Evaluation of probe chemistries and platforms to improve the detection limit of real-time PCR

Journal of Microbiological Methods

Volumn 66, Issue 2, 2006, Pages 206-216

  Reynisson, E ^a   Josefsen, M H ^b   Krause, M ^b   Hoorfar, J ^b  

^a Icelandic Fisheries Laboratories   (Iceland)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Diagnostic; PCR; Probe; Real time; Salmonella

Indexed keywords

LOCKED NUCLEIC ACID;

ARTICLE; CHICKEN; DNA PROBE; FECES; GENE; NONHUMAN; NUCLEIC ACID PROBE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SALMONELLA; SWINE; TEMPERATURE; TTR GENE;

ANIMALS; CHICKENS; DNA PRIMERS; DNA PROBES; DNA, BACTERIAL; FECES; FISH PRODUCTS; FLUORESCENT DYES; FOOD MICROBIOLOGY; POLYMERASE CHAIN REACTION; SALMONELLA TYPHIMURIUM; SENSITIVITY AND SPECIFICITY; TAQ POLYMERASE;

SALMONELLA; SCORPIONES; SUS SCROFA;

EID: 33745160325     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2005.11.006     Document Type: Article

References (21)

1. Anonymous. Salmonella. Detection in foods. Nordic Committee Food Analysis 71 (1999) 1-9
2. Fiandaca M.J., Hyldig-Nielsen J.J., Gildea B.D., and Coull J.M. Self-reporting PNA/DNA primers for PCR analysis. Genome Res. 11 (2001) 609-613
3. Hagen R.M., Seegmuller I., Navai J., Kappstein I., Lehn N., and Miethke T. Development of a real-time PCR assay for rapid identification of methicillin-resistant Staphylococcus aureus from clinical samples. Int. J. Med. Microbiol. 295 (2005) 77-86
4. Hoorfar J., Wolffs P., and Radstrom P. Diagnostic PCR: validation and sample preparation are two sides of the same coin. Apmis 112 (2004) 808-814
5. Johansson M.K., Fidder H., Dick D., and Cook R.M. Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes. J. Am. Chem. Soc. 124 (2002) 6950-6956
6. Josefsen M.H., Jacobsen N.R., and Hoorfar J. Enrichment followed by quantitative PCR both for rapid detection and as a tool for quantitative risk assessment of food-borne thermotolerant campylobacters. Appl. Environ. Microbiol. 70 (2004) 3588-3592
7. Kumar R., Singh S.K., Koshkin A.A., Rajwanshi V.K., Meldgaard M., and Wengel J. The first analogues of LNA (locked nucleic acids): phosphorothioate-LNA and 2′-thio-LNA. Bioorg. Med. Chem. Lett. 8 (1998) 2219-2222
8. Kutyavin I.V., Afonina I.A., Mills A., Gorn V.V., Lukhtanov E.A., Belousov E.S., Singer M.J., Walburger D.K., Lokhov S.G., Gall A.A., Dempcy R., Reed M.W., Meyer R.B., and Hedgpeth J. 3′-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res. 28 (2000) 655-661
9. Letertre C., Perelle S., Dilasser F., Arar K., and Fach P. Evaluation of the performance of LNA and MGB probes in 5′-nuclease PCR assays. Mol. Cell. Probes 17 (2003) 307-311
10. Lukhtanov E.A., Metcalf M., and Reed M.W. Fluorogenic DNA probes for multicolor hybridization assays. Am. Biotechnol. Lab. 68 (2001) 69
11. Mackay I.M. Real-time PCR in the microbiology laboratory. Clin. Microbiol. Infect. 10 (2004) 190-212
12. Malorny B., and Hoorfar J. Toward standardization of diagnostic PCR testing of fecal samples: lessons from the detection of salmonellae in pigs. J. Clin. Microbiol. 43 (2005) 3033-3037
13. Malorny B., Paccassoni E., Fach P., Bunge C., Martin A., and Helmuth R. Diagnostic real-time PCR for detection of Salmonella in food. Appl. Environ. Microbiol. 70 (2004) 7046-7052
14. McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E., Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., and Wilson R.K. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413 (2001) 852-856
15. Moreira B.G., You Y., Behlke M.A., and Owczarzy R. Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem. Biophys. Res. Commun. 327 (2005) 473-484
16. Proudnikov D., Yuferov V., Zhou Y., LaForge K.S., Ho A., and Kreek M.J. Optimizing primer-probe design for fluorescent PCR. J. Neurosci. Methods 123 (2003) 31-45
17. Radstrom P., Knutsson R., Wolffs P., Dahlenborg M., and Lofstrom C. Pre-PCR processing of samples. Methods Mol. Biol. 216 (2003) 31-50
18. Rodriguez-Lazaro D., Jofre A., Aymerich T., Hugas M., and Pla M. Rapid quantitative detection of Listeria monocytogenes in meat products by real-time PCR. Appl. Environ. Microbiol. 70 (2004) 6299-6301
19. Solinas A., Brown L.J., McKeen C., Mellor J.M., Nicol J., Thelwell N., and Brown T. Duplex Scorpion primers in SNP analysis and FRET applications. Nucleic Acids Res. 29 (2001) E96
20. Thelwell N., Millington S., Solinas A., Booth J., and Brown T. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. 28 (2000) 3752-3761
21. Whitcombe D., Theaker J., Guy S.P., Brown T., and Little S. Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17 (1999) 804-816