Skip to main content

PNA-Mediated PCR Clamping

Applications and Methods

  • Protocol
Peptide Nucleic Acids

Part of the book series: Methods in Molecular Biology ((MIMB,volume 208))

Abstract

About 90% of sequence variants in humans are differences in single bases of DNA, called single nucleotide polymorphisms (SNPs). When two individuals are compared, their genomic DNA differs at ∼1/1000 nucleotides (1). Neutral polymorphisms may be responsible for subtle differences between individuals, such as hair and eye color, or may be silent identifiers of variability and relatedness. Other polymorphisms cause genetic diseases such as hemophilia and are referred to as mutations. Polymorphisms within an individual may cause cancer or other diseases, are responsible for the variability of our immune response, and have been implicated in the aging process. Identification of polymorphisms can therefore be useful in diagnosis of genetic disease, detection of tumors, study of immune response and aging, identification of microbial strains, and developing relatedness trees between humans or other organisms.

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. Kwok P. Y., Deng Q., Zakeri H., Taylor S. L., and Nickerson D. A. (1996) Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics 31, 123–126.

    Article  PubMed  CAS  Google Scholar 

  2. Kwok S., Kellogg D. E., McKinney N., Spasic D., Goda L., Levenson C., and Sninsky J. J. (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res. 18, 999–1005.

    Article  PubMed  CAS  Google Scholar 

  3. Ørum H., Nielsen P. E., Egholm M., Berg R. H., Buchardt O., and Stanley C. (1993) Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Res. 21, 5332–5336.

    Article  PubMed  Google Scholar 

  4. Kyger E. M., Krevolin M. D., and Powell M. J. (1998) Detection of the hereditary hemochromatosis gene mutation by real-time fluorescence polymerase chain reaction and peptide nucleic acid clamping. Anal. Biochem. 260, 142–148.

    Article  PubMed  CAS  Google Scholar 

  5. Murdock D. G., Christacos N. C., and Wallace D. C. (2000) The agerelated accumulation of a mitochondrial DNA control region mutation in muscle, but not brain, detected by a sensitive PNA-directed PCR clamping based method. Nucleic Acids Res. 28, 4350–4355.

    Article  PubMed  CAS  Google Scholar 

  6. Behn M. and Schuermann M. (1998) Simple and reliable factor V genotyping by PNA-mediated PCR clamping. Thromb. Haemost. 79, 773–777.

    PubMed  CAS  Google Scholar 

  7. Thiede C., Bayerdorffer E., Blasczyk R., Wittig B., and Neubauer A. (1996) Simple and sensitive detection of mutations in the ras protooncogenes using PNA-mediated PCR clamping. Nucleic Acids Res. 24, 983–984.

    Article  PubMed  CAS  Google Scholar 

  8. Behn M., Thiede C., Neubauer A., Pankow W., and Schuermann M. (2000) Facilitated detection of oncogene mutations from exfoliated tissue material by a PNA-mediated ‘enriched PCR’ protocol. J. Pathol. 190, 69–75.

    Article  PubMed  CAS  Google Scholar 

  9. Rhodes C. H., Honsinger C., Porter D. M., and Sorenson G. D. (1997) Analysis of the allele-specific PCR method for the detection of neoplastic disease. Diagn. Mol. Pathol. 6, 49–57.

    Article  PubMed  CAS  Google Scholar 

  10. Myal Y., Blanchard A., Watson P., Corrin M., Shiu R., and Iwasiow B. (2000) Detection of genetic point mutations by peptide nucleic acid-mediated polymerase chain reaction clamping using paraffin-embedded specimens. Anal. Biochem. 285, 169–172.

    Article  PubMed  CAS  Google Scholar 

  11. Bianco P., Riminucci M., Majolagbe A., Kuznetsov S. A., Collins M. T., Mankani M. H., et al. (2000) Mutations of the GNAS1 gene, stromal cell dysfunction, and osteomalacic changes in non-McCune-Albright fibrous dysplasia of bone. J. Bone Min. Res. 15, 120–128.

    Article  CAS  Google Scholar 

  12. Zhong S., Nguyen N. Y., and Eggerman T. L. (1999) Detection of apolipoprotein B mRNA editing by peptide nucleic acid mediated PCR clamping. Biochem. Biophys. Res. Comm. 259, 311–313.

    Article  PubMed  CAS  Google Scholar 

  13. vonWintzingerode F., Landt O., Ehrlich A., and Gobel U. B. (2000) Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity. Appl. Environ. Microbiol. 66, 549–557.

    Article  Google Scholar 

  14. Feder J. N., Tsuchihashi Z., Irrinki A., Lee V. K., Mapa F. A., Morikang, E., et al. (1997) The hemochromatosis founder mutation in HLA-H disrupts beta2-microglobulin interaction and cell surface expression. J. Biol. Chem. 272, 14,025–14,028.

    Article  PubMed  CAS  Google Scholar 

  15. Takahashi S., Chi X. J., Yamaguchi Y., Suzuki H., Sugaya S., Kita K., et al. (2001) Mutagenicity of bisphenol A and its suppression by interferon-alpha in human RSa cells. Mutat. Res. 490, 199–207.

    PubMed  CAS  Google Scholar 

  16. Behn M. and Schuermann M. (1998) Sensitive detection of p53 gene mutations by a ‘mutant enriched’ PCR-SSCP technique. Nucleic Acids Res. 26, 1356–1358.

    Article  PubMed  CAS  Google Scholar 

  17. Cochet O., Martin E., Fridman W. H., and Teillaud J. L. (1999) Selective PCR amplification of functional immunoglobulin light chain from hybridoma containing the aberrant MOPC 21-derived V kappa by PNA-mediated PCR clamping. Biotechniques 26, 818–820, 822.

    PubMed  CAS  Google Scholar 

  18. Mrozikiewicz P. M., Landt O., Cascorbi I., and Roots I. (1997) Peptide nucleic acid-mediated polymerase chain reaction clamping allows allelic allocation of CYP1A1 mutations. Anal. Biochem. 250, 256–257.

    Article  PubMed  CAS  Google Scholar 

  19. Aynacioglu A. S., Cascorbi I., Mrozikiewicz P. M., and Roots I. (1998) High frequency of CYP1A1 mutations in a Turkish population. Arch. Toxicol. 72, 215–218.

    Article  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

© 2002 Humana Press Inc.

About this protocol

Cite this protocol

Murdock, D.G., Wallace, D.C. (2002). PNA-Mediated PCR Clamping. In: Nielsen, P.E. (eds) Peptide Nucleic Acids. Methods in Molecular Biology, vol 208. Springer, Totowa, NJ. https://doi.org/10.1385/1-59259-290-2:145

Download citation

  • DOI: https://doi.org/10.1385/1-59259-290-2:145

  • Publisher Name: Springer, Totowa, NJ

  • Print ISBN: 978-0-89603-976-6

  • Online ISBN: 978-1-59259-290-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics