Skip to main content

Linear-After-The-Exponential Polymerase Chain Reaction and Allied Technologies

Real-Time Detection Strategies for Rapid, Reliable Diagnosis from Single Cells

  • Protocol
Single Cell Diagnostics

Part of the book series: Methods in Molecular Medicineā„¢ ((MIMM,volume 132))

Abstract

Accurate detection of gene sequences in single cells is the ultimate challenge to polymerase chain reaction (PCR) sensitivity. Unfortunately, commonly used conventional and real-time PCR techniques are often too unreliable at that level to provide the accuracy needed for clinical diagnosis. Here we provide details of linear-after-the-exponential-PCR (LATE-PCR), a method similar to asymmetric PCR in the use of primers at different concentrations, but with novel design criteria to ensure high efficiency and specificity. Compared with conventional PCR, LATE-PCR increases the signal strength and allele discrimination capability of oligonucleotide probes such as molecular beacons and reduces variability among replicate samples. The analysis of real-time kinetics of LATEPCR signals provides a means for improving the accuracy of single cell genetic diagnosis.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

Institutional subscriptions

References

  1. Tyagi, S. and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303ā€“308.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  2. Heid, C. A., Stevens, J., Livak, K. J., and Williams, P. M. (1996) Real Time Quantitative PCR. Genome Res. 6, 86ā€“94.

    ArticleĀ  Google ScholarĀ 

  3. Kostrikis, L. G., Tyagi, S., Mhlanga, M. M., Ho, D. D., and Kramer, F. R. (1998) Spectral genotyping of human alleles. Science 27, 1228, 1229.

    ArticleĀ  Google ScholarĀ 

  4. Gyllensten, U. B. and Erlich, H. A. (1988) Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc. Natl. Acad. Sci. USA 85, 7652ā€“7656.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  5. Sanchez, J. A., Pierce, K. E., Rice, J. E., and Wangh, L. J. (2004) Linear-After-The-Exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc. Natl. Acad. Sci. USA 101, 1933ā€“1938.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  6. Pierce, K. E., Rice, J. E., Sanchez, J. A., and Wangh, L. J. (2005) LATE-PCR: primer design criteria for high yields of specific single-stranded DNA and improved real-time detection. Proc. Natl. Acad. Sci. USA, 102, 8609ā€“8614.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  7. Pierce, K. E., Rice, J. E., Sanchez, J. A., and Wangh, L. J. (2003) Detection of cystic fibrosis alleles from single cells using molecular beacons and a novel method of asymmetric real-time PCR. Mol. Hum. Reprod. 9, 815ā€“820.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  8. Pierce, K. E., Rice, J. E., Sanchez, J. A., and Wangh, L. J. (2002) QuantiLyseā„¢: reliable DNA amplification from single cells. BioTechniques 32, 1106ā€“1111.

    CASĀ  PubMedĀ  Google ScholarĀ 

  9. Allawi, H. T. and SantaLucia, J. (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36, 10,581ā€“10,584.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  10. SantaLucia, J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 5, 1460ā€“1465.

    ArticleĀ  Google ScholarĀ 

  11. Owczarzy, R., Vallone, P. M., Gallo, F. J., Paner, T. M., Lane, M. J., and Benight, A. S. (1998) Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers 44, 217ā€“223.

    ArticleĀ  Google ScholarĀ 

  12. Breslauer, K. J. (1986) Methods for obtaining thermodynamic data on oligonucleotide transitions, in Thermodynamic Data for Biochemistry and Biotechnology (Hinz H. ed.), Springer-Verlag, New York, pp. 402ā€“427.

    Google ScholarĀ 

  13. Le NovĆØre, N. (2001) MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 17, 1226, 1227.

    ArticleĀ  PubMedĀ  Google ScholarĀ 

  14. SantaLucia, J., Allawi, H. T., and Seneviratne, P. A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555ā€“3562.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  15. Wetmur, J. G. (1991) DNA probes: applications of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol. 26, 227ā€“235.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  16. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406ā€“3415.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  17. Marras, S. A. E., Kramer, F. R., and Tyagi, S. (2003) Genotyping single nucleotide polymorphisms with molecular beacons, in Single Nucleotide Polymorphisms: Methods and Protocols, vol. 212 (Kwok, P. Y., ed.), Humana Press, Totowa, NJ, pp. 111ā€“128.

    Google ScholarĀ 

  18. 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, 154ā€“160.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  19. Pierce, K. E., Rice, J. E., Sanchez, J. A., Brenner, C., and Wangh, L. J. (2000) Real-time PCR using molecular beacons for accurate detection of the Y chromosome in single human blastomeres. Mol. Hum. Reprod. 6, 1155ā€“1164.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  20. Rice, J. E., Sanchez, J. A., Pierce, K. E., and Wangh, L. J. (2002) Real-time PCR with molecular beacons provides a highly accurate assay for Tay-Sachs alleles in single cells. Prenat. Diagn. 22, 1130ā€“1134.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  21. Rosner, B. (1995) Fundamentals of Biostatistics, Wadsworth Publishing, Belmont, CA, pp. 277ā€“282.

    Google ScholarĀ 

  22. Rechitsky, S., Verlinsky, O., Amet, T., Rechitsky, M., Kouliev, T., Strom, C., and Verlinsky, Y. (2001) Reliability of preimplantation diagnosis for single gene disorders. Mol. Cell. Endocrinol. 183, S65ā€“S68.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  23. Al-Soud, W. A., Jonsson, L. J., and Radstrom, P. (2000) Identification and characterization of immunoglobulin G in blood as a major inhibitor of diagnostic PCR. J. Clin. Microbiol. 38, 345ā€“350.

    CASĀ  PubMedĀ  Google ScholarĀ 

  24. Al-Soud, W. A. and Radstrom, P. (2001) Purification and characterization of PCR-inhibitory components in blood cells. J. Clin. Microbiol. 3, 485ā€“493.

    ArticleĀ  Google ScholarĀ 

  25. Cui, X. F., Li, H. H., Goradia, T. M., Lange, K., Kazazian, H. H. Jr, Galas, D., and Arnheim, N. (1989) Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers. Proc. Natl. Acad. Sci. USA 86, 9389ā€“9393.

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  26. Li, Q., Luan, G., Guo, Q., and Liang, J. (2002) A new class of homogeneous nucleic acid probes based on specific displacement hybridization. Nucleic Acids Res. 30, e5.

    ArticleĀ  PubMedĀ  Google ScholarĀ 

  27. Cheng, J., Zhang, Y., and Li, Q. (2004) Real-time PCR genotyping using displacing probes. Nucleic Acids Res. 32, e61.

    ArticleĀ  PubMedĀ  Google ScholarĀ 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

Ā© 2007 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Pierce, K.E., Wangh, L.J. (2007). Linear-After-The-Exponential Polymerase Chain Reaction and Allied Technologies. In: Thornhill, A. (eds) Single Cell Diagnostics. Methods in Molecular Medicineā„¢, vol 132. Humana Press. https://doi.org/10.1007/978-1-59745-298-4_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-298-4_7

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-578-1

  • Online ISBN: 978-1-59745-298-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics