Skip to main content
Book cover

Medical Biomethods Handbook pp 293–303Cite as

Oligonucleotide Ligation Assay

  • Protocol

  • 2035 Accesses

Part of the Springer Protocols Handbooks book series (SPH)

Abstruct

Advances in molecular genetics and biotechnology are changing the practice of medicine. Completion of the human genome sequence and development of high-throughput semiautomated DNA analysis techniques have resulted in an exponential increase in the rate of discovery of new disease genes. The challenge of understanding complex, multigenic diseases, and the role of genetic variability in disease risk is now within reach. Identification of genetic mutation is assuming increasing importance in cancer diagnosis and in the detection and characterization of infectious agents. The emerging field of molecular genetic medicine has resulted in a need for new technologies capable of probing large numbers of gene sequences with sufficient selectivity to distinguish single-nucleotide differences.

Keywords

  • Oligonucleotide Probe
  • Ligation Product
  • Polymerase Chain Reaction Amplicon
  • Mobility Modifier
  • Padlock Probe

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1385/1-59259-870-6:293
  • Chapter length: 11 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   169.00
Price excludes VAT (USA)
  • ISBN: 978-1-59259-870-0
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   219.99
Price excludes VAT (USA)
Learn about institutional subscriptions
Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.

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

References

  1. Cotton, R. (1997) Mutation Detection, Oxford University Press, New York.

    Google Scholar 

  2. Mashal, R. and Sklar, J. (1996) Practical methods of mutation detection. Curr. Opin. Genet. Dev. 6, 275–280.

    PubMed  CAS  CrossRef  Google Scholar 

  3. Landegren, U. (1996) Laboratory Protocols for Mutation Detection. Oxford University Press, New York.

    Google Scholar 

  4. Landegren, U. (1993) Ligation-based DNA diagnostics. BioEssays 15, 761–764.

    PubMed  CAS  CrossRef  Google Scholar 

  5. Jarvius, J., Nilsson, M., and Landegren, U. (2003) Oligonucleotide ligation assay, in Single Nucleotide Polymorphisms: Methods and Protocols (Kwok, P.-Y., ed.), Humana, Totowa, NJ, pp. 215–228.

    Google Scholar 

  6. Barany, F. (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88, 189–193.

    PubMed  CAS  CrossRef  Google Scholar 

  7. Luo, J, Bergstrom, D. and Barany, F. (1996) Improving the fidelity of Thermus thermophilus DNA ligase. Nucleic Acids Res. 24, 3071–3087.

    PubMed  CAS  CrossRef  Google Scholar 

  8. Luo, J. and Barany, F. (1996) Identification of essential residues in Thermus thermoophilus DNA ligase. Nucleic Acids Res. 24, 3079–3085.

    PubMed  CAS  CrossRef  Google Scholar 

  9. Pritchard, C. and Southern, E. (1997) Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases. Nucleic Acids Res. 25, 3403–3407.

    PubMed  CAS  CrossRef  Google Scholar 

  10. Wu, D. and Wallace, R. (1989) The ligation amplification reaction (LAR)-amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 5, 560–569.

    CrossRef  Google Scholar 

  11. Wiedmann, M., Wilson, W., Czajka, J., Luo, J., Barany, F., and Batt, C. (1994) Ligase chain reaction (LCR)-overview and applications. PCR Methods Applic. 3, S51–S64.

    CAS  Google Scholar 

  12. Nilsson, M., Malmgre, H., Samiotaki, M., Kwiatkowski, M., Chowdhary, B., and Landegren, U. (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265, 2085–2088.

    PubMed  CAS  CrossRef  Google Scholar 

  13. Nilsson, M., Krejci, K., Koch, J., Kwiatkowski, M., Gustavsson, P., and Landegren, U. (1997) Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nature Genet. 16, 252–255.

    PubMed  CAS  CrossRef  Google Scholar 

  14. Baner, J., Nilsson, M., Mendel-Hartvig, M., and Landegren, U. (1998) Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res. 26, 5073–5078.

    PubMed  CAS  CrossRef  Google Scholar 

  15. Nickerson, D., Kaiser, R., Lappin, S., Stewart, J., Hood, L., and Landegren, U. (1990) Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. Proc. Natl. Acad. Sci. USA 87, 8923–8927.

    PubMed  CAS  CrossRef  Google Scholar 

  16. Samiotaki, M., Kwiatkowski, M., Parik, J., and Landegren, U. (1994) Dual-color detection of DNA sequence variants through ligase-mediated analysis. Genomics 20, 238–242.

    PubMed  CAS  CrossRef  Google Scholar 

  17. Grossman, P., Bloch, W., Brinson, E., et al. (1994) High-density multiplex detection of nucleic acid sequences: oligonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res. 22, 4527–4534.

    PubMed  CAS  CrossRef  Google Scholar 

  18. Eggerding, F., Iovannisci, D., Brinson, E., Grossman, P., and Winn-Deen, E. (1995) Fluorescencebased oligonucleotide ligation assay for analysis of cystic fibrosis transmembrane conductance regulator gene mutations. Hum. Mutat. 5, 153–165.

    PubMed  CAS  CrossRef  Google Scholar 

  19. Brinson, E., Adriano, T., Bloch, W., et al. (1997) introduction to PCR/OLA/SCS, a multiplex DNA test, and its application to cystic fibrosis. Genet. Test. 1, 61–68.

    PubMed  CAS  Google Scholar 

  20. Eggerding, F. (1995) A one-step coupled amplification and oligonucleotide ligation procedure for multiplex genetic typing. PCR Methods Applic. 4, 337–345.

    CAS  Google Scholar 

  21. Landegren, U., Kaiser, R., Sanders, J., and Hood, L. (1988) A ligase-mediated gene detection technique. Science 241, 1077–1080.

    PubMed  CAS  CrossRef  Google Scholar 

  22. Day, N., Tadin, M., Christiano, A., Lanzano, P, Piomelli, S., and Brown, S. (2002) Rapid prenatal diagnosis of sickle cell diseases using oligonucleotide ligation assay coupled with laser-induced capillary fluorescence detection. Prenat. Diagn. 22, 686–691.

    PubMed  CAS  CrossRef  Google Scholar 

  23. Chakravarty, A., Hansen, T., Horder, M., and Kristensen, S. (1997) A fast and robust dual-label nonradioactive oligonucleotide ligation assay for detection of factor V Leiden. Thromb. Haemost. 78, 1234–1236.

    PubMed  CAS  Google Scholar 

  24. Eggerding, F. (2000) Fluorescent oligonucleotide ligation technology for identification of ras oncogene mutations. Mol. Biotechnol. 14, 223–233.

    PubMed  CAS  CrossRef  Google Scholar 

  25. Edelstein, R., Nickerson, D., Tobe, V., Manns-Arcuino, L., and Frenkel, L. (1998) Oligonucleotide ligation assay for detecting mutations in the human immunodeficiency virus type 1 pol gene that are associated with resistance to zidovudine, didanosine, and lamivudine. J. Clin. Microbiol. 36, 569–572.

    PubMed  CAS  Google Scholar 

  26. Beck, I., Mahalanabis, M., Pepper, G., et al. (2002) Rapid and sensitive oligonucleotide ligation assay for detection of mutations in human immunodeficiency virus type 1 associated with high-level resistance to protease inhibitors. J. Clin. Microbiol. 40, 1413–1419.

    PubMed  CAS  CrossRef  Google Scholar 

  27. Bui, M-H., Stone, G., Nilius, A., Almer, L., and Flamm, R. (2003) PCR-oligonucleotide ligation assay for detection of point mutations associated with quinolone resistance in Streptococcus pneumoniae. Antimicrob. Agents Chemother. 47, 1456–1459.

    CAS  CrossRef  Google Scholar 

  28. Stone, G., Shortridge, D., Versalovic, J., et al. (1997) A PCR-oligonucleotide ligation assay to determine the prevalence of 23S rRNA gene mutations in clarithromycin-resistant Helicobacter pylori. Antimicrob. Agents Chnemother. 41, 712–714.

    CAS  Google Scholar 

  29. Delahunty, C., Ankener, J. W., Deng, Q., Eng, J., and Nickerson, D. (1996) Testing the feasibility of DNA typing for human identification by PCR and an oligonucleotide ligation assay. Am. J. Hum. Genet. 58, 1239–1246.

    PubMed  CAS  Google Scholar 

  30. Tobe, V., Taylor, S., and Nickerson D. (1996) Single-well genotyping of diallelic sequence variations by a two-color ELISA-based oligonucleotide ligation assay. Nucleic Acids Res. 24, 3728–3732.

    PubMed  CAS  CrossRef  Google Scholar 

  31. Chen, X., Livak, K., and Kwok, P.-Y. (1998) A homogeneous, ligase-mediated DNA diagnostic test. Genome Res. 8, 549–556.

    PubMed  CAS  Google Scholar 

  32. Iannone, M., Taylor J., Chen, J., et al. (2000) Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39, 131–140.

    PubMed  CAS  CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Huntington Medical Research Institutes, Pasadena, CA

    Faye A. Eggerding

Authors
  1. Faye A. Eggerding
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Hertfordshire, Hatfield, UK

    John M. Walker & Ralph Rapley & 

Rights and permissions

Reprints and Permissions

Copyright information

© 2005 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Eggerding, F.A. (2005). Oligonucleotide Ligation Assay. In: Walker, J.M., Rapley, R. (eds) Medical Biomethods Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1385/1-59259-870-6:293

Download citation

  • DOI: https://doi.org/10.1385/1-59259-870-6:293

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-288-9

  • Online ISBN: 978-1-59259-870-0

  • eBook Packages: Springer Protocols