Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 May 25;21(10):2343–2348. doi: 10.1093/nar/21.10.2343

Energetics of Z-DNA formation in poly d(A-T), poly d(G-C), and poly d(A-C) poly d(G-T).

H H Klump 1, E Schmid 1, M Wosgien 1
PMCID: PMC309530  PMID: 8506132

Abstract

The conformational change for the alternating purine-pyrimidine polydeoxyribonucleotides i.e. poly d(A-T), poly d(G-C), and poly d(A-C) poly d(G-T) from a right-handed conformation at room temperature to the left-handed Z-DNA like double helix at elevated temperatures has been studied by UV spectroscopy, Raman spectroscopy, and by adiabatic differential scanning microcalorimetry (DSC) in the presence of Na+ and Mg2+ or Ni2+ respectively as counterions. The differential UV spectra reveal through a hyperchromic shift at around 280nm and a hypochromic shift at 260nm that a conformational change to the left-handed conformation occurs. The Raman spectra clearly show characteristic changes, a drastic decrease of the band at 680cm-1 and the appearance of a new band at 628cm-1, due to the change of the purine bases to the syn conformation upon inversion of the helix-handedness. The course of the transition as function of temperature can be followed quantitatively by plotting the change in the excess heat capacity vs. temperature. The transition enthalpy delta H for the B- to Z-DNA transition per mole base pairs (mbp) amounts to 2.0 +/- 0.2kcal for poly d(G-C), to 4.0 +/- 0.4kcal for poly d(A-T), and to 3.1 +/- 0.3kcal for poly d(A-C) poly d(G-T). The enthalpy change due to the Z-DNA to coil transitions (per mole base pairs) amounts to 11kcal for poly d(G-C), 10.5kcal for poly d(A-T) and 11.3kcal for poly d(A-C) poly d(G-T).

Full text

PDF
2343

Selected References

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

  1. Adam S., Bourtayre P., Liquier J., Taillandier E. Interaction of transition metal ions with Z form poly d(A-C).poly d(G-T) and poly d(A-T) studied by I.R. spectroscopy. Nucleic Acids Res. 1986 Apr 25;14(8):3501–3513. doi: 10.1093/nar/14.8.3501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chaires J. B., Sturtevant J. M. Thermodynamics of the B to Z transition in poly(m5dG-dC). Proc Natl Acad Sci U S A. 1986 Aug;83(15):5479–5483. doi: 10.1073/pnas.83.15.5479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ghomi M., Letellier R., Taillandier E. A critical review of the nucleosidic vibration modes appearing in the 800-500-cm-1 spectral region, based on new harmonic dynamics calculations. Biopolymers. 1988 Apr;27(4):605–616. doi: 10.1002/bip.360270405. [DOI] [PubMed] [Google Scholar]
  4. Hall K. B., Maestre M. F. Temperature-dependent reversible transition of poly(dCdG).poly(dCdG) in ethanolic and methanolic solutions. Biopolymers. 1984 Nov;23(11 Pt 1):2127–2139. doi: 10.1002/bip.360231103. [DOI] [PubMed] [Google Scholar]
  5. Jaworski A., Hsieh W. T., Blaho J. A., Larson J. E., Wells R. D. Left-handed DNA in vivo. Science. 1987 Nov 6;238(4828):773–777. doi: 10.1126/science.3313728. [DOI] [PubMed] [Google Scholar]
  6. Jollès B., Chinsky L., Laigle A. Contribution of the resonance Raman spectroscopy to the identification of Z DNA. J Biomol Struct Dyn. 1984 Jun;1(6):1335–1346. doi: 10.1080/07391102.1984.10507524. [DOI] [PubMed] [Google Scholar]
  7. Klump H. H., Jovin T. M. Formation of a left-handed RNA double helix: energetics of the A-Z transition of poly[r(G-C)] in concentrated NaClO4 solutions. Biochemistry. 1987 Aug 11;26(16):5186–5190. doi: 10.1021/bi00390a043. [DOI] [PubMed] [Google Scholar]
  8. Klump H., Ackermann T. Experimental thermodynamics of the helix--random coil transition. IV. Influence of the base composition of DNA on the transition enthalpy. Biopolymers. 1971;10(3):513–522. doi: 10.1002/bip.360100307. [DOI] [PubMed] [Google Scholar]
  9. Krueger W. C., Prairie M. D. A low-salt form of poly(dG-5M-dC).poly(dG-5M-dC). Biopolymers. 1985 May;24(5):905–910. doi: 10.1002/bip.360240513. [DOI] [PubMed] [Google Scholar]
  10. Miskovsky P., Chinsky L., Laigle A., Turpin P. Y. The Z-conformation of poly(dA-dT).poly(dA-dT) in solution as studied by ultraviolet resonance Raman spectroscopy. J Biomol Struct Dyn. 1989 Dec;7(3):623–637. doi: 10.1080/07391102.1989.10508511. [DOI] [PubMed] [Google Scholar]
  11. Miskovsky P., Laigle A., Chinsky L., Turpin P. Y. Ultraviolet resonance Raman marker bands of the right to left helix structure transitions in DNA and polynucleotide model compounds. J Biomol Struct Dyn. 1992 Aug;10(1):169–179. doi: 10.1080/07391102.1992.10508636. [DOI] [PubMed] [Google Scholar]
  12. Mojzes P., Chinsky L., Turpin P. Y., Miskovsky P. Salt-induced conformational transition of poly(d2NH2A-dT) studied by ultraviolet resonance Raman spectroscopy. J Biomol Struct Dyn. 1992 Aug;10(1):181–194. doi: 10.1080/07391102.1992.10508637. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. van de Sande J. H., McIntosh L. P., Jovin T. M. Mn2+ and other transition metals at low concentration induce the right-to-left helical transformation of poly[d(G-C)]. EMBO J. 1982;1(7):777–782. doi: 10.1002/j.1460-2075.1982.tb01247.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES