Advertisement

Probe Design, Production, and Applications

  • Marilena Aquino de Muro
Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

A probe is a nucleic acid molecule (single-stranded DNA or RNA) with a strong affinity with a specific target (DNA or RNA sequence). Probe and target base sequences must be complementary to each other, but depending on conditions, they do not necessarily have to be exactly complementary. The hybrid (probe-target combination) can be revealed when appropriate labeling and detection systems are used. Gene probes are used in various blotting and in situ techniques for the detection of nucleic acid sequences. In medicine, they can help in the identification of microorganisms and the diagnosis of infectious, inherited, and other diseases.

Keywords

Oligonucleotide Probe Gene Probe Nucleic Acid Sequence Polymerase Chain Reaction Cycle Slot Blotting 
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.

References

  1. 1.
    Keller, G. H. and Manak, M. M. (1989) DNA Probes, Stockton, New York.Google Scholar
  2. 2.
    Sambrook, J. and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
  3. 3.
    Karcher, S. J. (1995) Molecular Biology: A Project Approach, Academic, San Diego, CA.Google Scholar
  4. 4.
    Hugenholtz, P., Tyson, G. W., and Blackall, L. L. (2002) Design and evaluation of 16S rRNAtargeted oligonucleotide probes for fluorescence in situ hybridization, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 29–42.Google Scholar
  5. 5.
    Boehringer Mannheim GmbH (1995) The DIG System User’s Guide for Filter Hybridisation, Boehringer Mannheim, Mannheim, Germany.Google Scholar
  6. 6.
    Boehringer Mannheim GmbH (1996) Nonradioactive In Situ Hybridisation Manual: Application Manual, 2nd ed. Boehringher Mannheim GmbH, Mannheim, Germany.Google Scholar
  7. 7.
    Alphey, L. and Parry, H. D. (1995) Making nucleic acid probes, in DNA cloning 1: Core Techniques (Glover, D. M. and Hames, B. D., eds.), IRL, Oxford, pp. 121–141.Google Scholar
  8. 8.
    Feinberg, A. P. and Vogelstein, B. (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Analy. Biochem. 132, 6–13.CrossRefGoogle Scholar
  9. 9.
    Feinberg, A. P. and Vogelstein, B. (1984) Addendum. Analy. Biochem. 137, 266–267.CrossRefGoogle Scholar
  10. 10.
    Aquino de Muro, M. and Priest, F. G. (1994) A colony hybridization procedure for the identification of mosquitocidal strains of Bacillus sphaericus on isolation plates. J. Invertebr. Pathol. 63, 310–313.CrossRefGoogle Scholar
  11. 11.
    Aquino de Muro, M. and Priest, F. G. (2000) Construction of chromosomal integrants of Bacillus sphaericus 2362 by conjugation with Escherichia coli. Res. Microbiol. 151, 547–555.Google Scholar
  12. 12.
    Garratt, L. C., McCabe, M. S., Power, J. B., and Davey, M. R. (2002) Detection of single-copy genes in DNA from transgenic plants, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 211–222.Google Scholar
  13. 13.
    Hilario, E. (2002) Photobiotin labeling, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 19–22.Google Scholar
  14. 14.
    Hilario, E. (2002) End labeling procedures, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 13–18.Google Scholar
  15. 15.
    Promega Corp. (1996) Protocols and Applications Guide, 3rd ed., Promega Corp., Madison, WI.Google Scholar
  16. 16.
    Schleicher & Schuell, Inc. (1995) Blotting, Hybridization and Detection: An S&S Laboratory Manual, 6th ed., Schleicher & Schuell, Inc., Keene, NH.Google Scholar
  17. 17.
    Stahl, D. A. and Amman, R. (1991) Development and application of nucleic acid probes, in Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M., eds.), Wiley, Chichester, pp. 205–244.Google Scholar
  18. 18.
    Brooker, J. D. Lockington, R. A. Attwood, G. T., and Miller, S. (1990) The use of gene and antibody probes in identification and enumeration of rumen bacterial species, in Gene Probes for Bacteria (Macario, A. J. L. and Conway de Macario, E., eds.), Academic, San Diego, CA, pp. 390–416.Google Scholar
  19. 19.
    Stahl, D. A. and Kane, M. D. (1992) Methods in microbial identification, tracking and monitoring of function. Curr. Opin. Biotechnol. 3, 244–252.CrossRefGoogle Scholar
  20. 20.
    Ward, D. M., Bateson, M. M., Weller, R., and Ruff-Roberts, A. L. (1992) Ribosomal RNA analysis of micro-organisms as they occur in nature. Adv. Microb. Ecol. 12, 219–286.Google Scholar
  21. 21.
    Orlow, I. and Cordon-Cardo, C. (2002) Evaluation of alterations in the tumor suppressor genes INK4A and INK4B in human bladder tumors, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 43–59.Google Scholar
  22. 22.
    Mendoza-Leon, A., Luis, L., and Martinez, C. (2002) The *b-tubulin gene region as a molecular marker to distinguish Leishmania parasites, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 61–83.Google Scholar
  23. 23.
    Brown, R. D. and Joy Ho, P. (2002) Detection of malignant plasma cells in the bone marrow and peripherical blood of patients with multiple myeloma, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 85–91.Google Scholar
  24. 24.
    Nuovo, G J. (2002) Diagnosis of human papillomavirus using in situ hybridization and in situ polymerase chain reaction, in Gene Probes: Principles and Protocols (Aquino de Muro, M. and Rapley, R., eds.), Humana, Totowa, NJ, pp. 113–136.Google Scholar
  25. 25.
    Wang, Y., Pang, D., Zhang, Z., Zheng, H., Cao, J., and Shen J. (2003) Visual gene diagnosis of HBV and HCV based on nanoparticle probe amplification and silver staining enhancement. J. Med. Virol. 70(2), 205–211.PubMedCrossRefGoogle Scholar
  26. 26.
    Cook, D. W., Bowers, J. C., and DePaola, A. (2002) Density of total and pathogenic (tdh+) Vibrio parahaemolyticus in Atlantic and Gulf Coast molluscan shellfish at harvest. J. Food Protect. 65(12), 1873–1880.Google Scholar
  27. 27.
    Dalsgaard, A., Serichantalergs, O., Forslund, A., et al. (2001) Clinical and environmental isolates of Vibrio cholerae serogroup O141 carry the CTX phage and the genes enconding the toxin-coregulated pili. J. Clin. Microbiol. 39(11), 4086–4092.PubMedCrossRefGoogle Scholar
  28. 28.
    Kondo, S., Kongmuang, U., Kalnauwakul, S., Matsumoto, C., Chen, C. H., and Nishibuchi, M. (2001) Molecular epidemiologic analysis of Vibrio cholerae O1 isolated during the 1997–8 cholera epidemic in southern Thailand. Epidemiol. Infect. 127(1), 7–16.PubMedCrossRefGoogle Scholar
  29. 29.
    Nair, G. B., Bag, P. K., Shimada, T., et al. (1995) Evaluation of DNA probes for specific detection of Vibrio cholerae O139 Bengal. J. Clin. Microbiol. 33(8), 2186–2187.PubMedGoogle Scholar
  30. 30.
    Frech, G. and Schwarz, S. (2000) Molecular analysis of tetracycline resistance in Salmonella enterica subsp. enterica serovars Typhimurium, Enteritidis, Dublin Choleraesuis, Hadar and Saintpaul: construction and application of specific gene probes. J. Appl. Microbiol. 89(4), 633–641.PubMedCrossRefGoogle Scholar
  31. 31.
    Mainil, J. G., Gerardin, J., and Jacquemin, E. (2000) Identification of the F17 fimbrial subunit-and adhesin-enconding (f17A and f17G) gene variants in necrotoxigenic Escherichia coli from cattle, pigs and humans. Vet. Microbiol. 73(4), 327–335.PubMedCrossRefGoogle Scholar
  32. 32.
    Fujimoto, S., Umene, K., Saito, M., Horikawa, K., and Blaser, M. J. (2000) Restriction fragmentlength polymorphism analysis using random chromosomal gene probes for epidemiological analysis of Campylobacter jejuni infections. J. Clin. Microbiol. 38(4), 1664–1667.PubMedGoogle Scholar
  33. 33.
    Kirkwood, C. D., Gentsch, J. R., and Glass, R. I. (1999) Sequence analysis of the NSP4 gene from human rotavirus strains isolated in the United States. Virus Genes 19(2), 113–122.PubMedCrossRefGoogle Scholar
  34. 34.
    Santos, M. R. M., Lorenzi, H., Porcile, P., et al. (1999) Physical mapping of a 670-kb region of chromosomes XVI and XVII from the human protozoan parasite Trypanosoma cruzi encompassing the genes for two immunodominant antigens. Genome Res. 9(12), 1268–1276.PubMedCrossRefGoogle Scholar
  35. 35.
    Radwanska, M., Magez, S., Perry-O’Keefe, H., et al. (2002) Direct detection and identification of African trypanosomes by fluorescence in situ hybridization with peptide nucleic acid probes. J. Clin. Microbiol. 40(11), 4295–4297.PubMedCrossRefGoogle Scholar
  36. 36.
    Higgins, G. A. and Mah, V. H. (1989) In situ hybridisation approaches to human neurological disease, in Gene Probes (Conn, P. M., ed.), Academic, San Diego, CA, pp. 183–196.Google Scholar
  37. 37.
    Rigby, S., Procop, G. W., Haase, G., et al. (2002) Fluorescence in situ hybridization with peptide nucleic acid probes for rapid identification of Candida albicans directly from blood culture bottles. J. Clin. Microbiol. 40(6), 2182–2186.PubMedCrossRefGoogle Scholar
  38. 38.
    Oliveira, K., Haase, G., Kurtzman, C., Hyldig-Nielsen, J. J., and Stender, H. (2001) Differentiation of Candida albicans and Candida dubliniensis by fluorescent in situ hybridization with peptide nucleic acid probes. J. Clin. Microbiol. 39(11), 4138–4141.PubMedCrossRefGoogle Scholar
  39. 39.
    Cloud, J. L., Neal, H., Rosenberry, R., et al. (2002) Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J. Clin. Microbiol. 40(2), 400–406.PubMedCrossRefGoogle Scholar
  40. 40.
    El Hajj, H. H., Marras, S. A. E., 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(11), 4131–4137.PubMedCrossRefGoogle Scholar
  41. 41.
    Oliveira, K., Procop, G. W., Wilson, D., Coull, J., and Stender, H. (2002) Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes. J. Clin. Microbiol. 40(1), 247–251.PubMedCrossRefGoogle Scholar
  42. 42.
    Reddy, C. C., Jayakumar, R., Kumanan, K., and Nainar, A. M. (2002) Detection of rabies virus genome in brain tissues by using in situ hybridization. Indian J. Anim. Sci. 72(1), 3–5.Google Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Marilena Aquino de Muro
    • 1
  1. 1.CABI Bioscience UK CentreEghamUK

Personalised recommendations