Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1985 Nov;56(2):457–465. doi: 10.1128/jvi.56.2.457-465.1985

Structure of simian virus 40-adeno-associated virus recombinant genomes.

Z Grossman, K I Berns, E Winocour
PMCID: PMC252600  PMID: 2997468

Abstract

The structures of recombinant genomes formed by recombination between simian virus 40 (SV40) and adeno-associated virus 2 (AAV) DNAs after either DNA cotransfection or coinfection by virions were characterized. Two types of structures were found. Group A structures, found after cotransfection and in one of seven recombinants arising from coinfection, represented a simple deletion of SV40 sequences replaced by a slightly shorter AAV sequence. Group B structures were found in six of seven recombinants arising after virion coinfection. All contained either the left or right terminal sequences (approximately 250 to 450 bases) of the AAV genome adjacent to the SV40 origin of DNA replication. Only 350 to 650 bases (including the origin) remained of the SV40 sequence. The joined SV40-AAV sequences were present in the recombinant genome as a tandem repeat of a size that can be packaged into SV40 capsids.

Full text

PDF
461

Images in this article

458Image
on p.458
460Image
on p.460
460Image
on p.460
461Image
on p.461

Selected References

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

  1. Berns K. I., Kort J., Fife K. H., Grogan E. W., Spear I. Study of the fine structure of adeno-associated virus DNA with bacterial restriction endonucleases. J Virol. 1975 Sep;16(3):712–719. doi: 10.1128/jvi.16.3.712-719.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Best A. N., Allison D. P., Novelli G. D. Purification of supercoiled DNA of plasmid col E1 by RPC-5 chromatography. Anal Biochem. 1981 Jul 1;114(2):235–243. doi: 10.1016/0003-2697(81)90476-0. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. Bullock P., Forrester W., Botchan M. DNA sequence studies of simian virus 40 chromosomal excision and integration in rat cells. J Mol Biol. 1984 Mar 25;174(1):55–84. doi: 10.1016/0022-2836(84)90365-6. [DOI] [PubMed] [Google Scholar]
  5. Chaconas G., van de Sande J. H. 5'-32P labeling of RNA and DNA restriction fragments. Methods Enzymol. 1980;65(1):75–85. doi: 10.1016/s0076-6879(80)65012-5. [DOI] [PubMed] [Google Scholar]
  6. Cheung A. K., Hoggan M. D., Hauswirth W. W., Berns K. I. Integration of the adeno-associated virus genome into cellular DNA in latently infected human Detroit 6 cells. J Virol. 1980 Feb;33(2):739–748. doi: 10.1128/jvi.33.2.739-748.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Deichaite I., Laver-Rudich Z., Dorsett D., Winocour E. Linear simian virus 40 DNA fragments exhibit a propensity for rolling-circle replication. Mol Cell Biol. 1985 Jul;5(7):1787–1790. doi: 10.1128/mcb.5.7.1787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Denhardt D. T. A membrane-filter technique for the detection of complementary DNA. Biochem Biophys Res Commun. 1966 Jun 13;23(5):641–646. doi: 10.1016/0006-291x(66)90447-5. [DOI] [PubMed] [Google Scholar]
  9. Dorsett D. L., Keshet I., Winocour E. Quantitation of a simian virus 40 nonhomologous recombination pathway. J Virol. 1983 Oct;48(1):218–228. doi: 10.1128/jvi.48.1.218-228.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dorsett D., Deichaite I., Winocour E. Circular and linear simian virus 40 DNAs differ in recombination. Mol Cell Biol. 1985 Apr;5(4):869–880. doi: 10.1128/mcb.5.4.869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Grossman Z., Winocour E., Berns K. I. Recombination between simian virus 40 and adeno-associated virus: virion coinfection compared to DNA cotransfection. Virology. 1984 Apr 15;134(1):125–137. doi: 10.1016/0042-6822(84)90278-2. [DOI] [PubMed] [Google Scholar]
  12. Gutai M. W., Nathans D. Evolutionary variants of simian virus 40: Cellular DNA sequences and sequences at recombinant joints of substituted variants. J Mol Biol. 1978 Dec 5;126(2):275–288. doi: 10.1016/0022-2836(78)90363-7. [DOI] [PubMed] [Google Scholar]
  13. Hanahan D., Meselson M. Plasmid screening at high colony density. Gene. 1980 Jun;10(1):63–67. doi: 10.1016/0378-1119(80)90144-4. [DOI] [PubMed] [Google Scholar]
  14. Hirt B. Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol. 1967 Jun 14;26(2):365–369. doi: 10.1016/0022-2836(67)90307-5. [DOI] [PubMed] [Google Scholar]
  15. Holmes D. S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981 Jun;114(1):193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
  16. Hu N., Messing J. The making of strand-specific M13 probes. Gene. 1982 Mar;17(3):271–277. doi: 10.1016/0378-1119(82)90143-3. [DOI] [PubMed] [Google Scholar]
  17. Laughlin C. A., Tratschin J. D., Coon H., Carter B. J. Cloning of infectious adeno-associated virus genomes in bacterial plasmids. Gene. 1983 Jul;23(1):65–73. doi: 10.1016/0378-1119(83)90217-2. [DOI] [PubMed] [Google Scholar]
  18. Lavi S., Winocour E. Acquisition of sequences homologous to host deoxyribonucleic acid by closed circular simian virus 40 deoxyribonucleic acid. J Virol. 1972 Feb;9(2):309–316. doi: 10.1128/jvi.9.2.309-316.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lefebvre R. B., Riva S., Berns K. I. Conformation takes precedence over sequence in adeno-associated virus DNA replication. Mol Cell Biol. 1984 Jul;4(7):1416–1419. doi: 10.1128/mcb.4.7.1416. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. McCutchan J. H., Pagano J. S. Enchancement of the infectivity of simian virus 40 deoxyribonucleic acid with diethylaminoethyl-dextran. J Natl Cancer Inst. 1968 Aug;41(2):351–357. [PubMed] [Google Scholar]
  21. Milman G., Herzberg M. Efficient DNA transfection and rapid assay for thymidine kinase activity and viral antigenic determinants. Somatic Cell Genet. 1981 Mar;7(2):161–170. doi: 10.1007/BF01567655. [DOI] [PubMed] [Google Scholar]
  22. Oren M., Lavi S., Winocour E. The structure of a cloned substituted SV40 genome. Virology. 1978 Apr;85(2):404–421. doi: 10.1016/0042-6822(78)90448-8. [DOI] [PubMed] [Google Scholar]
  23. Rigby P. W., Berg P. Does simian virus 40 DNA integrate into cellular DNA during productive infection? J Virol. 1978 Nov;28(2):475–489. doi: 10.1128/jvi.28.2.475-489.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rose J. A., Berns K. I., Hoggan M. D., Koczot F. J. Evidence for a single-stranded adenovirus-associated virus genome: formation of a DNA density hybrid on release of viral DNA. Proc Natl Acad Sci U S A. 1969 Nov;64(3):863–869. doi: 10.1073/pnas.64.3.863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Samulski R. J., Berns K. I., Tan M., Muzyczka N. Cloning of adeno-associated virus into pBR322: rescue of intact virus from the recombinant plasmid in human cells. Proc Natl Acad Sci U S A. 1982 Mar;79(6):2077–2081. doi: 10.1073/pnas.79.6.2077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Samulski R. J., Srivastava A., Berns K. I., Muzyczka N. Rescue of adeno-associated virus from recombinant plasmids: gene correction within the terminal repeats of AAV. Cell. 1983 May;33(1):135–143. doi: 10.1016/0092-8674(83)90342-2. [DOI] [PubMed] [Google Scholar]
  27. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Scott W. A., Wigmore D. J. Sites in simian virus 40 chromatin which are preferentially cleaved by endonucleases. Cell. 1978 Dec;15(4):1511–1518. doi: 10.1016/0092-8674(78)90073-9. [DOI] [PubMed] [Google Scholar]
  29. Sebring E. D., Kelly T. J., Jr, Thoren M. M., Salzman N. P. Structure of replicating simian virus 40 deoxyribonucleic acid molecules. J Virol. 1971 Oct;8(4):478–490. doi: 10.1128/jvi.8.4.478-490.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Senapathy P., Carter B. J. Molecular cloning of adeno-associated virus variant genomes and generation of infectious virus by recombination in mammalian cells. J Biol Chem. 1984 Apr 10;259(7):4661–4666. [PubMed] [Google Scholar]
  31. Senapathy P., Tratschin J. D., Carter B. J. Replication of adeno-associated virus DNA. Complementation of naturally occurring rep- mutants by a wild-type genome or an ori- mutant and correction of terminal palindrome deletions. J Mol Biol. 1984 Oct 15;179(1):1–20. doi: 10.1016/0022-2836(84)90303-6. [DOI] [PubMed] [Google Scholar]
  32. Smith G. E., Summers M. D. The bidirectional transfer of DNA and RNA to nitrocellulose or diazobenzyloxymethyl-paper. Anal Biochem. 1980 Nov 15;109(1):123–129. doi: 10.1016/0003-2697(80)90019-6. [DOI] [PubMed] [Google Scholar]
  33. Smith M., Leung D. W., Gillam S., Astell C. R., Montgomery D. L., Hall B. D. Sequence of the gene for iso-1-cytochrome c in Saccharomyces cerevisiae. Cell. 1979 Apr;16(4):753–761. doi: 10.1016/0092-8674(79)90091-6. [DOI] [PubMed] [Google Scholar]
  34. 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]
  35. Srivastava A., Lusby E. W., Berns K. I. Nucleotide sequence and organization of the adeno-associated virus 2 genome. J Virol. 1983 Feb;45(2):555–564. doi: 10.1128/jvi.45.2.555-564.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Straus S. E., Sebring E. D., Rose J. A. Concatemers of alternating plus and minus strands are intermediates in adenovirus-associated virus DNA synthesis. Proc Natl Acad Sci U S A. 1976 Mar;73(3):742–746. doi: 10.1073/pnas.73.3.742. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Vogelstein B., Gillespie D. Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci U S A. 1979 Feb;76(2):615–619. doi: 10.1073/pnas.76.2.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Winocour E., Keshet I. Indiscriminate recombination in simian virus 40-infected monkey cells. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4861–4865. doi: 10.1073/pnas.77.8.4861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Winocour E., Lavie V., Keshet I. Structure of simian virus 40-phiX174 recombinant genomes isolated from single cells. J Virol. 1983 Oct;48(1):229–238. doi: 10.1128/jvi.48.1.229-238.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES