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. 1986 Oct 24;14(20):8167–8182. doi: 10.1093/nar/14.20.8167

Structural forms, stabilities and transitions in double-helical poly(dG-dC) as a function of hydration and NaCl content. An infrared spectroscopic study.

P B Keller, K A Hartman
PMCID: PMC311842  PMID: 3774555

Abstract

The poly(dG-dC) helical duplex forms a modified, B-family structure (B*) at very high hydration and a normal B structure at slightly lower hydration. The B* structure is slightly different in sugar-phosphate and base-stacking conformations than the B structure. Increasing the hydration or decreasing the NaCl content stabilizes B* with respect to B. Poly(dG-dC) forms the Z structure at low NaCl contents when the hydration is sufficiently reduced. At moderate NaCl content, the B to Z transition is sharp and cooperative for hydration with D2O. Hydration with H2O broadens the transition which occurs at lower hydration. This suggests that hydrogen bonding is stronger in the Z structure and helps stabilize Z over B. IR spectra may be used to quantitatively estimate the fractions of B and Z structures present in a sample. Some new indicator bands are described.

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Selected References

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

  1. Arnott S., Chandrasekaran R., Puigjaner L. C., Walker J. K., Hall I. H., Birdsall D. L., Ratliff R. L. Wrinkled DNA. Nucleic Acids Res. 1983 Mar 11;11(5):1457–1474. doi: 10.1093/nar/11.5.1457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Behe M. J. Vacuum UV CD of the low-salt Z-forms of poly(rG-dC).poly(rG-dC), and poly(dG-m5dC).poly(dG-m5dC). Biopolymers. 1986 Mar;25(3):519–523. doi: 10.1002/bip.360250310. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. DiRico D. E., Jr, Keller P. B., Hartman K. A. The infrared spectrum and structure of the type I complex of silver and DNA. Nucleic Acids Res. 1985 Jan 11;13(1):251–260. doi: 10.1093/nar/13.1.251. [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. Dutta S., Parrack P. K., Sasisekharan V. Fibre diffraction of lithium DNA shows structural variability and deviation from a regular helical structure for the B-form. FEBS Lett. 1984 Oct 15;176(1):110–114. doi: 10.1016/0014-5793(84)80922-9. [DOI] [PubMed] [Google Scholar]
  7. Feuerstein B. G., Marton L. J., Keniry M. A., Wade D. L., Shafer R. H. New DNA polymorphism: evidence for a low salt, left-handed form of poly(dG-m5dC). Nucleic Acids Res. 1985 Jun 11;13(11):4133–4141. doi: 10.1093/nar/13.11.4133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Howard F. B., Frazier J., Miles H. T. Interbase vibrational coupling in G:C polynucleotide helices. Proc Natl Acad Sci U S A. 1969 Oct;64(2):451–458. doi: 10.1073/pnas.64.2.451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. KAUZMANN W. Some factors in the interpretation of protein denaturation. Adv Protein Chem. 1959;14:1–63. doi: 10.1016/s0065-3233(08)60608-7. [DOI] [PubMed] [Google Scholar]
  10. Krimm S., Abe Y. Intermolecular interaction effects in the amide I vibrations of polypeptides. Proc Natl Acad Sci U S A. 1972 Oct;69(10):2788–2792. doi: 10.1073/pnas.69.10.2788. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Leslie A. G., Arnott S., Chandrasekaran R., Ratliff R. L. Polymorphism of DNA double helices. J Mol Biol. 1980 Oct 15;143(1):49–72. doi: 10.1016/0022-2836(80)90124-2. [DOI] [PubMed] [Google Scholar]
  12. MILES H. T. Tautomeric forms in a polynucleotide helix and their bearing on the structure of DNA. Proc Natl Acad Sci U S A. 1961 Jun 15;47:791–802. doi: 10.1073/pnas.47.6.791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Pilet J., Leng M. Comparison of poly(dG-dC).poly(dG-dC) conformations in oriented films and in solution. Proc Natl Acad Sci U S A. 1982 Jan;79(1):26–30. doi: 10.1073/pnas.79.1.26. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. 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]
  16. Roy K. B., Miles H. T. A thermally driven interconversion of B and Z-dna. Biochem Biophys Res Commun. 1983 Aug 30;115(1):100–105. doi: 10.1016/0006-291x(83)90974-9. [DOI] [PubMed] [Google Scholar]
  17. Taboury J. A., Bourtayre P., Liquier J., Taillandier E. Interaction of Z form poly(dG-dC).poly(dG-dC) with divalent metal ions: localization of the binding sites by I.R. spectroscopy. Nucleic Acids Res. 1984 May 25;12(10):4247–4258. doi: 10.1093/nar/12.10.4247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Taillandier E., Taboury J., Liquier J., Sautière P., Couppez M. Structural transitions in DNAs and nucleohistones studied by I.R. spectroscopy. Biochimie. 1981 Nov-Dec;63(11-12):895–898. doi: 10.1016/s0300-9084(82)80282-4. [DOI] [PubMed] [Google Scholar]
  19. Wang A. J., Quigley G. J., Kolpak F. J., van der Marel G., van Boom J. H., Rich A. Left-handed double helical DNA: variations in the backbone conformation. Science. 1981 Jan 9;211(4478):171–176. doi: 10.1126/science.7444458. [DOI] [PubMed] [Google Scholar]
  20. Woisard A., Fazakerley G. V., Guschlbauer W. Z-DNA is formed by poly (dC-dG) and poly (dm5C-dG) at micro or nanomolar concentrations of some zinc(II) and copper(II) complexes. J Biomol Struct Dyn. 1985 Jun;2(6):1205–1220. doi: 10.1080/07391102.1985.10507633. [DOI] [PubMed] [Google Scholar]

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