Mediator probe PCR: Detection of real-time PCR by label-free probes and a universal fluorogenic reporter

Methods in Molecular Biology

Volumn 1160, Issue , 2014, Pages 55-73

  Wadle, Simon ^a   Rubenwolf, Stefanie ^a   Lehnert, Michael ^a   Faltin, Bernd ^a   Weidmann, Manfred ^a   Hufert, Frank ^a   Zengerle, Roland ^a   von Stetten, Felix ^a  

^a NONE

Author keywords

Mediator probe; Mediator probe PCR; Real time PCR; Universal reporter; Universal sequence dependent nucleic acid detection

Indexed keywords

NUCLEIC ACID; OLIGONUCLEOTIDE; FLUORESCENT DYE; VIRUS DNA;

ARTICLE; CHEMICAL REACTION; CONTROLLED STUDY; DNA DETERMINATION; ENZYME ANALYSIS; ENZYME MODIFICATION; FLUORESCENCE ANALYSIS; HYDROLYSIS; MEDIATOR PROBE POLYMERASE CHAIN REACTION; MOLECULAR HYBRIDIZATION; MOLECULAR PROBE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRACTICE GUIDELINE; PRIORITY JOURNAL; PROCESS DESIGN; REACTION ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA ANALYSIS; UNIVERSAL FLUOROGENIC REPORTER; CHEMISTRY; CONFORMATION; GENETICS; NUCLEIC ACID HYBRIDIZATION; PROCEDURES;

BASE SEQUENCE; DNA, VIRAL; FLUORESCENT DYES; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84921425253     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0733-5_6     Document Type: Article

References (26)

1. Livak KJ, Flood SJ, Marmaro J et al (1995) 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.
2. Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14: 303-308.
3. Wittwer CT, Herrmann MG, Moss AA et al (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 22: 130-138.
4. Gardner SN, Kuczmarski TA, Vitalis EA et al (2003) Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis a, B, C, and E viruses and human immunodeficiency virus. J Clin Microbiol 41: 2417-2427.
5. Lunge VR, Miller BJ, Livak KJ et al (2002) Factors affecting the performance of 5′ nuclease PCR assays for Listeria monocytogenes detection. J Microbiol Methods 51: 361-368.
6. SantaLucia J Jr (2007) Physical principles and visual-OMP software for optimal PCR design. In: Yuryev A (ed) Methods in Molecular Biology, vol 402. Humana Press, Totowa, pp 3-34.
7. Livak KJ (1999) Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet Anal 14: 43-149.
8. Althaus CF, Gianella S, Rieder P et al (2010) Rational design of HIV-1 fluorescent hydrolysis probes considering phylogenetic variation and probe performance. J Virol Methods 165: 151-160.
9. Marras SAE, Kramer FR, Tyagi S (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res 30: e122.
10. Wong ML, Medrano JF (2005) Real-time PCR for MRNA quantitation. Biotechniques 39: 75-85.
11. Letertre C, Perelle S, Dilasser F et al (2003) Evaluation of the performance of LNA and MGB probes in 5′-nuclease PCR assays. Mol Cell Probes 17: 307-311.
12. Faltin B, Zengerle R, von Stetten F (2013) Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications. Clin Chem 59: 1567-1582.
13. Mokany E, Bone SM, Young PE et al (2010) MNAzymes, a versatile New class of nucleic acid enzymes that Can function as biosensors and molecular switches. J Am Chem Soc 132: 1051-1059.
14. http://www. illumina. com/products/nupcr. ilmn. Accessed June 2013.
15. http://www. seegene. com/en/research/core_040. php. Accessed June 2013.
16. Faltin B, Wadle S, Roth G et al (2012) Mediator probe PCR: a novel approach for detection of real-time PCR based on label-free primary probes and standardized secondary universal fluorogenic reporters. Clin Chem 58: 1546-1556.
17. King N (2010) Methods in Molecular Biology, 2nd edn, RT-PCR protocols. Humana, Totowa.
18. Kennedy S, Oswald N (2011) PCR troubleshooting and optimization: the essential guide. Caister Academic Press, Poole.
19. http://frodo. wi. mit. edu. Accessed June 2013.
20. http://eu. idtdna. com/PrimerQuest/Home/Index.
21. http://www. dnasoftware. com/product/visual-omp. Accessed June 2013.
22. http://rna. tbi. univie. ac. at/cgi-bin/RNAfold. cgi. Accessed June 2013.
23. Deprez RHL, Fijnvandraat AC, Ruijter JM et al (2002) Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions. Anal Biochem 307: 63-69.
24. http://blast. ncbi. nlm. nih. gov. Accessed June 2013.
25. http://www. faculty. ucr. edu/~mmaduro/random. htm. Accessed June 2013.
26. Gunson R, Gillespie G, Carman F (2003) Optimisation of PCR reactions using primer chessboarding. J Clin Virol 26: 369-373.