Sensitivity comparison of real-time PCR probe designs on a model DNA plasmid

Analytical Biochemistry

Volumn 344, Issue 2, 2005, Pages 257-265

  Wang, L ^a   Blasic Jr , J R ^a   Holden, M J ^a   Pires, R ^b  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^b Invitrogen Corporation   (United States)

Author keywords

5 Exonuclease activity; Detection sensitivity; DNA plasmid; Fluorescence quantum yield; Melting temperature; Molecular beacon; Probe design; Quantitative real time PCR; Shared stem molecular beacon; Signal to background ratio; TaqMan

Indexed keywords

DNA; FLUORESCENCE; MELTING POINT; PROBES; QUANTUM YIELD;

DETECTION SENSITIVITY; DNA PLASMIDS; EXONUCLEASE ACTIVITY; FLUORESCENCE QUANTUM YIELD; MOLECULAR BEACON; PROBE DESIGN; QUANTITATIVE REAL TIME PCR; SIGNAL-TO-BACKGROUND RATIO; TAQMAN;

POLYMERASE CHAIN REACTION;

PLASMID DNA;

AMPLICON; ARTICLE; DNA CLEAVAGE; FLUORESCENCE; MELTING POINT; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; QUANTUM CHEMISTRY; SIGNAL NOISE RATIO;

EID: 23944455623     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2005.06.038     Document Type: Article

References (30)

1. S. Meuer C.T. Wittwer K. Nakagawara Rapid Cycle Real-Time PCR: Methods and Applications 1999 Springer Berlin
2. C.T. Wittwer, M.G. Herrmann, A.A. Moss, and R.P. Rasmussen Continuous fluorescence monitoring of rapid cycle DNA amplification BioTechniques 22 1997 130 138
3. M. Nakao, J.W.G. Janssen, T. Flohr, and C.R. Bartram Rapid and reliable quantification of minimal residual disease in acute lymphoblastic leukemia using rearranged immunoglobulin and T-cell receptor Loci by LightCycler technology Cancer Res. 60 2000 3281 3289
4. A.K. Dhar, M.M. Roux, and K.R. Klimpel Detection and quantification of infectious hypodermal and hematopoietic necrosis virus and white spot virus in shrimp using real-time quantitative PCR and SYBR Green chemistry J. Clin. Microbiol. 39 2001 2835 2845
5. S. Tyagi, and F.R. Kramer Molecular beacons: probes that fluoresce upon hybridization Nat. Biotechnol. 14 1996 303 308
6. K. Szuhai, E. Sandhaus, S.M. Kolkman-Uljee, M. Lemaitre, J.C. Truffert, R.W. Dirks, H.J. Tanke, G.J. Fleuren, E. Schuuring, and A.K. Raap A novel strategy for human papillomavirus detection and genotyping with SYBR Green and molecular beacon polymerase chain reaction Am. J. Pathol. 159 2001 1651 1660
7. I. Nazarenko, B. Lowe, M. Darfler, P. Ikonomi, D. Schuster, and A. Rashtchian Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore Nucleic Acids Res. 30 2002 e37
8. Y.S. Lie, and C.J. Petropoulos Advances in quantitative PCR technology: 5′ nuclease assays Curr. Opin. Biotechnol. 9 1998 43 48
9. E. Barragan, P. Bolufer, I. Moreno, G. Martin, J. Nomdedeu, S. Brunet, P. Fernandez, C. Rivas, and M.A. Sanz Quantitative detection of AML1-ETO rearrangement by real-time RT-PCR using fluorescently labeled probes Leuk. Lymphoma 42 2001 747 756
10. J. Vandesompele, A. De Paepe, and F. Speleman Elimination of primer-dimer artifacts and genomic coamplification using a two-step SYBR Green I real-time RT-PCR Anal. Biochem. 303 2002 95 98
11. K.P. Mouillesseaux, K.R. Klimpel, and A.K. Dhar Improvement in the specificity and sensitivity of detection for the Taura syndrome virus and yellow head virus of penaeid shrimp by increasing the amplicon size in SYBR Green real-time RT-PCR J. Virol. Methods 111 2003 121 127
12. S.A.E. Marras, F.R. Kramer, and S. Tyagi Multiplex detection of single-nucleotide variations using molecular beacons Genet. Anal. Biomol. E 14 1999 151 156
13. G. Breen, D. Harold, S. Ralston, D. Shaw, and D.St. Clair Determining SNP allele frequencies in DNA pools BioTechniques 28 2000 464 470
14. S.R. Lewin, M. Vesanen, L. Kostrikis, A. Hurley, M. Duran, L. Zhang, D.D. Ho, and M. Markowitz Use of real-time PCR and molecular beacons to detect virus replication in human immunodeficiency virus type 1-infected individuals on prolonged effective antiretroviral therapy J. Virol. 73 1999 6099 6103
15. K. Szuhai, J. Ouweland, R. Dirks, M. Lemaitre, J. Truffert, G. Janssen, H. Tanke, E. Holme, J. Maassen, and A. Raap Simultaneous A8344G heteroplasmy and mitochondrial DNA copy number quantitation in myoclonus epilepsy and ragged-red fibers (MERRF) syndrome by a multiplex molecular beacon based real-time fluorescence PCR Nucleic Acids Res. 29 2001 e13
16. C. Eckert, O. Landt, T. Taube, K. Seeger, B. Beyermann, J. Proba, and G. Henze Potential of LightCycler technology for quantification of minimal residual disease in childhood acute lymphoblastic leukemia Leukemia 14 2000 316 323
17. A. Tsourkas, M.A. Behlke, and G. Bao Structure-function relationships of shared-stem and conventional molecular beacons Nucleic Acids Res. 30 2002 4208 4215
18. L.Y. Bustamante, A. Crooke, J. Martínez, A. Díez, and J.M. Bautista Dual-function stem molecular beacons to assess mRNA expression in AT-rich transcripts of Plasmodium falciparum BioTechniques 36 2004 488 494
19. K.A. Browne Sequence-specific, self-reporting hairpin inversion probes J. Am. Chem. Soc. 127 2005 1989 1994
20. D-M. Kong, L. Gu, H-X. Shen, and H-F. Mi A modified molecular beacon combining the properties of TaqMan probe Chem. Commun. 8 2002 854 855
21. M. Zuker Mfold Web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31 2003 3406 3415
22. B. Mullah, and A. Andrus Automated synthesis of double dye-labeled oligonucleotides using tetramethylrhodamine (TAMRA) solid supports Tetrahedron Lett. 38 1997 5751 5754
23. W.P.C. Stemmer, A. Crameri, K.D. Ha, T.M. Brennan, and H.L. Heyneker Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Gene 164 1995 49 53
24. F.M. Ausubel R. Brent R.E. Kingston D.D. Moore J.G. Seidman J.A. Smith K. Struhl Short Protocols in Molecular Biology third ed. 1997 John Wiley New York
25. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
26. N. Klonis, A.H.A. Clayton, E.W. Voss, and W.H. Sawyer Spectral properties of fluorescein in solvent-water mixtures: applications as a probe of hydrogen bonding environments in biological systems Photochem. Photobiol. 67 1998 500 510
27. G.K. Turner An absolute spectrofluorimeter Science 146 1964 183 189
28. J.E. Noble, L. Wang, K.D. Cole, and A.K. Gaigalas The effect of overhanging nucleotides on fluorescence properties of hybridizing oligonucleotides labeled with Alexa-488 and FAM fluorophores Biophys. Chem. 113 2005 255 263
29. I. Nazarenko, R. Pires, B. Lowe, M. Obaidy, and A. Rashtchian Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes Nucleic Acids Res. 30 2002 2089 2095
30. A.O. Crockett, and C.T. Wittwer Fluorescein-labeled oligonucleotides for real-time PCR: using the inherent quenching of deoxyguanosine nucleotides Anal. Biochem. 290 2001 89 97