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. 1979 Sep 11;7(1):107–120. doi: 10.1093/nar/7.1.107

Comparison of the A-T rich regions and the Bacillus subtilis RNA polymerase binding sites in phage phi 29 DNA.

J M Sogo, P Rodeño, T Koller, E Viñuela, M Salas
PMCID: PMC327999  PMID: 114982

Abstract

By using a modification of the BAC spreading method for mounting the DNA for electron microscopy, partial denaturation maps of protein-free phi 29 DNA and of phi 29 DNA containing protein p3 were obtained. In phi 29 p3-DNA1 the protein does not seem to influence the melting of the ends of the molecules. The comparison of the partial denaturation map and the B. subtilis RNA polymerase binding sites indicates that five of the seven early promoters (A1, A2, A3, B2 and C2) are located in A-T rich DNA regions whereas the other two early promoters (B1 and C1) are located in less A-T rich sites.

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Selected References

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

  1. Botchan P. An electron microscopic comparison of transcription on linear and superhelical DNA. J Mol Biol. 1976 Jul 25;105(1):161–176. doi: 10.1016/0022-2836(76)90201-1. [DOI] [PubMed] [Google Scholar]
  2. Carrascosa J. L., Camacho A., Moreno F., Jiménez F., Mellado R. P., Viñuela E., Salas M. Bacillus subtilis phage phi29. Characterization of gene products and functions. Eur J Biochem. 1976 Jul 1;66(2):229–241. doi: 10.1111/j.1432-1033.1976.tb10512.x. [DOI] [PubMed] [Google Scholar]
  3. Carrascosa J. L., Viñuela E., Salas M. Proteins induced in Bacillus subtilis infected with bacteriophage phi 29. Virology. 1973 Nov;56(1):291–299. [PubMed] [Google Scholar]
  4. Dasgupta S., Allison D. P., Snyder C. E., Mitra S. Base-unpaired regions in supercoiled replicative form DNA of coliphage M13. J Biol Chem. 1977 Aug 25;252(16):5916–5923. [PubMed] [Google Scholar]
  5. Freifelder D. Electron microscopic study of the ethidium bromide-DNA complex. J Mol Biol. 1971 Sep 14;60(2):401–403. doi: 10.1016/0022-2836(71)90303-2. [DOI] [PubMed] [Google Scholar]
  6. Gómez B., Lang D. Denaturation map of bacteriophage T7 DNA and direction of DNA transcription. J Mol Biol. 1972 Sep 28;70(2):239–251. doi: 10.1016/0022-2836(72)90536-0. [DOI] [PubMed] [Google Scholar]
  7. Hagen E. W., Reilly B. E., Tosi M. E., Anderson D. L. Analysis of gene function of bacteriophage phi 29 of Bacillus subtilis: identification of cistrons essential for viral assembly. J Virol. 1976 Aug;19(2):501–517. doi: 10.1128/jvi.19.2.501-517.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Harding N. E., Ito J., David G. S. Identification of the protein firmly bound to the ends of bacteriophage phi 29 DNA. Virology. 1978 Feb;84(2):279–292. doi: 10.1016/0042-6822(78)90248-9. [DOI] [PubMed] [Google Scholar]
  9. Hawley L. A., Reilly B. E., Hagen E. W., Anderson D. L. Viral protein synthesis in bacteriophage phi 29-infected Bacillus subtilis. J Virol. 1973 Nov;12(5):1149–1159. doi: 10.1128/jvi.12.5.1149-1159.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Inciarte M. R., Lázaro J. M., Salas M., Vińuela E. Physical map of bacteriophage phi29 DNA. Virology. 1976 Oct 15;74(2):314–323. [PubMed] [Google Scholar]
  11. Inman R. B. A denaturation map of the lambda phage DNA molecule determined by electron microscopy. J Mol Biol. 1966 Jul;18(3):464–476. doi: 10.1016/s0022-2836(66)80037-2. [DOI] [PubMed] [Google Scholar]
  12. Ito J. Bacteriophage phi29 terminal protein: its association with the 5' termini of the phi29 genome. J Virol. 1978 Dec;28(3):895–904. doi: 10.1128/jvi.28.3.895-904.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Jones B. B., Chan H., Rothstein S., Wells R. D., Reznikoff W. S. RNA polymerase binding sites in lambdaplac5 DNA. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4914–4918. doi: 10.1073/pnas.74.11.4914. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Koller T., Kübler O., Portmann R., Sogo J. M. High resolution physical mapping of specific binding sites of Escherichia coli RNA polymerase on the DNA of bacteriophage T7 . J Mol Biol. 1978 Mar 25;120(1):121–131. doi: 10.1016/0022-2836(78)90298-x. [DOI] [PubMed] [Google Scholar]
  15. Koller T., Sogo J. M., Bujard H. An electron microscopic method for studying nucleic acid-protein complexes. Visualization of RNA polymerase bound to the DNA of bacteriophages T7 and T3. Biopolymers. 1974 May;13(5):995–1009. doi: 10.1002/bip.1974.360130514. [DOI] [PubMed] [Google Scholar]
  16. Mellado R. P., Moreno F., Viñuela E., Salas M., Reilly B. E., Anderson D. L. Genetic analysis of bacteriophage phi 29 of Bacillus subtilis: integration and mapping of reference mutants of two collections. J Virol. 1976 Aug;19(2):495–500. doi: 10.1128/jvi.19.2.495-500.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Portmann R., Schaffner W., Birnstiel M. Partial denaturation mapping of cloned histone DNA from the sea urchin Psammechinus miliaris. Nature. 1976 Nov 4;264(5581):31–34. doi: 10.1038/264031a0. [DOI] [PubMed] [Google Scholar]
  18. Reilly B. E., Nelson R. A., Anderson D. L. Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: mapping and functional analysis of the head fiber gene. J Virol. 1977 Oct;24(1):363–377. doi: 10.1128/jvi.24.1.363-377.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Rubio V., Salas M., Viñuela E., Usobiaga P., Saiz J. L., Llopis J. F. Biophysical properties of bacteriophage phi29. Virology. 1974 Jan;57(1):112–121. doi: 10.1016/0042-6822(74)90112-3. [DOI] [PubMed] [Google Scholar]
  20. Salas M., Mellado R. P., Viñuela E. Characterization of a protein covalently linked to the 5' termini of the DNA of Bacillus subtilis phage phi29. J Mol Biol. 1978 Feb 25;119(2):269–291. doi: 10.1016/0022-2836(78)90438-2. [DOI] [PubMed] [Google Scholar]
  21. Sogo J. M., Inciarte M. R., Corral J., Viñuela E., Salas M. RNA polymerase binding sites and transcription map of the DNA of Bacillus subtilis phage phi29. J Mol Biol. 1979 Feb 5;127(4):411–436. doi: 10.1016/0022-2836(79)90230-4. [DOI] [PubMed] [Google Scholar]
  22. Talavera A., Salas M., Viñuela E. Temperature-sensitive mutants affected in DNA synthesis in phage phi29 of Bacillus subtilis. Eur J Biochem. 1972 Dec 4;31(2):367–371. doi: 10.1111/j.1432-1033.1972.tb02542.x. [DOI] [PubMed] [Google Scholar]
  23. Thomas J. O., Kolb A., Szer W. Structure of single-stranded nucleic acids in the presence of ribosomal protein S1. J Mol Biol. 1978 Aug 5;123(2):163–176. doi: 10.1016/0022-2836(78)90319-4. [DOI] [PubMed] [Google Scholar]
  24. Thomas J. O., Sternberg N., Weisberg R. Altered arrangement of the DNA in injection-defective lambda bacteriophage. J Mol Biol. 1978 Aug 5;123(2):149–161. doi: 10.1016/0022-2836(78)90318-2. [DOI] [PubMed] [Google Scholar]
  25. Vollenweider H. J., Sogo J. M., Koller T. A routine method for protein-free spreading of double- and single-stranded nucleic acid molecules. Proc Natl Acad Sci U S A. 1975 Jan;72(1):83–87. doi: 10.1073/pnas.72.1.83. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Vollenweider H. J., Szybalski W. Electron microscopic mapping of RNA polymerase binding to coliphage lambda DNA. J Mol Biol. 1978 Aug 15;123(3):485–498. doi: 10.1016/0022-2836(78)90092-x. [DOI] [PubMed] [Google Scholar]
  27. Yanofsky S., Kawamura F., Ito J. Thermolabile transfecting DNA from temperature-sensitive mutant of phage phi29. Nature. 1976 Jan 1;259(5538):60–63. doi: 10.1038/259060a0. [DOI] [PubMed] [Google Scholar]
  28. Yehle C. O. Genome-linked protein associated with the 5' termini of bacteriophage phi29 DNA. J Virol. 1978 Sep;27(3):776–783. doi: 10.1128/jvi.27.3.776-783.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]

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