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. 1985 Sep 11;13(17):6205–6221. doi: 10.1093/nar/13.17.6205

Site-specific nicking at the avian retrovirus LTR circle junction by the viral pp32 DNA endonuclease.

D P Grandgenett, A C Vora
PMCID: PMC321947  PMID: 2995920

Abstract

The avian retrovirus pp32 DNA endonuclease prefers to nick supercoiled DNA containing long terminal repeat (LTR) circle junction sequences at one or the other of two sites, each which mapped two nucleotides back from the circle junction. The sequence at the sites of nicking was (sequence: see text) where increases indicates the positions of the two alternative nicked sites. This site-specific nicking was observed when the circle junction LTR DNA was present in supercoiled form, the divalent metal ion was Mg2+ and the molar ratio of protein to DNA was low. The majority of other LTR DNA sites nicked by pp32 in the presence of Mg2+ were adjacent to or within the dinucleotide CA.

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Selected References

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

  1. Better M., Lu C., Williams R. C., Echols H. Site-specific DNA condensation and pairing mediated by the int protein of bacteriophage lambda. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5837–5841. doi: 10.1073/pnas.79.19.5837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chiu I. M., Callahan R., Tronick S. R., Schlom J., Aaronson S. A. Major pol gene progenitors in the evolution of oncoviruses. Science. 1984 Jan 27;223(4634):364–370. doi: 10.1126/science.6197754. [DOI] [PubMed] [Google Scholar]
  3. Copeland T. D., Grandgenett D. P., Oroszlan S. Amino acid sequence analysis of reverse transcriptase subunits from avian myeloblastosis virus. J Virol. 1980 Oct;36(1):115–119. doi: 10.1128/jvi.36.1.115-119.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Craig N. L., Nash H. A. E. coli integration host factor binds to specific sites in DNA. Cell. 1984 Dec;39(3 Pt 2):707–716. doi: 10.1016/0092-8674(84)90478-1. [DOI] [PubMed] [Google Scholar]
  5. Donehower L. A., Varmus H. E. A mutant murine leukemia virus with a single missense codon in pol is defective in a function affecting integration. Proc Natl Acad Sci U S A. 1984 Oct;81(20):6461–6465. doi: 10.1073/pnas.81.20.6461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Duyk G., Leis J., Longiaru M., Skalka A. M. Selective cleavage in the avian retroviral long terminal repeat sequence by the endonuclease associated with the alpha beta form of avian reverse transcriptase. Proc Natl Acad Sci U S A. 1983 Nov;80(22):6745–6749. doi: 10.1073/pnas.80.22.6745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Eisenman R. N., Mason W. S., Linial M. Synthesis and processing of polymerase proteins of wild-type and mutant avian retroviruses. J Virol. 1980 Oct;36(1):62–78. doi: 10.1128/jvi.36.1.62-78.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Golomb M., Grandgenett D. P. Endonuclease activity of purified RNA-directed DNA polymerase from avian myeloblastosis virus. J Biol Chem. 1979 Mar 10;254(5):1606–1613. [PubMed] [Google Scholar]
  9. Grandgenett D. P., Golomb M., Vora A. C. Activation of an Mg2+-dependent DNA endonuclease of avian myeloblastosis virus alpha beta DNA polymerase by in vitro proteolytic cleavage. J Virol. 1980 Jan;33(1):264–271. doi: 10.1128/jvi.33.1.264-271.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Grandgenett D., Quinn T., Hippenmeyer P. J., Oroszlan S. Structural characterization of the avian retrovirus reverse transcriptase and endonuclease domains. J Biol Chem. 1985 Jul 15;260(14):8243–8249. [PubMed] [Google Scholar]
  12. Hippenmeyer P. J., Grandgenett D. P. Mutants of the Rous sarcoma virus reverse transcriptase gene are nondefective in early replication events. J Biol Chem. 1985 Jul 15;260(14):8250–8256. [PubMed] [Google Scholar]
  13. Hippenmeyer P. J., Grandgenett D. P. Requirement of the avian retrovirus pp32 DNA binding protein domain for replication. Virology. 1984 Sep;137(2):358–370. doi: 10.1016/0042-6822(84)90228-9. [DOI] [PubMed] [Google Scholar]
  14. Klevan L., Wang J. C. Deoxyribonucleic acid gyrase-deoxyribonucleic acid complex containing 140 base pairs of deoxyribonucleic acid and an alpha 2 beta 2 protein core. Biochemistry. 1980 Nov 11;19(23):5229–5234. doi: 10.1021/bi00564a012. [DOI] [PubMed] [Google Scholar]
  15. Knaus R. J., Hippenmeyer P. J., Misra T. K., Grandgenett D. P., Müller U. R., Fitch W. M. Avian retrovirus pp32 DNA binding protein. Preferential binding to the promoter region of long terminal repeat DNA. Biochemistry. 1984 Jan 17;23(2):350–359. doi: 10.1021/bi00297a026. [DOI] [PubMed] [Google Scholar]
  16. Leis J., Duyk G., Johnson S., Longiaru M., Skalka A. Mechanism of action of the endonuclease associated with the alpha beta and beta beta forms of avian RNA tumor virus reverse transcriptase. J Virol. 1983 Feb;45(2):727–739. doi: 10.1128/jvi.45.2.727-739.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  18. Misra T. K., Grandgenett D. P., Parsons J. T. Avian retrovirus pp32 DNA-binding protein. I. Recognition of specific sequences on retrovirus DNA terminal repeats. J Virol. 1982 Oct;44(1):330–343. doi: 10.1128/jvi.44.1.330-343.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Panganiban A. T., Temin H. M. Circles with two tandem LTRs are precursors to integrated retrovirus DNA. Cell. 1984 Mar;36(3):673–679. doi: 10.1016/0092-8674(84)90347-7. [DOI] [PubMed] [Google Scholar]
  20. Panganiban A. T., Temin H. M. The retrovirus pol gene encodes a product required for DNA integration: identification of a retrovirus int locus. Proc Natl Acad Sci U S A. 1984 Dec;81(24):7885–7889. doi: 10.1073/pnas.81.24.7885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Panganiban A. T., Temin H. M. The terminal nucleotides of retrovirus DNA are required for integration but not virus production. Nature. 1983 Nov 10;306(5939):155–160. doi: 10.1038/306155a0. [DOI] [PubMed] [Google Scholar]
  22. Payvar F., DeFranco D., Firestone G. L., Edgar B., Wrange O., Okret S., Gustafsson J. A., Yamamoto K. R. Sequence-specific binding of glucocorticoid receptor to MTV DNA at sites within and upstream of the transcribed region. Cell. 1983 Dec;35(2 Pt 1):381–392. doi: 10.1016/0092-8674(83)90171-x. [DOI] [PubMed] [Google Scholar]
  23. Rogers J. Molecular biology. CACA sequences - the ends and the means? Nature. 1983 Sep 8;305(5930):101–102. doi: 10.1038/305101a0. [DOI] [PubMed] [Google Scholar]
  24. Saigo K., Kugimiya W., Matsuo Y., Inouye S., Yoshioka K., Yuki S. Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster. Nature. 1984 Dec 13;312(5995):659–661. doi: 10.1038/312659a0. [DOI] [PubMed] [Google Scholar]
  25. Samuel K. P., Papas T. S., Chirikjian J. G. DNA endonucleases associated with the avian myeloblastosis virus DNA polymerase. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2659–2663. doi: 10.1073/pnas.76.6.2659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Schmid K., Thomm M., Laminet A., Laue F. G., Kessler C., Stetter K. O., Schmitt R. Three new restriction endonucleases MaeI, MaeII and MaeIII from Methanococcus aeolicus. Nucleic Acids Res. 1984 Mar 26;12(6):2619–2628. doi: 10.1093/nar/12.6.2619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Swanstrom R., DeLorbe W. J., Bishop J. M., Varmus H. E. Nucleotide sequence of cloned unintegrated avian sarcoma virus DNA: viral DNA contains direct and inverted repeats similar to those in transposable elements. Proc Natl Acad Sci U S A. 1981 Jan;78(1):124–128. doi: 10.1073/pnas.78.1.124. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Tapper D. P., Clayton D. A. Altered mobility of polydeoxyribonucleotides in high resolution polyacrylamide gels due to removal of terminal phosphates. Nucleic Acids Res. 1981 Dec 21;9(24):6787–6794. doi: 10.1093/nar/9.24.6787. [DOI] [PMC free article] [PubMed] [Google Scholar]

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