Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1985 Aug 12;13(15):5645–5656. doi: 10.1093/nar/13.15.5645

Diepoxybutane forms a monoadduct with B-form (dG-dC)n.(dG-dC)n and a crosslinked diadduct with the left-handed Z-form.

D S Kang, S C Harvey, R D Wells
PMCID: PMC321895  PMID: 2994006

Abstract

The characteristics of the reactions of DL-diepoxybutane (DEB) with (dG-dC)n.(dG-dC)n in the right-handed B-form or the left-handed Z-form were investigated. DEB does react with right-handed B-DNA since less salt is required to convert the modified B-form to Z-form than for the unmodified DNA. However, the product appears to be a monoadduct rather than the crosslinked diadduct formed with the Z-form. The modified B-form can be isolated, converted to a Z-form with l mM MnCl2, and then this activated complex further reacts intramolecularly to give the crosslinked Z-product. This modified Z-form cannot be reverted to the B-form unless the crosslink is cleaved with periodate. Only MnCl2, and to a lesser extent ZnCl2, was effective in facilitating the intramolecular conversion of the B-DNA monoadduct to the Z-DNA diadduct; lmM MgCl2 and 4M NaCl were ineffective suggesting that somewhat different types of modified left-handed conformations were generated by the different salts. DEB also cleaves DNA under our reaction conditions thus precluding studies with supercoiled recombinant plasmids harboring segments that adopt Z-structures.

Full text

PDF
5648

Selected References

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

  1. Castleman H., Hanau L. H., Erlanger B. F. Stabilization of (dG-dC)n.(dG-dC)n in the Z conformation by a crosslinking reaction. Nucleic Acids Res. 1983 Dec 10;11(23):8421–8429. doi: 10.1093/nar/11.23.8421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Crawford J. L., Kolpak F. J., Wang A. H., Quigley G. J., van Boom J. H., van der Marel G., Rich A. The tetramer d(CpGpCpG) crystallizes as a left-handed double helix. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4016–4020. doi: 10.1073/pnas.77.7.4016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Dickerson R. E., Drew H. R., Conner B. N., Kopka M. L., Pjura P. E. Helix geometry and hydration in A-DNA, B-DNA, and Z-DNA. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):13–24. doi: 10.1101/sqb.1983.047.01.004. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. Harvey S. C. DNA structural dynamics: longitudinal breathing as a possible mechanism for the B in equilibrium Z transition. Nucleic Acids Res. 1983 Jul 25;11(14):4867–4878. doi: 10.1093/nar/11.14.4867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hill R. J., Stollar B. D. Dependence of Z-DNA antibody binding to polytene chromosomes on acid fixation and DNA torsional strain. Nature. 1983 Sep 22;305(5932):338–340. doi: 10.1038/305338a0. [DOI] [PubMed] [Google Scholar]
  7. Jovin T. M., van de Sande J. H., Zarling D. A., Arndt-Jovin D. J., Eckstein F., Füldner H. H., Greider C., Grieger I., Hamori E., Kalisch B. Generation of left-handed Z-DNA in solution and visualization in polytene chromosomes by immunofluorescence. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):143–154. doi: 10.1101/sqb.1983.047.01.019. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. Kłysik J., Stirdivant S. M., Wells R. D. Left-handed DNA. Cloning, characterization, and instability of inserts containing different lengths of (dC-dG) in Escherichia coli. J Biol Chem. 1982 Sep 10;257(17):10152–10158. [PubMed] [Google Scholar]
  11. Lawley P. D., Brookes P. Interstrand cross-linking of DNA by difunctional alkylating agents. J Mol Biol. 1967 Apr 14;25(1):143–160. doi: 10.1016/0022-2836(67)90285-9. [DOI] [PubMed] [Google Scholar]
  12. Mitra C. K., Sarma M. H., Sarma R. H. Left-handed deoxyribonucleic acid double helix in solution. Biochemistry. 1981 Mar 31;20(7):2036–2041. doi: 10.1021/bi00510a046. [DOI] [PubMed] [Google Scholar]
  13. Möller A., Nordheim A., Nichols S. R., Rich A. 7-Methylguanine in poly(dG-dC).poly(dG-dC) facilitates z-DNA formation. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4777–4781. doi: 10.1073/pnas.78.8.4777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nordheim A., Pardue M. L., Lafer E. M., Möller A., Stollar B. D., Rich A. Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature. 1981 Dec 3;294(5840):417–422. doi: 10.1038/294417a0. [DOI] [PubMed] [Google Scholar]
  15. Patel D. J., Canuel L. L., Pohl F. M. "Alternating B-DNA" conformation for the oligo(dG-dC) duplex in high-salt solution. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2508–2511. doi: 10.1073/pnas.76.6.2508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Pohl F. M., Jovin T. M., Baehr W., Holbrook J. J. Ethidium bromide as a cooperative effector of a DNA structure. Proc Natl Acad Sci U S A. 1972 Dec;69(12):3805–3809. doi: 10.1073/pnas.69.12.3805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Pohl F. M., Jovin T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J Mol Biol. 1972 Jun 28;67(3):375–396. doi: 10.1016/0022-2836(72)90457-3. [DOI] [PubMed] [Google Scholar]
  18. Rich A. Right-handed and left-handed DNA: conformational information in genetic material. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):1–12. doi: 10.1101/sqb.1983.047.01.003. [DOI] [PubMed] [Google Scholar]
  19. Singleton C. K., Kilpatrick M. W., Wells R. D. S1 nuclease recognizes DNA conformational junctions between left-handed helical (dT-dG n. dC-dA)n and contiguous right-handed sequences. J Biol Chem. 1984 Feb 10;259(3):1963–1967. [PubMed] [Google Scholar]
  20. 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]
  21. Stirdivant S. M., Kłysik J., Wells R. D. Energetic and structural inter-relationship between DNA supercoiling and the right- to left-handed Z helix transitions in recombinant plasmids. J Biol Chem. 1982 Sep 10;257(17):10159–10165. [PubMed] [Google Scholar]
  22. Thamann T. J., Lord R. C., Wang A. H., Rich A. The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions. Nucleic Acids Res. 1981 Oct 24;9(20):5443–5457. doi: 10.1093/nar/9.20.5443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Wang J. C., Peck L. J., Becherer K. DNA supercoiling and its effects on DNA structure and function. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):85–91. doi: 10.1101/sqb.1983.047.01.011. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Wells R. D., Brennan R., Chapman K. A., Goodman T. C., Hart P. A., Hillen W., Kellogg D. R., Kilpatrick M. W., Klein R. D., Klysik J. Left-handed DNA helices, supercoiling, and the B-Z junction. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):77–84. doi: 10.1101/sqb.1983.047.01.010. [DOI] [PubMed] [Google Scholar]
  26. Wells R. D., Goodman T. C., Hillen W., Horn G. T., Klein R. D., Larson J. E., Müller U. R., Neuendorf S. K., Panayotatos N., Stirdivant S. M. DNA structure and gene regulation. Prog Nucleic Acid Res Mol Biol. 1980;24:167–267. doi: 10.1016/s0079-6603(08)60674-1. [DOI] [PubMed] [Google Scholar]
  27. Wells R. D., Larson J. E., Grant R. C., Shortle B. E., Cantor C. R. Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. J Mol Biol. 1970 Dec 28;54(3):465–497. doi: 10.1016/0022-2836(70)90121-x. [DOI] [PubMed] [Google Scholar]
  28. Zacharias W., Larson J. E., Klysik J., Stirdivant S. M., Wells R. D. Conditions which cause the right-handed to left-handed DNA conformational transitions. Evidence for several types of left-handed DNA structures in solution. J Biol Chem. 1982 Mar 25;257(6):2775–2782. [PubMed] [Google Scholar]

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

RESOURCES