Skip to main content

Mutation Detection by Fluorescent Hybridization Probe Melting Curves

  • Chapter
Rapid Cycle Real-Time PCR

Abstract

Sequence analysis of nucleic acids is used in many fields of science and for a variety of purposes. Although direct sequencing remains the gold standard for initially characterizing a new region of DNA, it is not a practical solution for the routine analysis of a sequence once it is known. For this reason, molecular techniques that facilitate the analysis of variants in established sequence have widespread application and continue to be developed. Conventionally, the target is first amplified by PCR and then further processed for mutation detection. Recently developed instrumentation couples rapid PCR with fluorescent hybridization probes, allowing target amplification and product analysis to be done consecutively, without sample handling and within 30 min [1].

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 74.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bernard PB, CT Wittwer (2000) Homogenous amplification and variant detection by fluorescent hybridization probes. Clin Chem 46: 147–148

    PubMed  CAS  Google Scholar 

  2. Wittwer CT, Ririe KM, Andrew RV, David DA, Gundry RA, UJ Balis (1997) The LightCycler: A microvolume multisample fluorimeter with rapid temperature control. Biotechniques 22: 176–181

    PubMed  CAS  Google Scholar 

  3. Ririe KM, Rasmussen RP, CT Wittwer (1997) Product differentiation by analysis of DNA melting curves during the Polymerase Chain Reaction. Anal Biochem 245: 154–160

    Article  PubMed  CAS  Google Scholar 

  4. Wittwer CT, Herrmann MG, Moss AA, RP Rasmussen (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 22: 130–138

    PubMed  CAS  Google Scholar 

  5. Lay MJ, CT Wittwer (1997) Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin Chem 43: 2262–2267

    PubMed  CAS  Google Scholar 

  6. Bernard PS, Lay MJ, CT Wittwer (1998) Integrated amplification and detection of the C677 T point mutation in the methylenetetrahydrofolate reductase gene by fluorescence resonance energy transfer and probe melting curves. Anal Biochem 255: 101–107

    Article  PubMed  CAS  Google Scholar 

  7. Bernard PS, Ajioka RS, Kushner JP, CT Wittwer (1998). Homogenous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes. Am J Pathol 153: 1055–1061

    Article  PubMed  CAS  Google Scholar 

  8. Gundry CN, Bernard PS, Herrmann MG, Reed GH, CT Wittwer (1999). Rapid F508del and F508 C assay using fluorescent hybridization probes. Genetic Testing 3: 365–370

    Article  PubMed  CAS  Google Scholar 

  9. Wetmur JG (1995) In: Meyers RA (ed) Molecular Biology and Biotechnology pp 605–608 VCH Publishers Inc., New York, NY

    Google Scholar 

  10. SantaLucia J Jr, Allawi HT, Seneviratne PA (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35: 3555–3562

    Article  PubMed  CAS  Google Scholar 

  11. Guo Z, Liu Q, Smith LM (1997) Enhanced discrimination of single nucleotide polymorphisme by artificial mismatch hybridization. Nature Biotech 4: 331–335

    Article  Google Scholar 

  12. Allawi HT, SantaLucia J Jr (1997). Thermodynamics and NMR of Internal G:T Mismatches in DNA. Biochemistry 36: 10581–10594

    Article  PubMed  CAS  Google Scholar 

  13. Allawi HT, SantaLucia J Jr (1998). Thermodynamics of internal C:T mismatches in DNA. Nucleic Acids Res 26: 2694–2701

    Article  PubMed  CAS  Google Scholar 

  14. Allawi HT, SantaLucia J Jr (1998). Nearest-neighbor thermodynamics of internal A:C mismatches in DNA: Sequence dependence and pH effects. Biochemistry 37: 9435–9444

    Google Scholar 

  15. Allawi HT, SantaLucia J Jr (1998). Nearest neighbor thermodynamic parameters for internal G:A mismatches in DNA. Biochemistry 37: 2170–2179

    Article  PubMed  CAS  Google Scholar 

  16. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr (1999). Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A:A, C:C, G:G, and T: T mismatches. Biochemistry 38: 3468–3477

    Google Scholar 

  17. Bernard PS, Pritham GH, Wittwer CT (1999) Color multiplexing hybridization probes using the apolipoprotein E locus as a model system for genotyping. Anal Biochem 273: 221–228

    CAS  Google Scholar 

  18. Schutz E, von Ahsen N (1999) Spreadsheet for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches. Biotechniques 27: 1218–1222

    PubMed  CAS  Google Scholar 

  19. Lyon E, Millson A, Phan T, Wittwer CT (1998). Detection and identification of base alterations within the region of factor V Leiden by fluorescent melting curves. Mol Diag 3: 203–210

    Article  CAS  Google Scholar 

  20. Mitchell RS, Stevenson E, Mouritsen CL, Bohling S, Lyon E (1999) A comparison of storage conditions for PCR mixtures with fluorescently labeled probes [Abstract]. J Mol Diag 1: 60

    Google Scholar 

  21. von Ahsen N, Schutz E, Armstrong VW Oellerich M (1999) Rapid detection of prothrombotic mutations of prothrombin (G20210), factor V (G1691 A), and methylenetetrahydrofolate reductase (C677 T) by real-time fluorescence PCR with the LightCycler. Clin Chem 45: 1875–1878

    Google Scholar 

  22. Aslanidis C, Schmitz G (1999) High-speed apolipoprotein E genotyping and apolipoprotein B3500 mutation detection using real-time fluorescence PCR and melting curves. Clin Chem 45: 1094–1097

    CAS  Google Scholar 

  23. Nauck MS, Gierens H, Nauck MA, Marz W, Wieland H (1999) Rapid genotyping of human platelet antigen 1 (HPA-1) with fluorophore-labeled hybridization probes on the LightCycler. Br J Haematol 105: 803–810

    Article  PubMed  CAS  Google Scholar 

  24. Blomeke B, Sieben S, Spotter D, Landt O, Merk HF (1999) Identification of N-acetyltransferase 2 genotypes by continuous monitoring of fluorogenic hybridization probes. Anal Biochem 275: 93–97

    Article  PubMed  CAS  Google Scholar 

  25. Nauck MS, Wieland H, Marz W (1999) Rapid, homogenous genotyping of the 4G/5G polymorphism in the promoter region of the PAII gene by fluorescence resonance energy transfer and probe melting curves. Clin Chem 45: 1141–1147

    PubMed  CAS  Google Scholar 

  26. Pals G, Pindolia K, Worsham MJ (1999) A rapid and sensitive approach to mutation detection using real-time polymerase chain reaction and melting curve analysis, using BRCA1 as an example. Mol Diag 4: 241–246

    Article  CAS  Google Scholar 

  27. Can PA, Cook P, Ratcliffe D, Multimer D, Pillay D (1999) Use of real-time PCR and fluorimetry to detect lamivudine resistance-associated mutations in hepatitis B virus. Antimicrob Agents Chemother 43: 1600–1608

    Google Scholar 

  28. Lee LG, Livak KJ, Mullah B, Graham RJ, Vinayak RS, Woudenberg TM (1999) Seven-color, homogenous detection of six PCR products. Biotechniques 27: 342–349

    PubMed  CAS  Google Scholar 

  29. von Ahsen N, Oellerich M, Schutz E (2000) Use of two reporter dyes without interference in a single-tube rapid cycle PCR: a.,-antitrypsin genotyping by multiplex real-time fluorescence PCR with the LightCycler. Clin Chem 46: 156–161

    Google Scholar 

  30. Herrmann MG, Dobrowolski SF, Wittwer CT (2000) Beta-globin genotyping by multiplexing probe Tm and color. Clin Chem 46: 425–428

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2001 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Bernard, P.S., Reiser, A., Pritham, G.H. (2001). Mutation Detection by Fluorescent Hybridization Probe Melting Curves. In: Meuer, S., Wittwer, C., Nakagawara, KI. (eds) Rapid Cycle Real-Time PCR. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-59524-0_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-59524-0_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-66736-0

  • Online ISBN: 978-3-642-59524-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics