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. 1985 Mar 25;13(6):1905–1922. doi: 10.1093/nar/13.6.1905

Removal of repeated sequences from hybridisation probes.

P G Sealey, P A Whittaker, E M Southern
PMCID: PMC341124  PMID: 4000947

Abstract

Pre-reassociation of human clone probes, containing dispersed highly repeated sequences, (e.g. Alu and KpnI families), with a large excess of sonicated total human DNA allows signal from single and low copy number components to be detected in transfer hybridisations. The signal from non-dispersed repeated sequences is reduced to single copy levels. The procedure, which is simple and quick, is illustrated using model combinations of well characterised cloned probes, and is applied to a sample of randomly chosen cosmid clones. A theoretical assessment is presented which may be useful to those wishing to use this procedure.

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Selected References

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  1. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brison O., Ardeshir F., Stark G. R. General method for cloning amplified DNA by differential screening with genomic probes. Mol Cell Biol. 1982 May;2(5):578–587. doi: 10.1128/mcb.2.5.578. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Britten R. J., Kohne D. E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science. 1968 Aug 9;161(3841):529–540. doi: 10.1126/science.161.3841.529. [DOI] [PubMed] [Google Scholar]
  4. Fisher J. H., Gusella J. F., Scoggin C. H. Molecular hybridization under conditions of high stringency permits cloned DNA segments containing reiterated DNA sequences to be assigned to specific chromosomal locations. Proc Natl Acad Sci U S A. 1984 Jan;81(2):520–524. doi: 10.1073/pnas.81.2.520. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fritsch E. F., Lawn R. M., Maniatis T. Molecular cloning and characterization of the human beta-like globin gene cluster. Cell. 1980 Apr;19(4):959–972. doi: 10.1016/0092-8674(80)90087-2. [DOI] [PubMed] [Google Scholar]
  6. Hamada H., Petrino M. G., Kakunaga T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6465–6469. doi: 10.1073/pnas.79.21.6465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Ish-Horowicz D., Burke J. F. Rapid and efficient cosmid cloning. Nucleic Acids Res. 1981 Jul 10;9(13):2989–2998. doi: 10.1093/nar/9.13.2989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Jelinek W. R., Toomey T. P., Leinwand L., Duncan C. H., Biro P. A., Choudary P. V., Weissman S. M., Rubin C. M., Houck C. M., Deininger P. L. Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1398–1402. doi: 10.1073/pnas.77.3.1398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lauer J., Shen C. K., Maniatis T. The chromosomal arrangement of human alpha-like globin genes: sequence homology and alpha-globin gene deletions. Cell. 1980 May;20(1):119–130. doi: 10.1016/0092-8674(80)90240-8. [DOI] [PubMed] [Google Scholar]
  10. Maniatis T., Hardison R. C., Lacy E., Lauer J., O'Connell C., Quon D., Sim G. K., Efstratiadis A. The isolation of structural genes from libraries of eucaryotic DNA. Cell. 1978 Oct;15(2):687–701. doi: 10.1016/0092-8674(78)90036-3. [DOI] [PubMed] [Google Scholar]
  11. Manuelidis L., Biro P. A. Genomic representation of the Hind II 1.9 kb repeated DNA. Nucleic Acids Res. 1982 May 25;10(10):3221–3239. doi: 10.1093/nar/10.10.3221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Orkin S. H. The duplicated human alpha globin genes lie close together in cellular DNA. Proc Natl Acad Sci U S A. 1978 Dec;75(12):5950–5954. doi: 10.1073/pnas.75.12.5950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Rinehart F. P., Ritch T. G., Deininger P. L., Schmid C. W. Renaturation rate studies of a single family of interspersed repeated sequences in human deoxyribonucleic acid. Biochemistry. 1981 May 26;20(11):3003–3010. doi: 10.1021/bi00514a003. [DOI] [PubMed] [Google Scholar]
  14. Ross J. A precursor of globin messenger RNA. J Mol Biol. 1976 Sep 15;106(2):403–420. doi: 10.1016/0022-2836(76)90093-0. [DOI] [PubMed] [Google Scholar]
  15. Schmid C. W., Deininger P. L. Sequence organization of the human genome. Cell. 1975 Nov;6(3):345–358. doi: 10.1016/0092-8674(75)90184-1. [DOI] [PubMed] [Google Scholar]
  16. Shafit-Zagardo B., Maio J. J., Brown F. L. KpnI families of long, interspersed repetitive DNAs in human and other primate genomes. Nucleic Acids Res. 1982 May 25;10(10):3175–3193. doi: 10.1093/nar/10.10.3175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Singh L., Jones K. W. The use of heparin as a simple cost-effective means of controlling background in nucleic acid hybridization procedures. Nucleic Acids Res. 1984 Jul 25;12(14):5627–5638. doi: 10.1093/nar/12.14.5627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Weiss E. H., Golden L., Fahrner K., Mellor A. L., Devlin J. J., Bullman H., Tiddens H., Bud H., Flavell R. A. Organization and evolution of the class I gene family in the major histocompatibility complex of the C57BL/10 mouse. Nature. 1984 Aug 23;310(5979):650–655. doi: 10.1038/310650a0. [DOI] [PubMed] [Google Scholar]

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