Giacca, M. Regulation of HIV-1 gene expression by histone acetylation and factor recruitment at the LTR promoter. EMBO J. 22, 6550-6561 (2003).
17. Deutsch, S. et al. Detection of aneuploidies by paralogous sequence quantification. J. Med. Genet 41, 908-915 (2004).
18. Liu, W., James, C.D., Frederick, L., Alderete, B.E. & Jenkins, R.B. PTEN/MMAC1 mutations and EGFR amplification in glioblastomas. Cancer Res. 57, 5254-5257 (1997).
19. Comar, M. et al. Dynamics of HIV-1 mRNA expression in patients with Long-term nonprogressive HIV-1 infection. J. Clin. Invest. 100, 893-903 (1997).
20. Grassi, G. et al. A rapid procedure for the quantitation of Low abundance RNAs by competitive reverse transcription-polymerase chain reaction. Nucleic Acids Res. 22, 4547-4549 (1994).
21. Tafuro, S., Zentilin, L., Falaschi, A. & Giacca, M. Rapid retrovirus titration using competitive polymerase chain reaction. Gene Ther. 3, 679-684 (1996).
22. Mileham, K.A. et al. Competitive titration for probing low-abundance ion channel mRNA molecules in normal and regionally-ischaemic heart tissue. Mol. Cell. Probes 8, 161-176 (1994).
23. Nie, G.Y., Wang, J., Li, Y. & Salamonsen, L.A. Construction and application of a multispecific competitor to quantify mRNA of matrix metalloproteinases and their tissue inhibitors in small human biopsies. J. Biochem. Biophys. Methods 40, 81-99 (1999).
24. McCulloch, R.K., Choong, C.S. & Hurley, D.M. An evaluation of competitor type and size for use in the determination of mRNA by competitive PCR. PCR Methods Appl. 4, 219-226 (1995).
25. Serth, J., Panitz, F., Herrmann, H. & Alves, J. Single-tube nested competitive PCR with homologous competitor for quantitation of DNA target sequences: Theoretical description of heteroduplex formation, evaluation of sensitivity, precision and linear range of the method. Nucleic Acids Res. 6, 4401-1408 (1998).
26. Giacca, M., Pelizon, C. & Falaschi, A. Mapping replication origins by quantifying relative abundance of nascent DNA strands using competitive polymerase chain reaction. Methods 13, 301-312 (1997).
27. Kato, K. Adaptor-tagged competitive PCR: A novel method for measuring relative gene expression. Nucleic Acids Res. 25, 4694-4696 (1997).
28. Kita-Matsuo, H. et al. Adaptor-tagged competitive polymerase chain reaction: Amplification bias and quantified gene expression levels. Anal. Biochem. 339, 15-28 (2005).
29. Grove, S., Faller, R., Soleim, K.B. & Dannevig, B.H. Absolute quantitation of RNA by a competitive real-time RT-PCR method using piscine nodavirus as a model. J. Virol. Methods 132, 104-112 (2006).
30. Locatelli, G. et al. Real-time quantitative PCR for human herpesvirus 6 DNA. J. Clin. Microbiol. 38, 4042-4048 (2000).
31. Widada, J. et al. Quantification of the carbazole 1,9a-dioxygenase gene by real-time competitive PCR combined with co-extraction of internal standards. FEMS Microbiol. Lett. 202, 51-57 (2001.
32. Ding, C. & Cantor, C.R. A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. Proc. Natl. Acad. Sci. USA 100 3059-3064 (2003).
33. Ding, C. & Cantor, C.R. Quantitative analysis of nucleic acids-the last few years of progress. J. Biochem. Mol. Biol. 37, 1-10 (2004).
34. McCullough, R.M., Cantor, C.R. & Ding, C. High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Nucleic Acids Res. 33, e99 (2005).
35. Elvidge, G.P., Price, T.S., Glenny, L. & Ragoussis, J. Development and evaluation of real competitive PCR for high-throughput quantitative applications. Anal. Biochem. 339, 231-241 (2005).
36. Ausubel, F.M. et al. Current Protocols in Molecular Biology (J. Wiley & Sons Inc., New York, NY, 2003).
37. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning. A Laboratory Manual 2nd edn. (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1989).