Skip to main content
NCBI 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
. 1987 Mar;84(6):1546–1549. doi: 10.1073/pnas.84.6.1546

Structure of A-DNA in solution.

E Charney, H H Chen
PMCID: PMC304472  PMID: 3470741

Abstract

The structure of DNA in aqueous trifluoroethanol solutions containing more than 70% (vol/vol) trifluoroethanol, where it has been proposed to have the A-conformation, has been studied by the technique of electric linear dichroism. The data demonstrate that both linear phi X174 DNA [5386 base pairs (bp) long] and a 172-bp fragment of sea urchin 5S RNA gene are in the double-helical A-form in the alcoholic solution and that two of the important structural parameters, the base tilt and the base-pair translation along the helical axis, are the same as in the A-form structure of crystalline double-helical d(GGTATACC). Despite its molecular length, the limiting reduced dichroism (-1.41) of the phi X174 DNA in low-salt aqueous solution is near the theoretical limit (-1.50) for DNA with base planes perpendicular to the helical axis. Transformation of this DNA and also of the 172-bp fragment to the A-structure in alcohol solutions reduces the experimental value of the dichroism to about -1.04, which agrees almost exactly with the value of -1.03 calculated for the A-form crystal. The base-pair translation along the helical axis was determined from relaxation of the DNA dichroism when the electric field is turned off. The 172-bp fragment is found to have a base-pair translation of only 2.6 A in the A-structure and is thus the same as in A-DNA fibers and in the A-form oligomers crystals. We conclude from the coincidence of the base-pair translation and the apparent values of the base tilt that the A structures are identical or nearly so in the solution and solid states. Comparison of the phi X174 data with data on smaller DNA fragments and with the data on the 172-bp sea urchin gene fragment unambiguously confirms that, in aqueous solution, the experimental reduced electric dichroism of B-DNA is highly dependent on molecular length, while the dichroism of the A-DNA form in alcoholic solutions is independent of molecular length at least in the range from 172 to 5386 bp.

Full text

PDF
1546

Selected References

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

  1. Arnott S., Hukins D. W. Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504–1509. doi: 10.1016/0006-291X(72)90243-4. [DOI] [PubMed] [Google Scholar]
  2. Arnott S., Hukins D. W. Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. J Mol Biol. 1973 Dec 5;81(2):93–105. doi: 10.1016/0022-2836(73)90182-4. [DOI] [PubMed] [Google Scholar]
  3. Arnott S., Wilkins M. H., Fuller W., Langridge R. Molecular and crystal structures of double-helical RNA. 3. An 11-fold molecular model and comparison of the agreement between the observed and calculated three-dimensional diffraction data for 10- and 11-fold models. J Mol Biol. 1967 Aug 14;27(3):535–548. doi: 10.1016/0022-2836(67)90057-5. [DOI] [PubMed] [Google Scholar]
  4. Causley G. C., Johnson W. C., Jr Polynucleotide conformation from flow dichroism studies. Biopolymers. 1982 Sep;21(9):1763–1780. doi: 10.1002/bip.360210907. [DOI] [PubMed] [Google Scholar]
  5. Charney E., Chen H. H., Henry E. R., Rau D. C. Structural information from electric dichroism measurements of DNA and alternating GC nucleic acids in solution: the question of base tilt. Biopolymers. 1986 May;25(5):885–904. doi: 10.1002/bip.360250510. [DOI] [PubMed] [Google Scholar]
  6. Chen H. H., Charney E., Rau D. C. Length changes in solution accompanying the B-Z transition of poly (dG-m5dC) induced by Co(NH3)63+. Nucleic Acids Res. 1982 Jun 11;10(11):3561–3571. doi: 10.1093/nar/10.11.3561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Clark L. B. Electronic spectra of crystalline 9-ethylguanine and guanine hydrochloride. J Am Chem Soc. 1977 Jun 8;99(12):3934–3938. doi: 10.1021/ja00454a006. [DOI] [PubMed] [Google Scholar]
  8. Dickerson R. E. Base sequence and helix structure variation in B and A DNA. J Mol Biol. 1983 May 25;166(3):419–441. doi: 10.1016/s0022-2836(83)80093-x. [DOI] [PubMed] [Google Scholar]
  9. Diekmann S., Hillen W., Jung M., Wells R. D., Pörschke D. Electric properties and structure of DNA-restriction fragments from measurements of the electric dichroism. Biophys Chem. 1982 May;15(2):157–167. doi: 10.1016/0301-4622(82)80028-8. [DOI] [PubMed] [Google Scholar]
  10. Edmondson S. P., Johnson W. C., Jr Base tilt of DNA in various conformations from flow linear dichroism. Biochemistry. 1985 Aug 27;24(18):4802–4806. doi: 10.1021/bi00339a013. [DOI] [PubMed] [Google Scholar]
  11. FULLER W., WILKINS M. H., WILSON H. R., HAMILTON L. D. THE MOLECULAR CONFIGURATION OF DEOXYRIBONUCLEIC ACID. IV. X-RAY DIFFRACTION STUDY OF THE A FORM. J Mol Biol. 1965 May;12:60–76. doi: 10.1016/s0022-2836(65)80282-0. [DOI] [PubMed] [Google Scholar]
  12. Lee C. H., Charney E. Solution conformation of DNA. J Mol Biol. 1982 Oct 25;161(2):289–303. doi: 10.1016/0022-2836(82)90154-1. [DOI] [PubMed] [Google Scholar]
  13. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys. 1978 May;11(2):179–246. doi: 10.1017/s0033583500002031. [DOI] [PubMed] [Google Scholar]
  14. Premilat S., Albiser G. Conformations of A-DNA and B-DNA in agreement with fiber X-ray and infrared dichroism. Nucleic Acids Res. 1983 Mar 25;11(6):1897–1908. doi: 10.1093/nar/11.6.1897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Shakked Z., Rabinovich D., Cruse W. B., Egert E., Kennard O., Sala G., Salisbury S. A., Viswamitra M. A. Crystalline A-dna: the X-ray analysis of the fragment d(G-G-T-A-T-A-C-C). Proc R Soc Lond B Biol Sci. 1981 Nov 24;213(1193):479–487. doi: 10.1098/rspb.1981.0076. [DOI] [PubMed] [Google Scholar]
  16. Sprecher C. A., Baase W. A., Johnson W. C., Jr Conformation and circular dichroism of DNA. Biopolymers. 1979 Apr;18(4):1009–1019. doi: 10.1002/bip.1979.360180418. [DOI] [PubMed] [Google Scholar]
  17. Wu H. M., Dattagupta N., Crothers D. M. Solution structural studies of the A and Z forms of DNA. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6808–6811. doi: 10.1073/pnas.78.11.6808. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Yamaoka K., Charney E. Electric dichroism studies of macromolecules in solutions. II. Measurements of linear dichroism and birefringence of deoxyribonucleic acid in orienting electric fields. Macromolecules. 1973 Jan-Feb;6(1):66–76. doi: 10.1021/ma60031a011. [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