Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1986 Feb 11;14(3):1479–1493. doi: 10.1093/nar/14.3.1479

Counterion distribution around DNA: variation with conformation and sequence.

G R Pack, L Wong, C V Prasad
PMCID: PMC339518  PMID: 3951990

Abstract

The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double helical DNA has been solved by an iterative procedure. These computations have been performed for 0.01M monovalent salt solutions. A systematic study of the ten possible sequences found among adjacent nucleotide base pairs is presented for the A, B, and C conformations of DNA. In addition, calculations of the electrostatic stabilities of these conformations of DNA allows for comparison of the charge accumulation around each of the three conformers.

Full text

PDF
1479

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., Selsing E. The conformation of C-DNA. J Mol Biol. 1975 Oct 15;98(1):265–269. doi: 10.1016/s0022-2836(75)80115-x. [DOI] [PubMed] [Google Scholar]
  3. Klein B. J., Pack G. R. Calculations of the spatial distribution of charge density in the environment of DNA. Biopolymers. 1983 Nov;22(11):2331–2352. doi: 10.1002/bip.360221103. [DOI] [PubMed] [Google Scholar]
  4. MARVIN D. A., SPENCER M., WILKINS M. H., HAMILTON L. D. The molecular configuration of deoxyribonucleic acid. III. X-ray diffraction study of the C form of the lithium salt. J Mol Biol. 1961 Oct;3:547–565. doi: 10.1016/s0022-2836(61)80021-1. [DOI] [PubMed] [Google Scholar]
  5. Miller K. J. Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix. Biopolymers. 1979 Apr;18(4):959–980. doi: 10.1002/bip.1979.360180415. [DOI] [PubMed] [Google Scholar]
  6. Pack G. R., Klein B. J. Generalized Poisson-Boltzmann calculation of the distribution of electrolyte ions around the B- and Z-conformers of DNA. Biopolymers. 1984 Dec;23(12):2801–2823. doi: 10.1002/bip.360231208. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. 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 Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES