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. 1987 Apr;84(8):2223–2227. doi: 10.1073/pnas.84.8.2223

Unusual conformational effect exerted by Z-DNA upon its neighboring sequences.

T Kohwi-Shigematsu, T Manes, Y Kohwi
PMCID: PMC304621  PMID: 3470786

Abstract

Supercoiled plasmid DNA harboring an insert of (dG-dC)16, a sequence known to form Z-DNA upon negative supercoiling, was reacted with chloroacetaldehyde. Chloroacetaldehyde, like bromoacetaldehyde, was found to be a specific probe for detecting unpaired DNA bases in supercoiled plasmid DNA. Under torsional stress (at bacterial superhelical density), chloroacetaldehyde reacted at multiple discrete regions within the neighboring sequences of the (dG-dC)16 insert. When the plasmid population was considered as a whole, the distribution of the chemically reactive bases exhibited a pattern of inversion symmetry with the center of inversion in the middle of the (dG-dC)16 insert. However, when a single supercoiled plasmid molecule was considered, chloroacetaldehyde reacted with only one of the neighboring sequences, either 5' or 3' of the (dG-dC)16 insert, but not with both. The possibility that the supercoiled plasmid DNA is in equilibrium with these two structural forms is discussed.

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Selected References

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

  1. 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]
  2. Herr W. Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA. Proc Natl Acad Sci U S A. 1985 Dec;82(23):8009–8013. doi: 10.1073/pnas.82.23.8009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Johnston B. H., Rich A. Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution. Cell. 1985 Oct;42(3):713–724. doi: 10.1016/0092-8674(85)90268-5. [DOI] [PubMed] [Google Scholar]
  4. Kang D. S., Wells R. D. B-Z DNA junctions contain few, if any, nonpaired bases at physiological superhelical densities. J Biol Chem. 1985 Jun 25;260(12):7783–7790. [PubMed] [Google Scholar]
  5. Kilpatrick M. W., Klysik J., Singleton C. K., Zarling D. A., Jovin T. M., Hanau L. H., Erlanger B. F., Wells R. D. Intervening sequences in human fetal globin genes adopt left-handed Z helices. J Biol Chem. 1984 Jun 10;259(11):7268–7274. [PubMed] [Google Scholar]
  6. Kimura K., Nakanishi M., Yamamoto T., Tsuboi M. A correlation between the secondary structure of DNA and the reactivity of adenine residues with chloroacetaldehyde. J Biochem. 1977 Jun;81(6):1699–1703. doi: 10.1093/oxfordjournals.jbchem.a131629. [DOI] [PubMed] [Google Scholar]
  7. Kohwi-Shigematsu T., Enomoto T., Yamada M. A., Nakanishi M., Tsuboi M. Exposure of DNA bases induced by the interaction of DNA and calf thymus DNA helix-destabilizing protein. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4689–4693. doi: 10.1073/pnas.75.10.4689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kohwi-Shigematsu T., Gelinas R., Weintraub H. Detection of an altered DNA conformation at specific sites in chromatin and supercoiled DNA. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4389–4393. doi: 10.1073/pnas.80.14.4389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kohwi-Shigematsu T., Kohwi Y. Poly(dG)-poly(dC) sequences, under torsional stress, induce an altered DNA conformation upon neighboring DNA sequences. Cell. 1985 Nov;43(1):199–206. doi: 10.1016/0092-8674(85)90024-8. [DOI] [PubMed] [Google Scholar]
  10. Leonard N. J., McDonald J. J., Henderson R. E., Reichmann M. E. Reaction of diethyl pyrocarbonate with nucleic acid components. Adenosine. Biochemistry. 1971 Aug 31;10(18):3335–3342. doi: 10.1021/bi00794a003. [DOI] [PubMed] [Google Scholar]
  11. Lilley D. M. Structural perturbation in supercoiled DNA: hypersensitivity to modification by a single-strand-selective chemical reagent conferred by inverted repeat sequences. Nucleic Acids Res. 1983 May 25;11(10):3097–3112. doi: 10.1093/nar/11.10.3097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. McCann J., Simmon V., Streitwieser D., Ames B. N. Mutagenicity of chloroacetaldehyde, a possible metabolic product of 1,2-dichloroethane (ethylene dichloride), chloroethanol (ethylene chlorohydrin), vinyl chloride, and cyclophosphamide. Proc Natl Acad Sci U S A. 1975 Aug;72(8):3190–3193. doi: 10.1073/pnas.72.8.3190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nordheim A., Lafer E. M., Peck L. J., Wang J. C., Stollar B. D., Rich A. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell. 1982 Dec;31(2 Pt 1):309–318. doi: 10.1016/0092-8674(82)90124-6. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. 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]
  17. 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]
  18. Singleton C. K., Klysik J., Stirdivant S. M., Wells R. D. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature. 1982 Sep 23;299(5881):312–316. doi: 10.1038/299312a0. [DOI] [PubMed] [Google Scholar]
  19. Van Duuren B. L., Goldschmidt B. M., Loewengart G., Smith A. C., Melchionne S., Seldman I., Roth D. Carcinogenicity of halogenated olefinic and aliphatic hydrocarbons in mice. J Natl Cancer Inst. 1979 Dec;63(6):1433–1439. [PubMed] [Google Scholar]
  20. Vincze A., Henderson R. E., McDonald J. J., Leonard N. J. Reaction of diethyl pyrocarbonate with nucleic acid components. Bases and nucleosides derived from guanine, cytosine, and uracil. J Am Chem Soc. 1973 Apr 18;95(8):2677–2682. doi: 10.1021/ja00789a045. [DOI] [PubMed] [Google Scholar]
  21. Wartell R. M., Klysik J., Hillen W., Wells R. D. Junction between Z and B conformations in a DNA restriction fragment: evaluation by Raman spectroscopy. Proc Natl Acad Sci U S A. 1982 Apr;79(8):2549–2553. doi: 10.1073/pnas.79.8.2549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Weintraub H. A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin. Cell. 1983 Apr;32(4):1191–1203. doi: 10.1016/0092-8674(83)90302-1. [DOI] [PubMed] [Google Scholar]

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