Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Nov 11;15(21):8899–8918. doi: 10.1093/nar/15.21.8899

Supercoiled induced transition to the Z-DNA conformation affects the ability of a d(CG/GC)12 sequence to be organized into nucleosome-cores.

J M Casasnovas 1, F Azorín 1
PMCID: PMC306412  PMID: 3684575

Abstract

Nucleosome-cores were reconstituted by the salt-dialysis method onto closed circular pDHg16 DNA which contains a d(CG/GC)12 sequence. Alternating d(CG/GC)n sequences form left-handed Z-DNA readily when contained in negatively supercoiled DNA. We have investigated the ability of the d(CG/GC)12 sequence to be organized into nucleosome-cores when stabilized as Z-DNA through negative supercoiling. We have found that nucleosome assembly at the d(CG/GC)12 insert is prevented when the sequence is stable in the Z-conformation but it is not affected at all when the sequence adopts the right-handed B-form.

Full text

PDF
8899

Images in this article

8903Image
on p.8903
8904Image
on p.8904
8907Image
on p.8907
8909Image
on p.8909
8910Image
on p.8910
8913Image
on p.8913

Selected References

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

  1. Axel R., Melchior W., Jr, Sollner-Webb B., Felsenfeld G. Specific sites of interaction between histones and DNA in chromatin. Proc Natl Acad Sci U S A. 1974 Oct;71(10):4101–4105. doi: 10.1073/pnas.71.10.4101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Azorin F., Hahn R., Rich A. Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA. Proc Natl Acad Sci U S A. 1984 Sep;81(18):5714–5718. doi: 10.1073/pnas.81.18.5714. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Azorin F., Nordheim A., Rich A. Formation of Z-DNA in negatively supercoiled plasmids is sensitive to small changes in salt concentration within the physiological range. EMBO J. 1983;2(5):649–655. doi: 10.1002/j.1460-2075.1983.tb01479.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Azorin F., Rich A. Isolation of Z-DNA binding proteins from SV40 minichromosomes: evidence for binding to the viral control region. Cell. 1985 Jun;41(2):365–374. doi: 10.1016/s0092-8674(85)80009-x. [DOI] [PubMed] [Google Scholar]
  5. Behe M., Felsenfeld G. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619–1623. doi: 10.1073/pnas.78.3.1619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Boseley P. G., Bradbury E. M., Butler-Browne G. S., Carpenter B. G., Stephens R. M. Physical studies of chromatin. The recombination of histones with DNA. Eur J Biochem. 1976 Feb 2;62(1):21–31. doi: 10.1111/j.1432-1033.1976.tb10093.x. [DOI] [PubMed] [Google Scholar]
  7. Ellison M. J., Kelleher R. J., 3rd, Wang A. H., Habener J. F., Rich A. Sequence-dependent energetics of the B-Z transition in supercoiled DNA containing nonalternating purine-pyrimidine sequences. Proc Natl Acad Sci U S A. 1985 Dec;82(24):8320–8324. doi: 10.1073/pnas.82.24.8320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Germond J. E., Hirt B., Oudet P., Gross-Bellark M., Chambon P. Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A. 1975 May;72(5):1843–1847. doi: 10.1073/pnas.72.5.1843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hamada H., Petrino M. G., Kakunaga T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6465–6469. doi: 10.1073/pnas.79.21.6465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Haniford D. B., Pulleyblank D. E. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature. 1983 Apr 14;302(5909):632–634. doi: 10.1038/302632a0. [DOI] [PubMed] [Google Scholar]
  11. Haniford D. B., Pulleyblank D. E. The in-vivo occurrence of Z DNA. J Biomol Struct Dyn. 1983 Dec;1(3):593–609. doi: 10.1080/07391102.1983.10507467. [DOI] [PubMed] [Google Scholar]
  12. Johns E. W. Studies on histones. 7. Preparative methods for histone fractions from calf thymus. Biochem J. 1964 Jul;92(1):55–59. doi: 10.1042/bj0920055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Keller W. Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4876–4880. doi: 10.1073/pnas.72.12.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kmiec E. B., Angelides K. J., Holloman W. K. Left-handed DNA and the synaptic pairing reaction promoted by Ustilago rec1 protein. Cell. 1985 Jan;40(1):139–145. doi: 10.1016/0092-8674(85)90317-4. [DOI] [PubMed] [Google Scholar]
  15. Kmiec E. B., Holloman W. K. Synapsis promoted by Ustilago rec1 protein. Cell. 1984 Mar;36(3):593–598. doi: 10.1016/0092-8674(84)90338-6. [DOI] [PubMed] [Google Scholar]
  16. Kornberg R. D., Thomas J. O. Chromatin structure; oligomers of the histones. Science. 1974 May 24;184(4139):865–868. doi: 10.1126/science.184.4139.865. [DOI] [PubMed] [Google Scholar]
  17. Kłysik J., Stirdivant S. M., Larson J. E., Hart P. A., Wells R. D. Left-handed DNA in restriction fragments and a recombinant plasmid. Nature. 1981 Apr 23;290(5808):672–677. doi: 10.1038/290672a0. [DOI] [PubMed] [Google Scholar]
  18. Lafer E. M., Sousa R., Rosen B., Hsu A., Rich A. Isolation and characterization of Z-DNA binding proteins from wheat germ. Biochemistry. 1985 Sep 10;24(19):5070–5076. doi: 10.1021/bi00340a017. [DOI] [PubMed] [Google Scholar]
  19. Miller F. D., Dixon G. H., Rattner J. B., van de Sande J. H. Assembly and characterization of nucleosomal cores on B- vs. Z-form DNA. Biochemistry. 1985 Jan 1;24(1):102–109. doi: 10.1021/bi00322a015. [DOI] [PubMed] [Google Scholar]
  20. Nickol J., Behe M., Felsenfeld G. Effect of the B--Z transition in poly(dG-m5dC) . poly(dG-m5dC) on nucleosome formation. Proc Natl Acad Sci U S A. 1982 Mar;79(6):1771–1775. doi: 10.1073/pnas.79.6.1771. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nordheim A., Rich A. The sequence (dC-dA)n X (dG-dT)n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc Natl Acad Sci U S A. 1983 Apr;80(7):1821–1825. doi: 10.1073/pnas.80.7.1821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Nordheim A., Tesser P., Azorin F., Kwon Y. H., Möller A., Rich A. Isolation of Drosophila proteins that bind selectively to left-handed Z-DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7729–7733. doi: 10.1073/pnas.79.24.7729. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Oudet P., Gross-Bellard M., Chambon P. Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell. 1975 Apr;4(4):281–300. doi: 10.1016/0092-8674(75)90149-x. [DOI] [PubMed] [Google Scholar]
  24. Peck L. J., Nordheim A., Rich A., Wang J. C. Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc Natl Acad Sci U S A. 1982 Aug;79(15):4560–4564. doi: 10.1073/pnas.79.15.4560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Rich A., Nordheim A., Wang A. H. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791–846. doi: 10.1146/annurev.bi.53.070184.004043. [DOI] [PubMed] [Google Scholar]
  26. Richmond T. J., Finch J. T., Rushton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 A resolution. Nature. 1984 Oct 11;311(5986):532–537. doi: 10.1038/311532a0. [DOI] [PubMed] [Google Scholar]
  27. Simpson R. T., Künzler P. Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. Nucleic Acids Res. 1979 Apr;6(4):1387–1415. doi: 10.1093/nar/6.4.1387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Simpson R. T., Thoma F., Brubaker J. M. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell. 1985 Oct;42(3):799–808. doi: 10.1016/0092-8674(85)90276-4. [DOI] [PubMed] [Google Scholar]
  29. Thomas T. J., Bloomfield V. A. Chain flexibility and hydrodynamics of the B and Z forms of poly(dG-dC).poly(dG-dC). Nucleic Acids Res. 1983 Mar 25;11(6):1919–1930. doi: 10.1093/nar/11.6.1919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Treco D., Arnheim N. The evolutionarily conserved repetitive sequence d(TG.AC)n promotes reciprocal exchange and generates unusual recombinant tetrads during yeast meiosis. Mol Cell Biol. 1986 Nov;6(11):3934–3947. doi: 10.1128/mcb.6.11.3934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]
  32. Woodcock C. L. Reconstitution of chromatin subunits. Science. 1977 Mar 25;195(4284):1350–1352. doi: 10.1126/science.841333. [DOI] [PubMed] [Google Scholar]
  33. Zimmerman S. B. The three-dimensional structure of DNA. Annu Rev Biochem. 1982;51:395–427. doi: 10.1146/annurev.bi.51.070182.002143. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES