Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1989 Oct;56(4):683–691. doi: 10.1016/S0006-3495(89)82715-8

Interaction of water with oriented DNA in the A- and B-form conformations.

R Brandes 1, A Rupprecht 1, D R Kearns 1
PMCID: PMC1280524  PMID: 2554988

Abstract

High resolution 2H nuclear magnetic resonance (NMR) was used to investigate the interaction of D2O with solid samples of uniaxially oriented Li-DNA (B-form DNA) and Na-DNA (A- and B-form DNA). At low levels of hydration, 0 approximately 4 D2O/nucleotide, the 2H spectra shows a very weak (due to short T2) broad single resonance, suggestive of unrestricted rotational diffusion of the water. At approximately 5 or more D2O/nucleotide, the Li-DNA (B-form) spectra suddenly exhibit a large doublet splitting, characteristic of partially ordered water. With increasing hydration, the general trend is a decrease of this splitting. From our analysis we show that the DNA water structure reorganizes as the DNA is progressively hydrated. The D2O interaction with Na-DNA is rather different than with Li-DNA. Below 10 D2O/nucleotide Na-DNA is normally expected to be in the A-form, and a small, or negligible splitting is observed. In the range 9-19 D2O/nucleotide, the splitting increases with increasing hydration. Above approximately 20 D2O/nucleotide Na-DNA converts entirely to the B-form and the D2O splittings are then similar to those found in Li-DNA. We show that the complex Na-DNA results obtained in the range 0-20 D2O/nucleotide are caused by a mixture of A- and B-DNA in those samples.

Full text

PDF
687

Selected References

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

  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Brandes R., Kearns D. R. Magnetic ordering of DNA liquid crystals. Biochemistry. 1986 Oct 7;25(20):5890–5895. doi: 10.1021/bi00368a008. [DOI] [PubMed] [Google Scholar]
  3. Brandes R., Kearns D. R., Rupprecht A. A 2H-NMR study of the DNA hydration water in solid Li-DNA assembles. Biopolymers. 1988 May;27(5):717–732. doi: 10.1002/bip.360270502. [DOI] [PubMed] [Google Scholar]
  4. Brandes R., Vold R. R., Kearns D. R., Rupprecht A. A 2H-NMR study of the A-DNA conformation in films of oriented Na-DNA: evidence of a disordered B-DNA contribution. Biopolymers. 1988 Jul;27(7):1159–1170. doi: 10.1002/bip.360270709. [DOI] [PubMed] [Google Scholar]
  5. Brandes R., Vold R. R., Kearns D. R., Rupprecht A. Static disorder and librational motions of the purine bases in films of oriented Li-DNA. J Mol Biol. 1988 Jul 20;202(2):321–332. doi: 10.1016/0022-2836(88)90461-5. [DOI] [PubMed] [Google Scholar]
  6. Brandes R., Vold R. R., Vold R. L., Kearns D. R. Effects of hydration on purine motion in solid DNA. Biochemistry. 1986 Nov 18;25(23):7744–7751. doi: 10.1021/bi00371a069. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Hélène C., Lancelot G. Interactions between functional groups in protein-nucleic acid associations. Prog Biophys Mol Biol. 1982;39(1):1–68. doi: 10.1016/0079-6107(83)90013-5. [DOI] [PubMed] [Google Scholar]
  9. Kennard O., Cruse W. B., Nachman J., Prange T., Shakked Z., Rabinovich D. Ordered water structure in an A-DNA octamer at 1.7 A resolution. J Biomol Struct Dyn. 1986 Feb;3(4):623–647. doi: 10.1080/07391102.1986.10508452. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Lindsay S. M., Lee S. A., Powell J. W., Weidlich T., DeMarco C., Lewen G. D., Tao N. J., Rupprecht A. The origin of the A to B transition in DNA fibers and films. Biopolymers. 1988 Jun;27(6):1015–1043. doi: 10.1002/bip.360270610. [DOI] [PubMed] [Google Scholar]
  12. Migchelsen C., Berendsen H. J., Rupprecht A. Hydration of DNA. Comparison of nuclear magnetic resonance results for oriented DNA in the A,B and C form. J Mol Biol. 1968 Oct 14;37(1):235–237. doi: 10.1016/0022-2836(68)90087-9. [DOI] [PubMed] [Google Scholar]
  13. Rhodes N. J., Mahendrasingam A., Pigram W. J., Fuller W., Brahms J., Vergne J., Warren R. A. The C conformation is a low salt form of sodium DNA. Nature. 1982 Mar 18;296(5854):267–269. doi: 10.1038/296267a0. [DOI] [PubMed] [Google Scholar]
  14. Rupprecht A. A wet spinning apparatus and auxiliary equipment suitable for preparing samples of oriented DNA. Biotechnol Bioeng. 1970 Jan;12(1):93–121. doi: 10.1002/bit.260120109. [DOI] [PubMed] [Google Scholar]
  15. Rupprecht A., Forslind B. Variation of electrolyte content in wet-spun lithium- and sodium-DNA. Biochim Biophys Acta. 1970 Apr 15;204(2):304–316. doi: 10.1016/0005-2787(70)90148-6. [DOI] [PubMed] [Google Scholar]
  16. Rupprecht A. Preparation of oriented DNA by wet spinning. Acta Chem Scand. 1966;20(2):494–504. doi: 10.3891/acta.chem.scand.20-0494. [DOI] [PubMed] [Google Scholar]
  17. Saenger W., Hunter W. N., Kennard O. DNA conformation is determined by economics in the hydration of phosphate groups. 1986 Nov 27-Dec 3Nature. 324(6095):385–388. doi: 10.1038/324385a0. [DOI] [PubMed] [Google Scholar]
  18. Texter J. Nucleic acid-water interactions. Prog Biophys Mol Biol. 1978;33(1):83–97. doi: 10.1016/0079-6107(79)90026-9. [DOI] [PubMed] [Google Scholar]
  19. Zimmerman S. B., Pheiffer B. H. Does DNA adopt the C form in concentrated salt solutions or in organic solvent water mixtures? An x-ray diffraction study of DNA fibers immersed in various media. J Mol Biol. 1980 Sep 25;142(3):315–330. doi: 10.1016/0022-2836(80)90275-2. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES