Skip to main content
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
. 1975 Nov;72(11):4275–4279. doi: 10.1073/pnas.72.11.4275

Conformational fluctuations of DNA helix.

D E Depew, J C Wang
PMCID: PMC388703  PMID: 172901

Abstract

Treatment of a homogeneous sample of circular DNA molecules that contain at least one single-strand scission per molecule with ligase yields a population of covalently closed circles heterogeneous in the topological winding number alpha. Under proper conditions, the product molecules with different values of alpha can all be resolved by gel electrophoresis. The distributions in alpha for several DNAs, covalently closed at different temperatures, have been determined and the results have been interpreted in terms of thermal fluctuations of the DNA helix.

Full text

PDF
4275

Images in this article

Selected References

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

  1. Arber W. Host specificity of DNA produced by Escherichia coli. 9. Host-controlled modification of bacteriophage fd. J Mol Biol. 1966 Oct;20(3):483–496. doi: 10.1016/0022-2836(66)90004-0. [DOI] [PubMed] [Google Scholar]
  2. Bauer W., Vinograd J. Interaction of closed circular DNA with intercalative dyes. II. The free energy of superhelix formation in SV40 DNA. J Mol Biol. 1970 Feb 14;47(3):419–435. doi: 10.1016/0022-2836(70)90312-8. [DOI] [PubMed] [Google Scholar]
  3. Cozzarelli N. R., Kelly R. B., Kornberg A. A minute circular DNA from Escherichia coli 15. Proc Natl Acad Sci U S A. 1968 Jul;60(3):992–999. doi: 10.1073/pnas.60.3.992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Davidson N. Effect of DNA length on the free energy of binding of an unwinding ligand to a supercoiled DNA. J Mol Biol. 1972 May 14;66(2):307–309. doi: 10.1016/0022-2836(72)90482-2. [DOI] [PubMed] [Google Scholar]
  5. Dugaiczyk A., Boyer H. W., Goodman H. M. Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures. J Mol Biol. 1975 Jul 25;96(1):171–184. doi: 10.1016/0022-2836(75)90189-8. [DOI] [PubMed] [Google Scholar]
  6. Espejo R. T., Canelo E. S., Sinsheimer R. L. DNA of bacteriophage PM2: a closed circular double-stranded molecule. Proc Natl Acad Sci U S A. 1969 Aug;63(4):1164–1168. doi: 10.1073/pnas.63.4.1164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hsieh T. S., Wang J. C. Thermodynamic properties of superhelical DNAs. Biochemistry. 1975 Feb 11;14(3):527–535. doi: 10.1021/bi00674a011. [DOI] [PubMed] [Google Scholar]
  8. Kriegstein H. J., Hogness D. S. Mechanism of DNA replication in Drosophila chromosomes: structure of replication forks and evidence for bidirectionality. Proc Natl Acad Sci U S A. 1974 Jan;71(1):135–139. doi: 10.1073/pnas.71.1.135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Liu L. F., Wang J. C. On the degree of unwinding of the DNA helix by ethidium. II. Studies by electron microscopy. Biochim Biophys Acta. 1975 Jul 23;395(4):401–412. [PubMed] [Google Scholar]
  10. Radloff R., Bauer W., Vinograd J. A dye-buoyant-density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells. Proc Natl Acad Sci U S A. 1967 May;57(5):1514–1521. doi: 10.1073/pnas.57.5.1514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Studier F. W. Analysis of bacteriophage T7 early RNAs and proteins on slab gels. J Mol Biol. 1973 Sep 15;79(2):237–248. doi: 10.1016/0022-2836(73)90003-x. [DOI] [PubMed] [Google Scholar]
  12. Thomas M., Davis R. W. Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975 Jan 25;91(3):315–328. doi: 10.1016/0022-2836(75)90383-6. [DOI] [PubMed] [Google Scholar]
  13. Wang J. C. Interactions between twisted DNAs and enzymes: the effects of superhelical turns. J Mol Biol. 1974 Aug 25;87(4):797–816. doi: 10.1016/0022-2836(74)90085-0. [DOI] [PubMed] [Google Scholar]
  14. Wang J. C. The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J Mol Biol. 1974 Nov 15;89(4):783–801. doi: 10.1016/0022-2836(74)90053-9. [DOI] [PubMed] [Google Scholar]
  15. Wang J. C. Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. J Mol Biol. 1969 Jul 14;43(1):25–39. doi: 10.1016/0022-2836(69)90076-x. [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