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. 1988 Mar 11;16(5 Pt A):1739–1758. doi: 10.1093/nar/16.5.1739

Compilation of DNA strand exchange sites for non-homologous recombination in somatic cells.

A K Konopka 1
PMCID: PMC338168  PMID: 2832826

Abstract

DNA sequences of 496 somatic cell illegitimate crossing over regions were compiled and analyzed. Sites for non-homologous recombination on linear DNAs transfected into mammalian cells (Transfected Linear DNAs; TLD) were analyzed separately from the remaining illegitimate recombination regions (IRR). Trinucleotides that are preferentially cleaved by rat liver topoisomerase I in vitro (CAT, CTY, GTY, RAT where R = purine, Y = pyrimidine) were present in the 10 base pair (bp) vicinity of the cross-over sites in 92% of IRR and 93% of TLD. Multiple repeats of these trinucleotides have been observed in 39% of IRR and 38% of TLD. Runs of five or more contiguous purines (or pyrimidines on the complementary strand) were found in 26% of IRR and 14% of TLD. Adenine-Thymine rich regions of five or more bases were found in 14% of IRR and 21% of TLD. Alternating purine-pyrimidine tracks longer than four nucleotides in length were found in 11% of IRR, though only in 4% of TLD. I discuss the possible biological significance of these findings and present an appendix containing the sequences in the 10 bp vicinity of the non-homologous recombination sites analyzed.

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Selected References

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

  1. Ahmed C. M., Lee E., Zain B. S. The nucleotide sequence at the recombination/integration sites of the hybrid viruses Ad2+ND3 and Ad2+ND5. Virology. 1984 Feb;133(1):233–237. doi: 10.1016/0042-6822(84)90445-8. [DOI] [PubMed] [Google Scholar]
  2. Anderson R. A., Kato S., Camerini-Otero R. D. A pattern of partially homologous recombination in mouse L cells. Proc Natl Acad Sci U S A. 1984 Jan;81(1):206–210. doi: 10.1073/pnas.81.1.206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arnott S., Chandrasekaran R., Hall I. H., Puigjaner L. C. Heteronomous DNA. Nucleic Acids Res. 1983 Jun 25;11(12):4141–4155. doi: 10.1093/nar/11.12.4141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Barsh G. S., Roush C. L., Bonadio J., Byers P. H., Gelinas R. E. Intron-mediated recombination may cause a deletion in an alpha 1 type I collagen chain in a lethal form of osteogenesis imperfecta. Proc Natl Acad Sci U S A. 1985 May;82(9):2870–2874. doi: 10.1073/pnas.82.9.2870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Been M. D., Burgess R. R., Champoux J. J. Nucleotide sequence preference at rat liver and wheat germ type 1 DNA topoisomerase breakage sites in duplex SV40 DNA. Nucleic Acids Res. 1984 Apr 11;12(7):3097–3114. doi: 10.1093/nar/12.7.3097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bendig M. M., Thomas T., Folk W. R. Regulatory mutants of polyoma virus defective in DNA replication and the synthesis of early proteins. Cell. 1980 Jun;20(2):401–409. doi: 10.1016/0092-8674(80)90626-1. [DOI] [PubMed] [Google Scholar]
  7. Bendig M. M., Thomas T., Folk W. R. Viable deletion mutant in the medium and large T-antigen-coding sequences of the polyoma virus genome. J Virol. 1980 Mar;33(3):1215–1220. doi: 10.1128/jvi.33.3.1215-1220.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Botchan M., Stringer J., Mitchison T., Sambrook J. Integration and excision of SV40 DNA from the chromosome of a transformed cell. Cell. 1980 May;20(1):143–152. doi: 10.1016/0092-8674(80)90242-1. [DOI] [PubMed] [Google Scholar]
  9. Bourgaux P., Sylla B. S., Chartrand P. Excision of polyoma virus DNA from that of a transformed mouse cell: identification of a hybrid molecule with direct and inverted repeat sequences at the viral-cellular joints. Virology. 1982 Oct 15;122(1):84–97. doi: 10.1016/0042-6822(82)90379-8. [DOI] [PubMed] [Google Scholar]
  10. Bullock P., Champoux J. J., Botchan M. Association of crossover points with topoisomerase I cleavage sites: a model for nonhomologous recombination. Science. 1985 Nov 22;230(4728):954–958. doi: 10.1126/science.2997924. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Bullock P., Miller J., Botchan M. Effects of poly[d(pGpT).d(pApC)] and poly[d(pCpG).d(pCpG)] repeats on homologous recombination in somatic cells. Mol Cell Biol. 1986 Nov;6(11):3948–3953. doi: 10.1128/mcb.6.11.3948. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Carbon J. Yeast centromeres: structure and function. Cell. 1984 Jun;37(2):351–353. doi: 10.1016/0092-8674(84)90363-5. [DOI] [PubMed] [Google Scholar]
  14. Carmichael G. G., Benjamin T. L. Identification of DNA sequence changes leading to loss of transforming ability in polyoma virus. J Biol Chem. 1980 Jan 10;255(1):230–235. [PubMed] [Google Scholar]
  15. Chang X. B., Wilson J. H. Formation of deletions after initiation of simian virus 40 replication: influence of packaging limit of the capsid. J Virol. 1986 May;58(2):393–401. doi: 10.1128/jvi.58.2.393-401.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Chu M. L., Gargiulo V., Williams C. J., Ramirez F. Multiexon deletion in an osteogenesis imperfecta variant with increased type III collagen mRNA. J Biol Chem. 1985 Jan 25;260(2):691–694. [PubMed] [Google Scholar]
  17. Corcoran L. M., Cory S., Adams J. M. Transposition of the immunoglobulin heavy chain enhancer to the myc oncogene in a murine plasmacytoma. Cell. 1985 Jan;40(1):71–79. doi: 10.1016/0092-8674(85)90310-1. [DOI] [PubMed] [Google Scholar]
  18. Dean M., Park M., Vande Woude G. F. Characterization of the rearranged tpr-met oncogene breakpoint. Mol Cell Biol. 1987 Feb;7(2):921–924. doi: 10.1128/mcb.7.2.921. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Dejean A., Bougueleret L., Grzeschik K. H., Tiollais P. Hepatitis B virus DNA integration in a sequence homologous to v-erb-A and steroid receptor genes in a hepatocellular carcinoma. Nature. 1986 Jul 3;322(6074):70–72. doi: 10.1038/322070a0. [DOI] [PubMed] [Google Scholar]
  20. Deuring R., Winterhoff U., Tamanoi F., Stabel S., Doerfler W. Site of linkage between adenovirus type 12 and cell DNAs in hamster tumour line CLAC3. Nature. 1981 Sep 3;293(5827):81–84. doi: 10.1038/293081a0. [DOI] [PubMed] [Google Scholar]
  21. Dhruva B. R., Shenk T., Subramanian K. N. Integration in vivo into simian virus 40 DNA of a sequence that resembles a certain family of genomic interspersed repeated sequences. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4514–4518. doi: 10.1073/pnas.77.8.4514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. DiMaio D., Nathans D. Cold-sensitive regulatory mutants of simian virus 40. J Mol Biol. 1980 Jun 15;140(1):129–142. doi: 10.1016/0022-2836(80)90359-9. [DOI] [PubMed] [Google Scholar]
  23. Ding D., Jones M. D., Leigh-Brown A., Griffin B. E. Mutant din-21, a variant of polyoma virus containing a mouse DNA sequence in the viral genome. EMBO J. 1982;1(4):461–466. doi: 10.1002/j.1460-2075.1982.tb01191.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Doerfler W., Gahlmann R., Stabel S., Deuring R., Lichtenberg U., Schulz M., Eick D., Leisten R. On the mechanism of recombination between adenoviral and cellular DNAs: the structure of junction sites. Curr Top Microbiol Immunol. 1984;109:193–228. doi: 10.1007/978-3-642-69460-8_9. [DOI] [PubMed] [Google Scholar]
  25. Edwards K. A., Halligan B. D., Davis J. L., Nivera N. L., Liu L. F. Recognition sites of eukaryotic DNA topoisomerase I: DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA. Nucleic Acids Res. 1982 Apr 24;10(8):2565–2576. doi: 10.1093/nar/10.8.2565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Efstratiadis A., Posakony J. W., Maniatis T., Lawn R. M., O'Connell C., Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M., Slightom J. L. The structure and evolution of the human beta-globin gene family. Cell. 1980 Oct;21(3):653–668. doi: 10.1016/0092-8674(80)90429-8. [DOI] [PubMed] [Google Scholar]
  27. Franklin N. C. Extraordinary recombinational events in Escherichia coli. Their independence of the rec+ function. Genetics. 1967 Apr;55(4):699–707. doi: 10.1093/genetics/55.4.699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Gahlmann R., Doerfler W. Integration of viral DNA into the genome of the adenovirus type 2-transformed hamster cell line HE5 without loss or alteration of cellular nucleotides. Nucleic Acids Res. 1983 Nov 11;11(21):7347–7361. doi: 10.1093/nar/11.21.7347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Gilliam A. C., Shen A., Richards J. E., Blattner F. R., Mushinski J. F., Tucker P. W. Illegitimate recombination generates a class switch from C mu to C delta in an IgD-secreting plasmacytoma. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4164–4168. doi: 10.1073/pnas.81.13.4164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Grandgenett D. P., Vora A. C., Schiff R. D. A 32,000-dalton nucleic acid-binding protein from avian retravirus cores possesses DNA endonuclease activity. Virology. 1978 Aug;89(1):119–132. doi: 10.1016/0042-6822(78)90046-6. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. Hasson J. F., Mougneau E., Cuzin F., Yaniv M. Simian virus 40 illegitimate recombination occurs near short direct repeats. J Mol Biol. 1984 Jul 25;177(1):53–68. doi: 10.1016/0022-2836(84)90057-3. [DOI] [PubMed] [Google Scholar]
  33. Hattori J., Carmichael G. G., Benjamin T. L. DNA sequence alterations in Hr-t deletion mutants of polyoma virus. Cell. 1979 Mar;16(3):505–513. doi: 10.1016/0092-8674(79)90025-4. [DOI] [PubMed] [Google Scholar]
  34. Hayday A., Ruley H. E., Fried M. Structural and biological analysis of integrated polyoma virus DNA and its adjacent host sequences cloned from transformed rat cells. J Virol. 1982 Oct;44(1):67–77. doi: 10.1128/jvi.44.1.67-77.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Hoffman-Liebermann B., Liebermann D., Troutt A., Kedes L. H., Cohen S. N. Human homologs of TU transposon sequences: polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo. Mol Cell Biol. 1986 Nov;6(11):3632–3642. doi: 10.1128/mcb.6.11.3632. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Hogan A., Faust E. A. Nonhomologous recombination in the parvovirus chromosome: role for a CTATTTCT motif. Mol Cell Biol. 1986 Aug;6(8):3005–3009. doi: 10.1128/mcb.6.8.3005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Hope T. J., Aguilera R. J., Minie M. E., Sakano H. Endonucleolytic activity that cleaves immunoglobulin recombination sequences. Science. 1986 Mar 7;231(4742):1141–1145. doi: 10.1126/science.3003919. [DOI] [PubMed] [Google Scholar]
  38. Jagadeeswaran P., Tuan D., Forget B. G., Weissman S. M. A gene deletion ending at the midpoint of a repetitive DNA sequence in one form of hereditary persistence of fetal haemoglobin. Nature. 1982 Apr 1;296(5856):469–470. doi: 10.1038/296469a0. [DOI] [PubMed] [Google Scholar]
  39. Jeang K. T., Hayward S. D. Organization of the Epstein-Barr virus DNA molecule. III. Location of the P3HR-1 deletion junction and characterization of the NotI repeat units that form part of the template for an abundant 12-O-tetradecanoylphorbol-13-acetate-induced mRNA transcript. J Virol. 1983 Oct;48(1):135–148. doi: 10.1128/jvi.48.1.135-148.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Jeffreys A. J., Wilson V., Thein S. L. Hypervariable 'minisatellite' regions in human DNA. Nature. 1985 Mar 7;314(6006):67–73. doi: 10.1038/314067a0. [DOI] [PubMed] [Google Scholar]
  41. Jennings M. W., Jones R. W., Wood W. G., Weatherall D. J. Analysis of an inversion within the human beta globin gene cluster. Nucleic Acids Res. 1985 Apr 25;13(8):2897–2906. doi: 10.1093/nar/13.8.2897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Johnson A. D., Barkan A., Mertz J. E. Nucleotide sequence analysis of the recombinant joints in 16 naturally arising deletion mutants of simian virus 40. Virology. 1982 Dec;123(2):464–469. doi: 10.1016/0042-6822(82)90281-1. [DOI] [PubMed] [Google Scholar]
  43. Konopka A. K., Reiter J., Jung M., Zarling D. A., Jovin T. M. Concordance of experimentally mapped or predicted Z-DNA sites with positions of selected alternating purine-pyrimidine tracts. Nucleic Acids Res. 1985 Mar 11;13(5):1683–1701. doi: 10.1093/nar/13.5.1683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Konopka A. K., Smythers G. W., Owens J., Maizel J. V., Jr Distance analysis helps to establish characteristic motifs in intron sequences. Gene Anal Tech. 1987 Jul-Aug;4(4):63–74. doi: 10.1016/0735-0651(87)90020-3. [DOI] [PubMed] [Google Scholar]
  45. Kopchick J. J., Harless J., Geisser B. S., Killam R., Hewitt R. R., Arlinghaus R. B. Endodeoxyribonuclease activity associated with Rauscher murine leukemia virus. J Virol. 1981 Jan;37(1):274–283. doi: 10.1128/jvi.37.1.274-283.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Koshy R., Koch S., von Loringhoven A. F., Kahmann R., Murray K., Hofschneider P. H. Integration of hepatitis B virus DNA: evidence for integration in the single-stranded gap. Cell. 1983 Aug;34(1):215–223. doi: 10.1016/0092-8674(83)90152-6. [DOI] [PubMed] [Google Scholar]
  47. Lehrman M. A., Russell D. W., Goldstein J. L., Brown M. S. Exon-Alu recombination deletes 5 kilobases from the low density lipoprotein receptor gene, producing a null phenotype in familial hypercholesterolemia. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3679–3683. doi: 10.1073/pnas.83.11.3679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Lehrman M. A., Schneider W. J., Südhof T. C., Brown M. S., Goldstein J. L., Russell D. W. Mutation in LDL receptor: Alu-Alu recombination deletes exons encoding transmembrane and cytoplasmic domains. Science. 1985 Jan 11;227(4683):140–146. doi: 10.1126/science.3155573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Ling L. E., Manos M. M., Gluzman Y. Sequence of the junction in adenovirus 2-SV40 hybrids: examples of illegitimate recombination. Nucleic Acids Res. 1982 Dec 20;10(24):8099–8112. doi: 10.1093/nar/10.24.8099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Maeda N., Yang F., Barnett D. R., Bowman B. H., Smithies O. Duplication within the haptoglobin Hp2 gene. Nature. 1984 May 10;309(5964):131–135. doi: 10.1038/309131a0. [DOI] [PubMed] [Google Scholar]
  51. Mager D. L., Henthorn P. S., Smithies O. A Chinese G gamma + (A gamma delta beta)zero thalassemia deletion: comparison to other deletions in the human beta-globin gene cluster and sequence analysis of the breakpoints. Nucleic Acids Res. 1985 Sep 25;13(18):6559–6575. doi: 10.1093/nar/13.18.6559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Maruyama K., Oda K. Two types of deletion within integrated viral sequences mediate reversion of simian virus 40-transformed mouse cells. J Virol. 1984 Feb;49(2):479–489. doi: 10.1128/jvi.49.2.479-489.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. McCutchan T., Singer M., Rosenberg M. Structure of simian virus 40 recombinants that contain both host and viral DNA sequences. II. The structure of variant 1103 and its comparison to variant CVPS/1P2 (EcoRI res). J Biol Chem. 1979 May 10;254(9):3592–3597. [PubMed] [Google Scholar]
  54. Molineaux S. M., Engh H., de Ferra F., Hudson L., Lazzarini R. A. Recombination within the myelin basic protein gene created the dysmyelinating shiverer mouse mutation. Proc Natl Acad Sci U S A. 1986 Oct;83(19):7542–7546. doi: 10.1073/pnas.83.19.7542. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Moser H. E., Dervan P. B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science. 1987 Oct 30;238(4827):645–650. doi: 10.1126/science.3118463. [DOI] [PubMed] [Google Scholar]
  56. 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]
  57. Nalbantoglu J., Hartley D., Phear G., Tear G., Meuth M. Spontaneous deletion formation at the aprt locus of hamster cells: the presence of short sequence homologies and dyad symmetries at deletion termini. EMBO J. 1986 Jun;5(6):1199–1204. doi: 10.1002/j.1460-2075.1986.tb04347.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Nalbantoglu J., Meuth M. DNA amplification--deletion in a spontaneous mutation of the hamster aprt locus: structure and sequence of the novel joint. Nucleic Acids Res. 1986 Nov 11;14(21):8361–8371. doi: 10.1093/nar/14.21.8361. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Nalbantoglu J., Phear G., Meuth M. DNA sequence analysis of spontaneous mutations at the aprt locus of hamster cells. Mol Cell Biol. 1987 Apr;7(4):1445–1449. doi: 10.1128/mcb.7.4.1445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Nicholls R. D., Fischel-Ghodsian N., Higgs D. R. Recombination at the human alpha-globin gene cluster: sequence features and topological constraints. Cell. 1987 May 8;49(3):369–378. doi: 10.1016/0092-8674(87)90289-3. [DOI] [PubMed] [Google Scholar]
  61. Nicholls R. D., Higgs D. R., Clegg J. B., Weatherall D. J. Alpha zero-thalassemia due to recombination between the alpha 1-globin gene and an AluI repeat. Blood. 1985 Jun;65(6):1434–1438. [PubMed] [Google Scholar]
  62. Nordheim A., Rich A. Negatively supercoiled simian virus 40 DNA contains Z-DNA segments within transcriptional enhancer sequences. Nature. 1983 Jun 23;303(5919):674–679. doi: 10.1038/303674a0. [DOI] [PubMed] [Google Scholar]
  63. Orkin S. H., Michelson A. Partial deletion of the alpha-globin structural gene in human alpha-thalassaemia. Nature. 1980 Jul 31;286(5772):538–540. doi: 10.1038/286538a0. [DOI] [PubMed] [Google Scholar]
  64. Parnes J. R., Sizer K. C., Seidman J. G., Stallings V., Hyman R. A mutational hot-spot within an intron of the mouse beta 2-microglobulin gene. EMBO J. 1986 Jan;5(1):103–111. doi: 10.1002/j.1460-2075.1986.tb04183.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Passananti C., Davies B., Ford M., Fried M. Structure of an inverted duplication formed as a first step in a gene amplification event: implications for a model of gene amplification. EMBO J. 1987 Jun;6(6):1697–1703. doi: 10.1002/j.1460-2075.1987.tb02420.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Pickup D. J., Ink B. S., Parsons B. L., Hu W., Joklik W. K. Spontaneous deletions and duplications of sequences in the genome of cowpox virus. Proc Natl Acad Sci U S A. 1984 Nov;81(21):6817–6821. doi: 10.1073/pnas.81.21.6817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Roth D. B., Porter T. N., Wilson J. H. Mechanisms of nonhomologous recombination in mammalian cells. Mol Cell Biol. 1985 Oct;5(10):2599–2607. doi: 10.1128/mcb.5.10.2599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Rovinski B., Munroe D., Peacock J., Mowat M., Bernstein A., Benchimol S. Deletion of 5'-coding sequences of the cellular p53 gene in mouse erythroleukemia: a novel mechanism of oncogene regulation. Mol Cell Biol. 1987 Feb;7(2):847–853. doi: 10.1128/mcb.7.2.847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Ruley H. E., Fried M. Clustered illegitimate recombination events in mammalian cells involving very short sequence homologies. Nature. 1983 Jul 14;304(5922):181–184. doi: 10.1038/304181a0. [DOI] [PubMed] [Google Scholar]
  70. Sambrook J., Greene R., Stringer J., Mitchison T., Hu S. L., Botchan M. Analysis of the sites of integration of viral DNA sequences in rat cells transformed by adenovirus 2 or SV40. Cold Spring Harb Symp Quant Biol. 1980;44(Pt 1):569–584. doi: 10.1101/sqb.1980.044.01.059. [DOI] [PubMed] [Google Scholar]
  71. Savageau M. A., Metter R., Brockman W. W. Statistical significance of partial base-pairing potential: implications for recombination of SV40 DNA in eukaryotic cells. Nucleic Acids Res. 1983 Sep 24;11(18):6559–6570. doi: 10.1093/nar/11.18.6559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  72. Schon E., Evans T., Welsh J., Efstratiadis A. Conformation of promoter DNA: fine mapping of S1-hypersensitive sites. Cell. 1983 Dec;35(3 Pt 2):837–848. doi: 10.1016/0092-8674(83)90116-2. [DOI] [PubMed] [Google Scholar]
  73. Schwartzberg P., Colicelli J., Goff S. P. Construction and analysis of deletion mutations in the pol gene of Moloney murine leukemia virus: a new viral function required for productive infection. Cell. 1984 Jul;37(3):1043–1052. doi: 10.1016/0092-8674(84)90439-2. [DOI] [PubMed] [Google Scholar]
  74. Seif I., Khoury G., Dhar R. A rapid enzymatic DNA sequencing technique: determination of sequence alterations in early simian virus 40 temperature sensitive and deletion mutants. Nucleic Acids Res. 1980 May 24;8(10):2225–2240. doi: 10.1093/nar/8.10.2225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. Sheflin L., Celeste A., Woodworth-Gutai M. Recombination in simian virus 40-infected cells. Structure of naturally arising variants ev-2114, ev-2102, and ev-1110. J Biol Chem. 1983 Dec 10;258(23):14315–14321. [PubMed] [Google Scholar]
  76. Smolar N., Griffin B. E. DNA sequences of polyoma virus early deletion mutants. J Virol. 1981 Jun;38(3):958–967. doi: 10.1128/jvi.38.3.958-967.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Soeda E., Griffin B. E. Sequences from the genome of a non-transforming mutant of polyoma virus. Nature. 1978 Nov 16;276(5685):294–298. doi: 10.1038/276294a0. [DOI] [PubMed] [Google Scholar]
  78. Spritz R. A., Orkin S. H. Duplication followed by deletion accounts for the structure of an Indian deletion beta (0)-thalassemia gene. Nucleic Acids Res. 1982 Dec 20;10(24):8025–8029. doi: 10.1093/nar/10.24.8025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Stabel S., Doerfler W. Nucleotide sequence at the site of junction between adenovirus type 12 DNA and repetitive hamster cell DNA in transformed cell line CLAC1. Nucleic Acids Res. 1982 Dec 20;10(24):8007–8023. doi: 10.1093/nar/10.24.8007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. Stringer J. R. DNA sequence homology and chromosomal deletion at a site of SV40 DNA integration. Nature. 1982 Mar 25;296(5855):363–366. doi: 10.1038/296363a0. [DOI] [PubMed] [Google Scholar]
  81. Stringer J. R. Integrated simian virus 40 DNA: nucleotide sequences at cell-virus recombinant junctions. J Virol. 1981 May;38(2):671–679. doi: 10.1128/jvi.38.2.671-679.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Stringer J. R. Recombination between poly[d(GT).d(CA)] sequences in simian virus 40-infected cultured cells. Mol Cell Biol. 1985 Jun;5(6):1247–1259. doi: 10.1128/mcb.5.6.1247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Subramani S., Berg P. Homologous and nonhomologous recombination in monkey cells. Mol Cell Biol. 1983 Jun;3(6):1040–1052. doi: 10.1128/mcb.3.6.1040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Sylla B. S., Huberdeau D., Bourgaux-Ramoisy D., Bourgaux P. Site-specific excision of integrated polyoma DNA. Cell. 1984 Jun;37(2):661–667. doi: 10.1016/0092-8674(84)90398-2. [DOI] [PubMed] [Google Scholar]
  85. Thimmappaya B., Shenk T. Nucleotide sequence analysis of viable deletion mutants lacking segments of the simian virus 40 genome coding for small t antigen. J Virol. 1979 Jun;30(3):668–673. doi: 10.1128/jvi.30.3.668-673.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Trifonov E. N., Konopka A. K., Jovin T. M. Unusual frequencies of certain alternating purine-pyrimidine runs in natural DNA sequences: relation to Z-DNA. FEBS Lett. 1985 Jun 3;185(1):197–202. doi: 10.1016/0014-5793(85)80769-9. [DOI] [PubMed] [Google Scholar]
  87. Van Heuverswyn H., Fiers W. Nucleotide sequence of the Hind-C fragment of simian virus 40 DNA. Comparison of the 5'-untranslated region of wild-type virus and of some deletion Mutants. Eur J Biochem. 1979 Oct;100(1):51–60. doi: 10.1111/j.1432-1033.1979.tb02032.x. [DOI] [PubMed] [Google Scholar]
  88. Vanin E. F., Henthorn P. S., Kioussis D., Grosveld F., Smithies O. Unexpected relationships between four large deletions in the human beta-globin gene cluster. Cell. 1983 Dec;35(3 Pt 2):701–709. doi: 10.1016/0092-8674(83)90103-4. [DOI] [PubMed] [Google Scholar]
  89. Visser L., Reemst A. C., van Mansfeld A. D., Rozijn T. H. Nucleotide sequence analysis of the linked left and right hand terminal regions of adenovirus type 5 DNA present in the transformed rat cell line 5RK20. Nucleic Acids Res. 1982 Apr 10;10(7):2189–2198. doi: 10.1093/nar/10.7.2189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  90. Wakamiya T., McCutchan T., Rosenberg M., Singer M. Structure of simian virus 40 recombinants that contain both host and viral DNA sequences. I. The structure of variant CVPS/1/P2 (EcoRI res). J Biol Chem. 1979 May 10;254(9):3584–3591. [PubMed] [Google Scholar]
  91. Wake C. T., Gudewicz T., Porter T., White A., Wilson J. H. How damaged is the biologically active subpopulation of transfected DNA? Mol Cell Biol. 1984 Mar;4(3):387–398. doi: 10.1128/mcb.4.3.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. Westin G., Visser L., Zabielski J., van Mansfeld A. D., Pettersson U., Rozijn T. H. Sequence organization of a viral DNA insertion present in the adenovirus-type-5-transformed hamster line BHK268-C31. Gene. 1982 Mar;17(3):263–270. doi: 10.1016/0378-1119(82)90142-1. [DOI] [PubMed] [Google Scholar]
  93. Westphal H. Genomic arrangement of an adenovirus-simian virus 40 hybrid virus, Ad2+ND4del. J Virol. 1981 Nov;40(2):526–532. doi: 10.1128/jvi.40.2.526-532.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. Wilkie T. M., Palmiter R. D. Analysis of the integrant in MyK-103 transgenic mice in which males fail to transmit the integrant. Mol Cell Biol. 1987 May;7(5):1646–1655. doi: 10.1128/mcb.7.5.1646. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Wilson J. H., Berget P. B., Pipas J. M. Somatic cells efficiently join unrelated DNA segments end-to-end. Mol Cell Biol. 1982 Oct;2(10):1258–1269. doi: 10.1128/mcb.2.10.1258. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Woodworth-Gutai M. Recombination in SV40-infected cells: nucleotide sequences at viral-viral recombinant joints in naturally arising variants. Virology. 1981 Mar;109(2):344–352. doi: 10.1016/0042-6822(81)90505-5. [DOI] [PubMed] [Google Scholar]
  97. Woodworth-Gutai M. Recombination in SV40-infected cells: viral DNA sequences at sites of circularization of transfecting linear DNA. Virology. 1981 Mar;109(2):353–365. doi: 10.1016/0042-6822(81)90506-7. [DOI] [PubMed] [Google Scholar]
  98. Zain B. S., Roberts R. J. Characterization and sequence analysis of a recombination site in the hybrid virus Ad2+ND. J Mol Biol. 1978 Mar 25;120(1):13–31. doi: 10.1016/0022-2836(78)90293-0. [DOI] [PubMed] [Google Scholar]

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