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. 1982;1(1):21–26. doi: 10.1002/j.1460-2075.1982.tb01118.x

Two distant regions of the Epstein-Barr virus genome with sequence homologies have the same orientation and involve small tandem repeats.

J Hudewentz, H Delius, U K Freese, U Zimber, G W Bornkamm
PMCID: PMC552989  PMID: 6325150

Abstract

The two regions of the Epstein-Barr virus genome (DSL and DSR) carrying homologous sequences at distant parts of the long unique region are described. Cleavage of cloned DNA containing the DSR region with restriction endonucleases revealed a so far unrecognized small tandem repeat of approximately 120 base pairs present in approximately 20 copies. Heteroduplexes of the DNA of two clones containing DSL and DSR respectively, visualized in the electron microscope by cytochrome c spreading, revealed that the region of homology is approximately 2.5 kb long, involves small tandem repeats, and has the same orientation in the viral genome. Mica adsorption of the heteroduplex showed, that the homologous region consists of approximately 1.5 kb with only partial homology including the small internal repeats and 0.9 kb with well-matched duplexes. When DNA containing the DSL region reanneals, it can give rise to two single-stranded loops of the same size at different positions suggesting the presence of a row of tandem repeats also in this region.

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Selected References

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

  1. Arrand J. R., Rymo L., Walsh J. E., Björck E., Lindahl T., Griffin B. E. Molecular cloning of the complete Epstein-Barr virus genome as a set of overlapping restriction endonuclease fragments. Nucleic Acids Res. 1981 Jul 10;9(13):2999–3014. doi: 10.1093/nar/9.13.2999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bornkamm G. W., Delius H., Zimber U., Hudewentz J., Epstein M. A. Comparison of Epstein-Barr virus strains of different origin by analysis of the viral DNAs. J Virol. 1980 Sep;35(3):603–618. doi: 10.1128/jvi.35.3.603-618.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Clewell D. B., Helinski D. R. Supercoiled circular DNA-protein complex in Escherichia coli: purification and induced conversion to an opern circular DNA form. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1159–1166. doi: 10.1073/pnas.62.4.1159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Crawford D. H., Epstein M. A., Bornkamm G. W., Achong B. G., Finerty S., Thompson J. L. Biological and biochemical observations on isolates of EB virus from the malignant epithelial cells of two nasopharyngeal carcinomas. Int J Cancer. 1979 Sep 15;24(3):294–302. doi: 10.1002/ijc.2910240305. [DOI] [PubMed] [Google Scholar]
  6. Dambaugh T., Nkrumah F. K., Biggar R. J., Kieff E. Epstein-Barr virus RNA in Burkitt tumor tissue. Cell. 1979 Feb;16(2):313–322. doi: 10.1016/0092-8674(79)90008-4. [DOI] [PubMed] [Google Scholar]
  7. Davis R. W., Thomas M., Cameron J., St John T. P., Scherer S., Padgett R. A. Rapid DNA isolations for enzymatic and hybridization analysis. Methods Enzymol. 1980;65(1):404–411. doi: 10.1016/s0076-6879(80)65051-4. [DOI] [PubMed] [Google Scholar]
  8. Delius H., Bornkamm G. W. Heterogeneity of Epstein-Barr virus. III. Comparison of a transforming and a nontransforming virus by partial denaturation mapping of their DNAs. J Virol. 1978 Jul;27(1):81–89. doi: 10.1128/jvi.27.1.81-89.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Favaloro J., Treisman R., Kamen R. Transcription maps of polyoma virus-specific RNA: analysis by two-dimensional nuclease S1 gel mapping. Methods Enzymol. 1980;65(1):718–749. doi: 10.1016/s0076-6879(80)65070-8. [DOI] [PubMed] [Google Scholar]
  10. Fischer D. K., Miller G., Gradoville L., Heston L., Westrate M. W., Maris W., Wright J., Brandsma J., Summers W. C. Genome of a mononucleosis Epstein-Barr virus contains DNA fragments previously regarded to be unique to Burkitt's lymphoma isolates. Cell. 1981 May;24(2):543–553. doi: 10.1016/0092-8674(81)90345-7. [DOI] [PubMed] [Google Scholar]
  11. Given D., Kieff E. DNA of Epstein-Barr virus. IV. Linkage map of restriction enzyme fragments of the B95-8 and W91 strains of Epstein-Barr Virus. J Virol. 1978 Nov;28(2):524–542. doi: 10.1128/jvi.28.2.524-542.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Given D., Kieff E. DNA of Epstein-Barr virus. VI. Mapping of the internal tandem reiteration. J Virol. 1979 Aug;31(2):315–324. doi: 10.1128/jvi.31.2.315-324.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Given D., Yee D., Griem K., Kieff E. DNA of Epstein-Barr virus. V. Direct repeats of the ends of Epstein-Barr virus DNA. J Virol. 1979 Jun;30(3):852–862. doi: 10.1128/jvi.30.3.852-862.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hayward S. D., Nogee L., Hayward G. S. Organization of repeated regions within the Epstein-Barr virus DNA molecule. J Virol. 1980 Jan;33(1):507–521. doi: 10.1128/jvi.33.1.507-521.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Heller M., Dambaugh T., Kieff E. Epstein-Barr virus DNA. IX. Variation among viral DNAs from producer and nonproducer infected cells. J Virol. 1981 May;38(2):632–648. doi: 10.1128/jvi.38.2.632-648.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hohn B., Collins J. A small cosmid for efficient cloning of large DNA fragments. Gene. 1980 Nov;11(3-4):291–298. doi: 10.1016/0378-1119(80)90069-4. [DOI] [PubMed] [Google Scholar]
  17. Kintner C. R., Sugden B. The structure of the termini of the DNA of Epstein-Barr virus. Cell. 1979 Jul;17(3):661–671. doi: 10.1016/0092-8674(79)90273-3. [DOI] [PubMed] [Google Scholar]
  18. Maniatis T., Jeffrey A., Kleid D. G. Nucleotide sequence of the rightward operator of phage lambda. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1184–1188. doi: 10.1073/pnas.72.3.1184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Morrison D. A. Transformation and preservation of competent bacterial cells by freezing. Methods Enzymol. 1979;68:326–331. doi: 10.1016/0076-6879(79)68023-0. [DOI] [PubMed] [Google Scholar]
  20. Priess H., Koller B., Hess B., Delius H. Electron microscopic mapping and sequence analysis of the terminator for the early message of E. coli phage T7. Mol Gen Genet. 1980 Apr;178(1):27–34. doi: 10.1007/BF00267209. [DOI] [PubMed] [Google Scholar]
  21. Raab-Traub N., Dambaugh T., Kieff E. DNA of Epstein-Barr virus VIII: B95-8, the previous prototype, is an unusual deletion derivative. Cell. 1980 Nov;22(1 Pt 1):257–267. doi: 10.1016/0092-8674(80)90173-7. [DOI] [PubMed] [Google Scholar]
  22. Raab-Traub N., Pritchett R., Kieff E. DNA of Epstein-Barr virus. III. Identification of restriction enzyme fragments that contain DNA sequences which differ among strains of Epstein-Barr virus. J Virol. 1978 Aug;27(2):388–398. doi: 10.1128/jvi.27.2.388-398.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  24. Rymo L., Forsblom S. Cleavage of Epstein-Barr virus DNA by restriction endonucleases EcoRI, HindIII and BamI. Nucleic Acids Res. 1978 Apr;5(4):1387–1402. doi: 10.1093/nar/5.4.1387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Rymo L., Lindahl T., Adams A. Sites of sequence variability in Epstein-Barr virus DNA from different sources. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2794–2798. doi: 10.1073/pnas.76.6.2794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Skare J., Strominger J. L. Cloning and mapping of BamHi endonuclease fragments of DNA from the transforming B95-8 strain of Epstein-Barr virus. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3860–3864. doi: 10.1073/pnas.77.7.3860. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  28. Yang V. W., Flint S. J. Synthesis and processing of adenoviral RNA in isolated nuclei. J Virol. 1979 Nov;32(2):394–403. doi: 10.1128/jvi.32.2.394-403.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]

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