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. 1993 Dec 11;21(24):5782–5785. doi: 10.1093/nar/21.24.5782

PCR primed with VNTR core sequences yields species specific patterns and hypervariable probes.

D D Heath 1, G K Iwama 1, R H Devlin 1
PMCID: PMC310549  PMID: 8284229

Abstract

The use of genomic DNA-based techniques in ecological and evolutionary studies has been limited by the availability of suitable probes for species of interest due to the technical difficulty of isolating and applying such probes. We have developed a simple technique that directs polymerase chain reaction (PCR) amplification to regions rich in variable number of tandem repeats (VNTRs). By using published VNTR core sequences as primers in PCRs, fragments were amplified that showed little variation within a species, but did show differences between species. When the amplified fragments were used as probes with genomic DNA Southern blots they produced hypervariable single-locus or few-locus patterns in fish, birds, and humans. We have named this procedure as Directed Amplification of Minisatellite-region DNA (DAMD).

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aquadro C. F. Why is the genome variable? Insights from Drosophila. Trends Genet. 1992 Oct;8(10):355–362. doi: 10.1016/0168-9525(92)90281-8. [DOI] [PubMed] [Google Scholar]
  2. Arnold M. L., Buckner C. M., Robinson J. J. Pollen-mediated introgression and hybrid speciation in Louisiana irises. Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1398–1402. doi: 10.1073/pnas.88.4.1398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chapco W., Ashton N. W., Martel R. K., Antonishyn N., Crosby W. L. A feasibility study of the use of random amplified polymorphic DNA in the population genetics and systematics of grasshoppers. Genome. 1992 Aug;35(4):569–574. doi: 10.1139/g92-085. [DOI] [PubMed] [Google Scholar]
  4. Don R. H., Cox P. T., Wainwright B. J., Baker K., Mattick J. S. 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 1991 Jul 25;19(14):4008–4008. doi: 10.1093/nar/19.14.4008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Feinberg A. P., Vogelstein B. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984 Feb;137(1):266–267. doi: 10.1016/0003-2697(84)90381-6. [DOI] [PubMed] [Google Scholar]
  6. Georges M., Lequarré A. S., Castelli M., Hanset R., Vassart G. DNA fingerprinting in domestic animals using four different minisatellite probes. Cytogenet Cell Genet. 1988;47(3):127–131. doi: 10.1159/000132529. [DOI] [PubMed] [Google Scholar]
  7. Hadrys H., Balick M., Schierwater B. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol. 1992 May;1(1):55–63. doi: 10.1111/j.1365-294x.1992.tb00155.x. [DOI] [PubMed] [Google Scholar]
  8. Jeffreys A. J., MacLeod A., Tamaki K., Neil D. L., Monckton D. G. Minisatellite repeat coding as a digital approach to DNA typing. Nature. 1991 Nov 21;354(6350):204–209. doi: 10.1038/354204a0. [DOI] [PubMed] [Google Scholar]
  9. Jeffreys A. J., Royle N. J., Wilson V., Wong Z. Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature. 1988 Mar 17;332(6161):278–281. doi: 10.1038/332278a0. [DOI] [PubMed] [Google Scholar]
  10. Nakamura Y., Carlson M., Krapcho K., Kanamori M., White R. New approach for isolation of VNTR markers. Am J Hum Genet. 1988 Dec;43(6):854–859. [PMC free article] [PubMed] [Google Scholar]
  11. Nakamura Y., Leppert M., O'Connell P., Wolff R., Holm T., Culver M., Martin C., Fujimoto E., Hoff M., Kumlin E. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science. 1987 Mar 27;235(4796):1616–1622. doi: 10.1126/science.3029872. [DOI] [PubMed] [Google Scholar]
  12. Nelson D. L., Ledbetter S. A., Corbo L., Victoria M. F., Ramírez-Solis R., Webster T. D., Ledbetter D. H., Caskey C. T. Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6686–6690. doi: 10.1073/pnas.86.17.6686. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Scott M. P., Haymes K. M., Williams S. M. Parentage analysis using RAPD PCR. Nucleic Acids Res. 1992 Oct 25;20(20):5493–5493. doi: 10.1093/nar/20.20.5493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Vassart G., Georges M., Monsieur R., Brocas H., Lequarre A. S., Christophe D. A sequence in M13 phage detects hypervariable minisatellites in human and animal DNA. Science. 1987 Feb 6;235(4789):683–684. doi: 10.1126/science.2880398. [DOI] [PubMed] [Google Scholar]
  15. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990 Dec 25;18(24):7213–7218. doi: 10.1093/nar/18.24.7213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Westneat D. F., Noon W. A., Reeve H. K., Aquadro C. F. Improved hybridization conditions for DNA 'fingerprints' probed with M13. Nucleic Acids Res. 1988 May 11;16(9):4161–4161. doi: 10.1093/nar/16.9.4161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Williams J. G., Kubelik A. R., Livak K. J., Rafalski J. A., Tingey S. V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990 Nov 25;18(22):6531–6535. doi: 10.1093/nar/18.22.6531. [DOI] [PMC free article] [PubMed] [Google Scholar]

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