Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1983 Oct;80(20):6206–6210. doi: 10.1073/pnas.80.20.6206

Energetics of B-to-Z transition in DNA.

L J Peck, J C Wang
PMCID: PMC394264  PMID: 6578505

Abstract

Analysis by two-dimensional gel electrophoresis of topoisomers of plasmids containing d(pCpG)n . d(pCpG)n inserts, in which n ranges between 8 and 21, shows that the B-to-Z transition within the alternating C-G is readily induced by negative supercoiling and is highly cooperative. The free energy parameters for the transition in dilute aqueous buffers have been evaluated from a statistical mechanical analysis of the data, and these parameters allow prediction of the superhelicities of plasmids at which the transition occurs in alternating C-G inserts over a wide range of lengths. In agreement with the crystal structures, the helical handedness of the B structure in solution and that of the Z structure are shown to be opposite to each other. Furthermore, it is found that the B form of the alternating C-G sequence in solution has a helical periodicity of 10.5 +/- 0.1 base pairs per turn, and the Z form has a helical periodicity of 11.6 +/- 0.3 base pairs per turn. There also appears to be a significant unwinding of the right-handed DNA duplex at each of the B/Z junctions.

Full text

PDF
6207

Images in this article

6207Image
on p.6207
6207Image
on p.6207
6209Image
on p.6209

Selected References

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

  1. 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]
  2. 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]
  3. Courey A. J., Wang J. C. Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions. Cell. 1983 Jul;33(3):817–829. doi: 10.1016/0092-8674(83)90024-7. [DOI] [PubMed] [Google Scholar]
  4. Depew D. E., Wang J. C. Conformational fluctuations of DNA helix. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4275–4279. doi: 10.1073/pnas.72.11.4275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dickerson R. E., Drew H. R., Conner B. N., Wing R. M., Fratini A. V., Kopka M. L. The anatomy of A-, B-, and Z-DNA. Science. 1982 Apr 30;216(4545):475–485. doi: 10.1126/science.7071593. [DOI] [PubMed] [Google Scholar]
  6. Fuller F. B. The writhing number of a space curve. Proc Natl Acad Sci U S A. 1971 Apr;68(4):815–819. doi: 10.1073/pnas.68.4.815. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gupta G., Bansal M., Sasisekharan V. Reversal of handedness in DNA: a stable link between RU and LZ helices. Biochem Biophys Res Commun. 1980 Dec 31;97(4):1258–1267. doi: 10.1016/s0006-291x(80)80002-7. [DOI] [PubMed] [Google Scholar]
  8. Ivanov V. I., Minchenkova L. E., Minyat E. E., Schyolkina A. K. Cooperative transitions in DNA with no separation of strands. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):243–250. doi: 10.1101/sqb.1983.047.01.029. [DOI] [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. Lee C. H., Mizusawa H., Kakefuda T. Unwinding of double-stranded DNA helix by dehydration. Proc Natl Acad Sci U S A. 1981 May;78(5):2838–2842. doi: 10.1073/pnas.78.5.2838. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lyamichev V. I., Panyutin I. G., Frank-Kamenetskii M. D. Evidence of cruciform structures in superhelical DNA provided by two-dimensional gel electrophoresis. FEBS Lett. 1983 Mar 21;153(2):298–302. doi: 10.1016/0014-5793(83)80628-0. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. Peck L. J., Wang J. C. Sequence dependence of the helical repeat of DNA in solution. Nature. 1981 Jul 23;292(5821):375–378. doi: 10.1038/292375a0. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Pohl F. M. Salt-induced transition between two double-helical forms of oligo (dC-dG). Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):113–117. doi: 10.1101/sqb.1983.047.01.014. [DOI] [PubMed] [Google Scholar]
  18. Pulleyblank D. E., Shure M., Tang D., Vinograd J., Vosberg H. P. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4280–4284. doi: 10.1073/pnas.72.11.4280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Roberts T. M., Kacich R., Ptashne M. A general method for maximizing the expression of a cloned gene. Proc Natl Acad Sci U S A. 1979 Feb;76(2):760–764. doi: 10.1073/pnas.76.2.760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Shure M., Pulleyblank D. E., Vinograd J. The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity. Nucleic Acids Res. 1977;4(5):1183–1205. doi: 10.1093/nar/4.5.1183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Wang J. C. DNA: bihelical structure, supercoiling, and relaxation. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):29–33. doi: 10.1101/sqb.1979.043.01.006. [DOI] [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. 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 Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES