Real-time PCR fluorescent chemistries

Methods in Molecular Biology

Volumn 353, Issue , 2007, Pages 237-261

  Mackay, John ^a   Landt, Olfert ^a  

^a NONE

Author keywords

Fluorescent chemistries; Hybridization probes; Hydrolysis probes; Melting curves; Molecular beacon probes; Quenched dye primers; Scorpion primers; SYBR green I

Indexed keywords

SCORPIONES;

DNA; FLUORESCENT DYE; ORGANIC COMPOUND; PRIMER DNA; SYBR GREEN I; UNCLASSIFIED DRUG;

ARTICLE; CHEMISTRY; GENETIC PROCEDURES; GENETICS; HYDROLYSIS; ISOLATION AND PURIFICATION; KINETICS; METHODOLOGY; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; THERMODYNAMICS;

DNA; DNA PRIMERS; FLUORESCENT DYES; HYDROLYSIS; KINETICS; MOLECULAR PROBE TECHNIQUES; OLIGONUCLEOTIDE PROBES; ORGANIC CHEMICALS; POLYMERASE CHAIN REACTION; THERMODYNAMICS;

EID: 34247198469     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-229-7:237     Document Type: Article

References (92)

1. Higuchi, R., Dollinger, G., Walsh, P. S., and Griffith, R. (1992) Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY) 10, 413-417.
2. Higuchi, R., Fockler, C., Dollinger, G., and Watson, R. (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. BioTechnology (NY) 11, 1026-1030.
3. Wittwer, C. T., Herrmann, M. G., Moss, A. A., and Rasmussen, R. P. (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22, 130-138.
4. Molecular Probes. (2003) SYBR Green I Product Information Sheet.
5. DNA detection with SYBR Green I, from www.lightcycler-online.com, Roche Applied Science, 1999.
6. Zipper, H., Branner, H., Bernhagen, J., and Vitzthum, F. (2004) Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nuc. Acids Res. 32, 12 el03.
7. Nucleic Acid Stains, Chapter 8.1, from The Handbook: A Guide to Fluorescent Probes and Labeling Technologies. Available from: http://probes.invitrogen.com.
8. Newby, D. T., Hadfield, T. L., and Roberto, F. F. (2003) Real-time PCR detection of Brucella abortus: a comparative study of SYBR Green I, 5' exonuclease and hybridization probe assays. App. Environ. Micro. 69, 4753-4759.
9. Schmittgen, T. D., Zakrajsek, B. A., Mills, A. G., Gorn, V., Singer, M. J., and Reed, M. W (2000) Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. Anal. Biochem. 15, 194-204.
10. Ririe, K. M., Rasmussen, R. P., and Wittwer, C. T. (1997) Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 245, 154-160.
11. Gingeras, T. R., Higuchi, R., Kricka, L. J., Lo, Y. M. D., and Wittwer, C. T. (2005) Fifty years of molecular (DNA/RNA) diagnostics. Clin. Chem. 51, 661-671.
12. Morrison, T. B., Weis, J. J., and Wittwer, C. T. (1998) Quantification of lowcopy transcripts by continuous SYBR Green I monitoring during amplification. BioTechniques 24, 954-962.
13. Ball, T. B., Plummer, F. A., and HayGlass, K. T. (2003) Improved mRNA quantification in LightCycler RT-PCR. Int. Arch. Allergy Immunology. 130, 82-86.
14. Simpson, D. A. C., Feeney, S., Boyle, C., and Stitt, A. W. (2000) Retinal VEGF mRNA measured by SYBR Green I fluorescence: a versatile approach to quantitative PCR. Mol. Vis. 6, 178-183.
15. Bengtsson, M., Karlsson, H. J., Westman, G., and Kubista, M. (2003) A new minor groove binding asymmetric cyanine reporter dye for real-time PCR. Nue. Acids Res. 31, e45.
16. Wittwer, C. T., Reed, G. H., Gundry, C. N., Vandersteen, J. G., and Pryor, R. J. (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem. 49, 853-860.
17. Vaughn, C. P. and Elenitoba-Johnson, K. S. J. (2004) High-resolution melting analysis for detection of internal tandem duplications. J. Mol. Diag. 6, 211-216.
18. Nath, K., Sarosy, J. W., Hahn, J., and Di Como, C. J. (2000) Effects of ethidium bromide and SYBR Green I on different polymerase chain reaction systems. J. Biochem Biophys. Meth. 42, 15-29.
19. Liew, M., Pryor, R., Palais, R., et al. (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin. Chem. 50, 1156-1164.
20. Zhou, L., Myers, A. N., Vandersteen, J. G., Wang, L., and Wittwer, C. T. (2004) Closed-tube genotyping with unlabelled oligonucleotide probes and a saturating DNA dye. Clin. Chem. 50, 1328-1335.
21. Monis, P. T., Giglio, S., and Saint, C. P. (2005) Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. Anal. Biochem. 340, 24-34.
22. Giglio, S., Monis, P. T., and Saint, C. P. (2003) Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR. Nucleic Acids Res. 31, el36.
23. Bon, M. A. M., van Oeveren-Dybicz, A., and van den Bergh, F. A. J. T. M. (2000) Genotyping of HLA-B27 by real-time PCR without hybridization probes. Clin. Chem. 46, 1000-1002.
24. Read, S. J., Mitchell, J. L., and Fink, C. G. (2001) LightCycler multiplex PCR for the laboratory diagnosis of common viral infections of the central nervous system. J. Clin. Micro. 39, 3056-3059.
25. Papin, J. F., Vahrson, W., and Dittmer, D. P. (2004) SYBR Green-based real-time quantitative PCR assay for detection of West Nile Virus circumvents false-negative results due to strain variability. J. Clin. Micro. 42, 1511-1518.
26. Drosten, C., Gottig, S., Schilling, S., et al. (2002) Rapid detection and quantification of RNA of Ebola and Marburg viruses, Lassa virus, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, dengue virus, and yellow fever virus by real-time reverse transcription-PCR. J. Clin. Micro. 40, 2323-2330.
27. Rajeevan, M. S., Vernon, S. D., Taysavang, N., and Unger, E. R. (2001) Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. J. Mol. Diag. 3, 26-31.
28. Mimmack, M. L., Brooking, J., and Bahn, S. (2004) Quantitative polymerase chain reaction: validation of microarray results from postmortem brain studies. Biol. Psychiatry 55, 337-345.
29. Rodríguez-Lázaro, D., Hernández, M., Scortii, M., Esteve, T., Vázquez-Boland, J. A., and Pla, M. (2004) Quantitative detection of Listeria monocytogenes and Listeria innocua by real-time PCR: assessment of hly, iap, and lin02483 targets and AmpliFluor technology. App. Environ. Micro. 70, 1366-1377.
30. Nazarenko, I., Lowe, B., Darfler, M., Ikonomi, P., Schuster, D., and Rashtchian, A. (2002) Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore Nuc. Acids Res 30, e37.
31. Crockett, A. O. and Wittwer, C. T. (2001) Fluorescein-labeled oligonucleotides for real-time PCR: using the inherent quenching of deoxyguanosine nucleotides. Anal. Biochem. 290, 89-97.
32. Kaboev, O. K., Luchkina, L. A., Tret'iakov, A. N., and Bahrmand, A. R. (2000) PCR hot start using primers with the structure of molecular beacons (hairpin-like structure). Nuc. Acids Res. 28, e94.
33. Chen, R., Huang, W., Lin, Z., Zhou, Z., Yu, H., and Zhu, D. (2004) Development of a novel real-time RT-PCR assay with LUX primer for the detection of swine transmissible gastroenteritis virus. J. Virol. Methods. 122, 57-61.
34. Fiandaca, M. J., Hyldig-Nielsen, J. J., Gildea, B. D., and Coull, J. M. (2001) Selfreporting PNA/DNA primers for PCR analysis. Genome Res. 11, 609-611.
35. Clegg, R. M. (1992) Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211, 353-388.
36. Holland, P. M., Abramson, R. D., Watson, R., and Gelfand, D. H. (1991) Detection of specific polymerase chain reaction product by utilizing the 5′ to 3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA 88, 7276-7280.
37. Livak, K. J., Flood, S. J. A., Marmara, J., Giusti, W., and Deetz, K. (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.
38. Gibson, U. E. M., Heid, C. A., and Williams, P. M. (1996) A novel method for real time quantitative RT-PCR. Genome Res. 6, 995-1001.
39. Marras, S. A., Kramer, F. R., and Tyagi, S. (2002). Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nuc. Acids Res. 30, el22.
40. Kutyavin, I. V., Afonina, I. A., Mills, A., et al. (2000) 3′-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nuc. Acids Res. 28, 655-661.
41. Lanciotti.R. S., Kerst, A. J., Nasci, R. S., et al. (2000) Rapid detection of West Nile Virus from human clinical specimens, field-collected mosquitoes, and avian samples by a TaqMan reverse transcriptase-PCR Assay. J. Clin. Micro. 38, 4066-4071.
42. Nijhuis, M., van Maarseveen, N., Schuurman, R., et al. (2002) Rapid and sensitive routine detection of all members of the genus Enterovirus in different clinical specimens by real-time PCR. J. Clin. Micro. 40, 3666-3670.
43. Tondella, M. L. C., Talkington, D. F., Holloway, B. P., et al. (2002) Development and evaluation of real-time PCR-based fluorescent assays for detection of Chlamydia pneumoniae. J. Clin. Micro. 40, 575-583.
44. Yoshida, T., Deguchi, T., Ito, M., Maeda, S.-L, Tamaki, M., and Ishiko, H. (2002) Quantitative detection of Mycoplasma genitalium from first-ass urine of men with urethritis and asymptomatic men by real-time PCR. J. Clin. Micro. 40, 1451-1455.
45. Yang, S., Lin, S., Kelen, G.D., et al. (2002) Quantitative multiprobe PCR assay for simultaneous detection and identification to species level of bacterial pathogens. J. Clin. Micro. 40, 3449-3454.
46. Livak, K. J. (1999) Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet. Anal. 14, 143-149.
47. Cradic, K. W., Wells, J. E., Allen, L., Kruckeberg, K. E., Singh, R. J., and Grebe, S. K. G. (2004) Substitution of 3′-phosphate cap with a carbon-based blocker reduces the possibility of fluorescent resonance energy transfer probe failure in real-time PCR assays. Clin. Chem. 50, 1080-1082.
48. Cane, P. A., Cook, P., Ratcliffe, D., Mutimer, D., and Pillay, D. (1999) use of realtime PCR and fluorimetry to detect lamivudine resistance-associated mutations in hepatitis B virus. Antimicrobial Agents Chemother. 43, 1600-1608.
49. Whalley, S. A., Brown, D., Tei, C. G., Dusheiko, G. M., and Saunders, N. A. (2001) Monitoring the emergence of hepatitis B virus polymerase gene variants during lamivudine therapy using the LightCycler. J. Clin. Micro. 39, 1456-1459.
50. Wilhelm, H., Pingoud, A., and Hahn, M. (2001) Comparison between Taq DNA polymerase and its Stoffel fragment for quantitative real-time PCR with hybridization probes. BioTechniques 30, 1052-1062.
51. Boll, I., Ebenbichler, C., and Ankenbauer, W. (2004) Establishing multiplex PCR assays using the new LightCycler multiplex DNA master and the LightCycler 2.0 instrument. Biochemica 2, 4-5.
52. Lyon, E. (2001) Mutation detection using fluorescent hybridization probes and melting curve analysis. Expert Rev. Mol. Diagn. 1, 92-101.
53. Teupser, D., Rupprecht, W., Lohse, P., and Thiery, J. (2001) Fluorescence-based detection of the CETP TaqIB polymorphism: false positives with the TaqManbased exonuclease assay attributable to a previously unknown gene variant. Clin. Chem. 47, 852-857.
54. Li, Q., Luan, G., Guo, Q., and Liang, J. (2002) A new class of homogeneous nucleic acid probes based on sequence displacement hybridization. Nuc. Acids. Res. 30, e5.
55. Mayall, F., Barratt, K., and Shanks, J. (2003) The detection of Simian virus 40 in mesotheliomas from New Zealand and England using real time FRET probe PCR protocols. J. Clin. Path. 56, 728-730.
56. Lay, M. and Wittwer, C. (1997) Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin. Chem. 43, 2262-2267.
57. Schutz, E., von Ahsen, N., and Ollerich, M. (2000) Genotyping of eight thiopurine methyltransferase mutations: three-color multiplexing, "two-color/shared" anchor, and fluorescence-quenching hybridization probe assays based on thermodynamic nearest-neighbor probe design. Clin. Chem. 46, 1728-1737.
58. Schutz, E. and von Ahsen, N. (1999) A simple and versatile standard spreadsheet software for the thermodynamic melting point prediction for oligonucleotide hybridization with and without mismatches. BioTechniques 26, 2018-1026.
59. Arjomand-Nahad, F., Diefenbach, K., Landt, O., Gaikovitch, E., and Roots, I. (2004) Genotyping of the triallelic variant G2677T/A in MDRl using LightCycler with locked-nucleic-acid-modifed hybridization probes. Anal. Biochem. 334, 201-203.
60. Op den Buijsch, R. A. M., Bekers, O., Wijnen, P. A. H. M., van Dieijen-Visser, M. P., and de Vries, J. E. (2005) Rapid genotyping of the OATP1B1 polymorphisms A388G and T521C with real-time PCR FRET assays. Pharmacogenomics 6, 393-397.
61. Stocher, M., Leb, V., Bozic, M., et al. (2003) Parallel detection of five human herpes virus DNAs by a set of real-time polymerase chain reactions in a single run. J. Clin. Virol. 26, 85-93.
62. Whiley, D. M., Syrmis, M. W., Mackay, I. M., and Sloots, T. P. (2002) Detection of human respiratory synctial virus in respiratory samples by LightCycler reverse transcriptase PCR. J. Clin. Micro. 40, 4418-4422.
63. Øster, B. and Höllsberg, P. (2002) A sensitive quantification of HHV-6B by realtime PCR. Biol. Proced. Online 4, 88-93.
64. Klaschik, D., Lehrmann, L. E., Raadts, A., Book, M., Hoeft, A., and Stuber, F. (2002) Real-time PCR for detection and differentiation of Gram-positive and Gram-negative bacteria. J. Clin. Micro. 40, 4304-4307.
65. Mygind, T., Bikelund, S., Falk, E., and Christiansen, G. (2001) Evaluation of realtime quantitative PCR for identification and quantification of Chlamydia pneumoniae by comparison with immunohistochemistry. J. Micro. Methods 46, 241-251.
66. Reischl, U., Linde, H.-J., Lehn, N., Landt, O., Barratt, K., and Wellinghausen, N. (2002) Direct detection and differentiation of Legionella spp. and Legionella pneumophila in clinical specimens by dual-colour real-time PCR and melting curve analysis. J. Clin. Micro. 30, 3814-3817.
67. Wellinghausen, N., Wirths, B., Franz, A. R., Karolyi, L., Marre, R., and Reischl, U. (2004) Algorithm for the the identification of bacterial pathogens in positive blood cultures by real-time LightCycler polymerase chain reaction (PCR) with sequencespecific probes. Diag. Micro. Infec. Disease 48, 229-241.
68. Pryce, T. M., Kay, I. D., Palladino, S., and Heath, C. H. (2003) Real-time automated polymerase chain reaction (PCR) to detect Candida albicans and Aspergillus fumigatus DNA in whole blood from high-risk patients. Diag. Micro Infect. Disease. 47, 487-496.
69. Loeffler, J., Henke, N., Hebart, H., et al. (2000) Quantification of fungal DNA by using fluorescence resonance energy transfer and the LightCycler system. J. Clin. Micro. 38, 586-590.
70. Loeffler, J., Swatoch, P., Akhawi-Araghi, D., Hebart, H., and Einsele, H. (2003) Automated RNA extraction by MagNA Pure followed by rapid quantification of cytokine and chemokine gene expression with use of fluorescence resonance energy transfer. Clin. Chem. 49, 955-958.
71. Richtsteiger, R., Henke-Gendo, C., Schmidtke, M., Harste, G., and Heim, A. (2003). Quantitative multiplex real-time PCR for the sensitive detection of inteferon βgene induction and viral suppression of interferon βexpression. Cytokine 24, 190-200.
72. Steffensen, R., Hoffmann, K., and Varming, K. (2003) Rapid genotyping of MBL2 gene mutations using real-time PCR with fluorescent hybridisation probes. J. Immunol. Meth. 278, 191-199.
73. Van den Bergh, A. J. T. M., van Oevereb-Dybicz, A. M., and Bon, M. A. M. (2000) Rapid single-tube genotyping of the factor V Leiden and prothrombin mutations by real-time PCR using dual-color detection. Clin. Chem. 46, 1191-1195.
74. Vet, J. A. M., Van der Rijt, B. J. M., and Blom, H. J. (2002) Molecular beacons: colorful analysis of nucleic acids. Expert Rev. Mol. Diagn. 2, 77-86.
75. Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49-53.
76. Tyagi, S., Marras, S. A. E., and Kramer, F. R. (2000) Wavelength-shifting molecular beacons Nat. Biotechnol. 18, 1191-1196.
77. Zuker, M. (2003) Mfold webserver for nucleic acid folding and hybridization prediction. Nuc. Acids. Res. 31, 3406-3415.
78. Nitin, N., Santangelo, P. J., Kim, G., Nie, S., and Bao, G. (2004) Peptide-linked molecular beacons for efficienct delivery and rapid mRNA detection in living cells. Nuc. Acids Res. 32, e58.
79. Perlette, J. and Tan, W. (2001) Real-time monitoring of intracellular mRNA hybridization inside single living cells. Anal. Chem. 73, 5544-5550.
80. Piatek, A. S., Tyagi, S., Pol, A. G., et al. (1998) Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol. 16, 359-363.
81. Hodgson, D. R., Foy, C. A., Partridge, M., Pateromichelakis, S., and Gibson, N. J. (2002) Development of a facile fluorescent assay for the detection of 80 mutations within the p53 gene. Mol. Med. 8, 227-237.
82. Abd El Galil, K. H., El Sokkary, M. A., Kheira, S. M., et al. (2004) Combined immunomagnetic separation molecular beacon reverse transcription PCR assay for detection of hepatitis A virus from environmental samples. Appl. Environ. Microbiol. 70, 4371-4374.
83. Liming, S. H. and Bhagwat, A. A. (2004) Application of a molecular beaconreal-time PCR technology to detect Salmonella species contaminating fruits and vegetables. Int. J. Food Micro. 95, 177-187.
84. Bergeron, M. G. and Ke, D. (2001) New DNA-based PCR approaches for rapid real-time detection and prevention of group B streptococcal infections in newborns and pregnant women. Expert Mol. Med. 380, 5a.
85. Whitcombe, D., Theaker, T., Guy, S. P., Brown, T., and Little, S. (1999) Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17, 804-807.
86. Thelwell, N., Millington, S., Solinas, A., Booth, J., and Brown, T. (2000) Mode of action and application of scorpion primers to mutation detection. Nuc. Acids Res. 28, 3752-3761.
87. Solinas, A., Brown, L. J., McKeen, C., et al. (2001) Duplex scorpion primers in SNP analysis and FRET applications. Nuc Acids Res. 29, 396.
88. Hart, K. W., Williams, O. M., Thelwell, N., et al. (2001) Novel method for detection, typing and quantification of human papillomaviruses in clincal samples. J. Clin. Micro. 39, 3204-3213.
89. Svanik, N., Westman, G., Wang, D., and Kubista, M. (2000) Light-up probes: thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution. Anal. Biochem. 281, 26-35.
90. Svanik, N., Ståhlberg, A., Sehlstedt, U., Sjöback, R., and Kubista, M. (2000) Detection of PCR products in real time using light-up probes. Anal. Biochem. 287, 179-182.
91. Francés, F., Corella, D., Sorlí, J., Guillen, M., González, J., and Portóles, O. (2005) Validating a rapid method for detecting common polymorphisms in the APOA5 gene by melting curve analysis using LightTyper. Clin. Chem. 51, 1279-1282.
92. Bennett, C. D., Campbell, M. N., Cook, C. J., et al. (2003) the LightTyper™: highthroughput genotyping using fluorescent melting curve analysis. BioTechniques 34, 1288-1295.