Skip to main content

Real-Time PCR

  • Protocol

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 266))

Abstract

The development of instruments that allow real-time monitoring of fluorescence within PCR reaction vessels is a significant advance in clinical bacteriology. The technology is very flexible, and many alternative instruments and fluorescent probe systems are currently available. Real-time PCR assays can be completed very rapidly, because no manipulations are required after amplification. Identification of amplification products by probe detection in real time is highly accurate compared with size analysis on gels. Analysis of the progress of the reaction allows accurate quantification of the target sequence over a very wide dynamic range, provided suitable standards are available. Finally, probe melting analysis can detect sequence variants including single base mutations.

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

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., et al. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.

    Article  PubMed  CAS  Google Scholar 

  2. Bach, H. J., Tomanova, J., Schloter, M., and Munch, J. C. (2002) Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification. J. Microbiol. Meth. 49, 235–245.

    Article  CAS  Google Scholar 

  3. Eishi, Y., Suga, M., Ishige, I., Kobayashi, D., Yamada, T., Takemura, T., et al. (2002) Quantitative analysis of mycobacterial and propionibacterial DNA in lymph nodes of Japanese and European patients with sarcoidosis. J. Clin. Microbiol. 40, 198–204.

    Article  PubMed  CAS  Google Scholar 

  4. Piesman, J., Schneider, B. S., and Zeidner, N. S. (2001) Use of quantitative PCR to measure density of Borrelia burgdorferi in the midgut and salivary glands of feeding tick vectors. J. Clin. Microbiol. 39, 4145–4148.

    Article  PubMed  CAS  Google Scholar 

  5. Brechtbuehl, K., Whalley, S. A., Dusheiko, G. M., and Saunders, N. A. (2001) A rapid real-time quantitative polymerase chain reaction for hepatitis B virus. J. Virol. Meth. 93, 105–113.

    Article  CAS  Google Scholar 

  6. Edwards, K. J., Metherell, L. A., Yates, M., and Saunders, N. A. (2001) Detection of rpoB mutations in Mycobacterium tuberculosis by biprobe analysis. J. Clin. Microbiol. 39, 3350–3352.

    Article  PubMed  CAS  Google Scholar 

  7. Edwards, K. J., Kaufmann, M. E., and Saunders, N. A. (2001) Rapid and accurate identification of coagulase-negative staphylococci by real-time PCR. J. Clin. Microbiol. 39, 3047–3051.

    Article  PubMed  CAS  Google Scholar 

  8. Whalley, S. A., Brown, D., Teo, 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. Microbiol. 39, 1456–1459.

    Article  PubMed  CAS  Google Scholar 

  9. McKie, A., Samuel, D., Cohen, B., and Saunders, N. A. (2002) A quantitative immuno-PCR assay for the detection of mumps-specific IgG. J. Immunol. Meth. 270, 135–141.

    CAS  Google Scholar 

  10. Mygind, T., Birkelund, S., Birkebaek, N., Oestergaard, L., Jensen, J., and Christiansen, G. (2002) Determination of PCR efficiency in chelex-100 purified clinical samples and comparison of real-time quantitative PCR and conventional PCR for detection of Chlamydia pneumoniae. BMC Microbiol. 2, 17.

    Article  PubMed  Google Scholar 

  11. Boom, R., Sol, C. J., Salimans, M. M., Jansen, C. L., Wertheim-van Dillen, P. M., and van der Noordaa, J. (1990) Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495–503.

    Google Scholar 

  12. Higuchi, R., Fockler, C., Dollinger, G., and Watson, R. (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology 11, 1026–1030.

    Article  PubMed  CAS  Google Scholar 

  13. Higuchi, R., Dollinger, G., Walsh, P. S., and Griffith, R. (1992) Simultaneous amplification and detection of specific DNA sequences. Biotechnology 10, 413–417.

    Article  PubMed  CAS  Google Scholar 

  14. 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.

    Article  PubMed  CAS  Google Scholar 

  15. Reischl, U., Linde, H. J., Metz, M., Leppmeier, B., and Lehn, N. (2000) Rapid identification of methicillin-resistant Staphylococcus aureus and simultaneous species confirmation using real-time fluorescence PCR. J. Clin. Microbiol. 38, 2429–2433.

    PubMed  CAS  Google Scholar 

  16. Lee, L. G., Livak, K. J., Mullah, B., Graham, R. J., Vinayak, R. S., and Woudenberg, T. M. (1999) Seven-color, homogeneous detection of six PCR products. Biotechniques 27, 342–349.

    PubMed  CAS  Google Scholar 

  17. Edwards, K. J. and Saunders, N. A. (2001) Real-time PCR used to measure stressinduced changes in the expression of the genes of the alginate pathway of Pseudomonas aeruginosa. J. Appl. Microbiol. 91, 29–37.

    Article  PubMed  CAS  Google Scholar 

  18. Kellogg, D. E., Rybalkin, I., Chen, S., Mukhamedova, N., Vlasik, T., Siebert, P. D., et al. (1994) TaqStart Antibody: “hot start” PCR facilitated by a neutralizing monoclonal antibody directed against Taq DNA polymerase. Biotechniques 16, 1134–1137.

    PubMed  CAS  Google Scholar 

  19. Wittwer, C. T., Ririe, K. M., Andrew, R. V., David, D. A., Gundry, R. A., and Balis, U. J. (1997) The LightCycler: a microvolume multisample fluorimeter with rapid temperature control. Biotechniques 22, 176–181.

    PubMed  CAS  Google Scholar 

  20. 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.

    Article  PubMed  CAS  Google Scholar 

  21. Perkin-Elmer. (1995) TaqMan Probe Design, Synthesis and Purification. Applied Biosystems, Foster City, CA.

    Google Scholar 

  22. Gelmini, S., Orlando, C., Sestini, R., Vona, G., Pinzani, P., Ruocco, L., et al. (1997) Quantitative polymerase chain reaction-based homogeneous assay with fluorogenic probes to measure c-erbB-2 oncogene amplification. Clin. Chem. 43, 752–758.

    PubMed  CAS  Google Scholar 

  23. Lee, M. A., Siddle, S. L., and Hunter, R. P. (2002) ResonSense: simple linear probes for quantitative homogenous rapid polymerase chain reaction. Anal. Chimic. Acta. 457, 61–70.

    Article  CAS  Google Scholar 

  24. El-Hajj, H. H., Marras, S. A., Tyagi, S., Kramer, F. R., and Alland, D. (2001) Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. J. Clin. Microbiol. 39, 4131–4137.

    Article  PubMed  CAS  Google Scholar 

  25. Whitcombe, D., Theaker, J., Guy, S. P., Brown, T., and Little, S. (1999) Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17, 804–807.

    Article  PubMed  CAS  Google Scholar 

  26. Solinas, A., Brown, L. J., McKeen, C., Mellor, J. M., Nicol, J., Thelwell, N., et al. (2001) Duplex Scorpion primers in SNP analysis and FRET applications. Nucl. Acids Res. 29, E96.

    Article  PubMed  CAS  Google Scholar 

  27. Solinas, A., Thelwell, N., and Brown, T. (2002) Intramolecular TaqMan probes for genetic analysis. Chem. Commun. 2002, 2272–2273.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Humana Press Inc.

About this protocol

Cite this protocol

Saunders, N.A. (2004). Real-Time PCR. In: Woodford, N., Johnson, A.P. (eds) Genomics, Proteomics, and Clinical Bacteriology. Methods in Molecular Biology™, vol 266. Humana Press. https://doi.org/10.1385/1-59259-763-7:191

Download citation

  • DOI: https://doi.org/10.1385/1-59259-763-7:191

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-218-6

  • Online ISBN: 978-1-59259-763-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics