New developments in quantitative real-time polymerase chain reaction technology

Current Issues in Molecular Biology

Volumn 16, Issue 1, 2014, Pages 1-6

  Gadkar, Vijay J ^a   Filion, Martin ^a  

^a UNIVERSITÉ DE MONCTON   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA POLYMERASE; LOCKED NUCLEIC ACID; RNA; DNA DIRECTED DNA POLYMERASE; OLIGONUCLEOTIDE; PRIMER DNA;

AMPLICON; ARTICLE; BIOENGINEERING; BIOTECHNOLOGY; DNA EXTRACTION; GENE EXPRESSION; GENETIC TRANSCRIPTION; ISOTHERM; MICROBIOLOGY; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID AMPLIFICATION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; SINGLE NUCLEOTIDE POLYMORPHISM; TEMPERATURE SENSITIVITY; ANIMAL; BIOSYNTHESIS; COMPUTER PROGRAM; DEVICES; ESSENTIAL GENE; GENETICS; HUMAN; METABOLISM; PROCEDURES; PROTEIN ENGINEERING; STANDARD; STANDARDS; SYNTHESIS; TRENDS;

ANIMALS; DNA PRIMERS; DNA-DIRECTED DNA POLYMERASE; GENES, ESSENTIAL; HUMANS; OLIGONUCLEOTIDES; PROTEIN ENGINEERING; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; SOFTWARE;

EID: 84876189248     PISSN: 14673037     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. Alm, E.W., and Stahl, D.A. (2000). Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. J. Microbiol. Methods 40, 153-162.
2. Al-Soud, W.A., and Rådström, P. (1998). Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol. 64, 3748-3753.
3. Arezi, B., McCarthy, M., and Hogrefe, H. (2010). Mutant of Moloney murine leukemia virus reverse transcriptase exhibits higher resistance to common RT-qPCR inhibitors. Anal. Biochem. 400, 301-303.
4. Baar, C., d'Abbadie, M., Vaisman, A., Arana, M.E., Hofreiter, M., Woodgate, R., Kunkel, T.A., and Holliger, P. (2011). Molecular breeding of polymerases for resistance to environmental inhibitors. Nucleic Acids Res. 39, e51
5. DeCoste, N.J., Gadkar, V.J., and Filion, M. (2011). Relative and absolute quantitative real-time PCR-based quantifications of hcnC and phlD gene transcripts in natural soil spiked with Pseudomonas sp. strain LBUM300. Appl. Environ. Microbiol. 77, 41-47.
6. Deer, D.M., Lampel, K.A., and González-Escalona, N. (2010). A versatile internal control for use as DNA in real-time PCR and as RNA in real-time reverse transcription PCR assays. Lett. Appl. Microbiol. 50, 366-372.
7. van Doorn, R., Klerks, M.M., van Gent-Pelzer, M.P., Speksnijder, A.G., Kowalchuk, G.A., and Schoen, C.D. (2009). Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel internal amplification control approach using Biotrove OpenArrays. Appl. Environ. Microbiol. 75, 7253-7260
8. Filion, M. (2012). Quantitative Real-time PCR in Applied Microbiology (Norfolk, UK: Caister Academic Press)
9. Gelfand, D.H. (1992). Taq DNA polymerase, PCR technology. In Principles and Applications for DNA Amplification, Erlich, H.A. ed. (Freeman and Company, New York), pp. 17-22.
10. Gill, P., and Ghaemi, A. (2008). Nucleic acid isothermal amplification technologies-a review. Nucleosides Nucleotides Nucleic Acids. 27, 224-243.
11. Goldmeyer, J., Kong, H., and Tang, W. (2007). Development of a novel one-tube isothermal reverse transcription thermophilic helicase-dependent amplification platform for rapid RNA detection. J. Mol. Diagn. 9, 639-644.
12. González-Escalona, N., Hammack, T.S., Russel, M., Jacobson, A.P., De Jesús, A.J., Brown, E.W., and Lampel, K.A. (2009). Detection of live Salmonella sp. cells in produce by a TaqMan-Based quantitative reverse transcriptase real-time PCR targeting invA mRNA. Appl. Environ. Microbiol. 75, 3714-3720.
13. Hendrix, C., Rosemeyer, H., De Bouvere, B., Van Aerschot, A., Seela, F., and Herdewijn, P. (1997). 1,5′-Anhydrohexitol oligonucleotides: hybridization and strand displacement with oligoribonucleotides, interaction with RNase H and HIV reverse transcriptase. Eur. J. Chem. 3, 1513-1520
14. Hoorfar, J., Cook, N., Malorny, B., Wagner, M., De Medici, D., Abdulmawjood, A., and Fach, P. (2003). Making internal amplification control mandatory for diagnostic PCR. J. Clin. Microbiol. 41, 5835.
15. Hoorfar, J., Cook, N., Malorny, B., Wagner, M., De Medici, D., Abdulmawjood, A., and Fach, P. (2004). Diagnostic PCR: making internal amplification control mandatory. Lett. Appl. Microbiol. 38, 79-80.
16. Hyrup, B., and Nielson, P.E. (1996). Peptide nucleic acids (PNA): synthesis, properties and nucleic acids, a new promising antisense construct. Bioorg. Med. Chem. 4, 5-23.
17. Johnson, M.P., Haupt, L.M., and Griffiths, L.R. (2004). Locked nucleic acids (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res. 32, e55.
18. Joneja, A., and Huang, X. (2011). Linear nicking endonuclease-mediated strand displacement DNA amplification, Anal. Biochem. 414, 58-69.
19. Kermekchiev, M.B., Kirilova, L.I., Vail, E.E., and Barnes, W.M. (2009). Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res. 37, e40
20. Kiesling, T., Cox, K., Davidson, E.A., Dretchen, K., Grater, G., Hibbard, S., Lasken, R.S., Leshin, J., Skowronski, E., and Danielsen, M. (2007). Sequence specific detection of DNA using nicking endonuclease signal amplification (NESA). Nucleic Acids Res. 35, e117.
21. Latorra, D., Campbell, K., Wolter, A., and Hurley, J.M. (2003). Enhanced allele-specific PCR discrimination in SNP genotyping using 3′ locked nucleic acid (LNA) primers. Hum. Mut. 22, 79-85.
22. Lorenz, M.G., and Wackernagel, W. (1987). Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl. Environ. Microbiol. 53, 2948-2952
23. Mahalanabis M., Do, J., Al-Muayad H., Zhang, J.Y., and Klapperich, C.M. (2010). An integrated disposable device for DNA extraction and helicase dependent amplification. Biomed. Microdev. 12, 353-359.
24. Moran, M.A., Torsvik, V.L., Torsvik, T., and Hodson, R.E. (1993). Direct extraction and purification of rRNA for ecological studies. Appl. Environ. Microbiol. 59, 915-918
25. Moreau, V., Voirin, E., Paris, C., Kotera, M., Nothisen, M., Rémy, J.S., Behr, J.P., Erbacher, P., and Lenne-Samuel, N. (2009). Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription. Nucleic Acids Res. 37, e130.
26. Nielson, P.E., and Haaima, G. (1997). Peptide nucleic acid (PNA): A DNA mimic with a pseudopeptide backbone. Chem. Soc. Rev. 26, 73-78.
27. Nolte, F.S. (2004). Novel internal controls for real-time PCR assays. Clin. Chem. 50, 801-802.
28. Nordstrom, J.L, Vickery, M.C, Blackstone, G.M., Murray, S.L., and DePaola, A. (2007). Development of a multiplex real-time PCR assay with an internal amplification control for the detection of total and pathogenic Vibrio parahaemolyticus bacteria in oysters. Appl. Environ. Microbiol. 73, 5840-5847.
29. Obika, S., Nanbu, D., Hari, Y., Andoh, J-i., Morio, K-i., Doi, T., and Imanishi, T. (1998). Stability and structural features of the duplexes containing nulcoeside analogs with a fixed N-type conformation. 2′-O, 4′-C methylene ribonucleosides. Tetrahedron Lett. 39, 5401-5404.
30. Oikonomou, I., Halatsi, K., and Kyriacou, A. (2008). Selective PCR: a novel internal amplification control strategy for enhanced sensitivity in Salmonella diagnosis. Lett. Appl. Microbiol. 46, 456-461.
31. Schaerli Y., Stein, V., Spiering, M.M., Benkovic, S.J., Abell, C., and Hollfelder, F. (2010). Isothermal DNA amplification using the T4 replisome: circular nicking endonuclease-dependent amplification and primase-based whole-genome amplification. Nucleic Acids Res. 38, e201.
32. Schulz, R.G., and Gryaznov, S.M. (1996). Oligo-2′-fluoro-2′-deoxynucleotide N3′->P5′ phosphoramidates: synthesis and properties. Nucleic Acids Res. 24, 2966-2973.
33. Scipioni, A., Bourgot, I., Mauroy, A., Ziant, D., Saegerman, C., Daube, G., and Thiry, E. (2008). Detection and quantification of human and bovine noro viruses by a TaqMan RT-PCR assay with a control for inhibition. Mol. Cell. Probes 22, 215-222.
34. Simeonov, A., and Nikiforov, T.T. (2002). Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. Nucleic Acids Res. 30, e91.
35. Singh, S.K., Nielsen, P., Koshkin, A.A., and Wengel, J. (1998). LNA (locked nucleic acids): synthesis and high affinity nucleic acid recognition. Chem. Commun. 4, 455-456.
36. Suslov, O., and Steindler, D.A. (2005). PCR inhibition by reverse transcriptase leads to an overestimation of amplification efficiency. Nucleic Acids Res. 33, e181
37. Tan, E., Erwin, B., Dames, S., Ferguson, T., Buechel, M., Irvine, B., Voelkerding, K., and Niemz, A. (2008). Specific versus nonspecific isothermal DNA amplification through thermophilic polymerase and nicking enzyme activities. Biochem. 47, 9987-9999.
38. Tong, Y., Tang, W., Kim, H.J., Pan, X., Ranalli, T., and Kong, H. (2008). Development of isothermal TaqMan assays for detection of biothreat organisms. Biotechniques 45, 543-557.
39. Ugozzoli, L.A., Latorra, D., Pucket, R., Arar, K., and Hamby, K. (2004). Real-time genotyping with oligonucleotide probes containing locked nucleic acids. Anal. Biochem. 324, 143-152.
40. Van Aerschot, A., Verheggen, I., Hendrix, C., and Herdewijn, P. (1995). 1,5-Anhydrohexitol nucleic acids, a new promising antisense construct. Angew Chem. Int. Ed. 34, 1338-1339.
41. Vincent, M., Xu, Y., and Kong, H. (2004). Helicase-dependent isothermal DNA amplification. EMBO Rep. 5, 795-800.
42. Voirin, E., Behr, J.P., and Kotera, M. (2007). Versatile synthesis of oligodeoxyribonucleotide-oligospermine conjugates. Nature Prot. 2, 1360-1367.