Skip to main content
PMC 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
. 1991 Jun 1;88(11):4631–4635. doi: 10.1073/pnas.88.11.4631

Computation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA.

R Klement 1, D M Soumpasis 1, T M Jovin 1
PMCID: PMC51719  PMID: 1711205

Abstract

We introduce an efficient computational methodology employing the potentials of mean force approach for estimating the detailed three-dimensional ionic distributions around arbitrarily complex charged biomolecular structures for all monovalent salt concentrations of practical interest (e.g., 0.1-5.0 M NaCl). Such distributions are required for specifying thermodynamic and structure-specific features of ion-mediated interactions of charged proteins, DNA and RNA, membranes, and macromolecular assemblies. As a first application, we present results for distributions around the B and ZI conformers of the DNA oligomer d(C-G)18.d(C-G)18. The ionic microenvironment depends strongly on the DNA conformation, sequence, and bulk salt concentrations.

Full text

PDF
4631

Images in this article

4633Image
on p.4633
4633Image
on p.4633
4633Image
on p.4633

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. Clementi E., Corongiu G. Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure. Biopolymers. 1982 Apr;21(4):763–777. doi: 10.1002/bip.360210404. [DOI] [PubMed] [Google Scholar]
  3. Drew H., Takano T., Tanaka S., Itakura K., Dickerson R. E. High-salt d(CpGpCpG), a left-handed Z' DNA double helix. Nature. 1980 Aug 7;286(5773):567–573. doi: 10.1038/286567a0. [DOI] [PubMed] [Google Scholar]
  4. García A. E., Soumpasis D. M. Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proc Natl Acad Sci U S A. 1989 May;86(9):3160–3164. doi: 10.1073/pnas.86.9.3160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Jayaram B., Sharp K. A., Honig B. The electrostatic potential of B-DNA. Biopolymers. 1989 May;28(5):975–993. doi: 10.1002/bip.360280506. [DOI] [PubMed] [Google Scholar]
  6. Klement R., Soumpasis D. M., Kitzing E. V., Jovin T. M. Inclusion of ionic interactions in force field calculations of charged biomolecules--DNA structural transitions. Biopolymers. 1990 May-Jun;29(6-7):1089–1103. doi: 10.1002/bip.360290620. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Record M. T., Jr, Anderson C. F., Lohman T. M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q Rev Biophys. 1978 May;11(2):103–178. doi: 10.1017/s003358350000202x. [DOI] [PubMed] [Google Scholar]
  9. Record M. T., Jr, Mazur S. J., Melançon P., Roe J. H., Shaner S. L., Unger L. Double helical DNA: conformations, physical properties, and interactions with ligands. Annu Rev Biochem. 1981;50:997–1024. doi: 10.1146/annurev.bi.50.070181.005025. [DOI] [PubMed] [Google Scholar]
  10. Soumpasis D. M., Robert-Nicoud M., Jovin T. M. B-Z DNA conformational transition in 1:1 electrolytes: dependence upon counterion size. FEBS Lett. 1987 Mar 23;213(2):341–344. doi: 10.1016/0014-5793(87)81519-3. [DOI] [PubMed] [Google Scholar]
  11. Soumpasis D. M. Salt dependence of DNA structural stabilities in solution. Theoretical predictions versus experiments. J Biomol Struct Dyn. 1988 Dec;6(3):563–574. doi: 10.1080/07391102.1988.10506507. [DOI] [PubMed] [Google Scholar]
  12. Soumpasis D. M. Statistical mechanics of the B----Z transition of DNA: contribution of diffuse ionic interactions. Proc Natl Acad Sci U S A. 1984 Aug;81(16):5116–5120. doi: 10.1073/pnas.81.16.5116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Soumpasis D. M., Wiechen J., Jovin T. M. Relative stabilities and transitions of DNA conformations in 1:1 electrolytes: a theoretical study. J Biomol Struct Dyn. 1987 Feb;4(4):535–552. doi: 10.1080/07391102.1987.10507658. [DOI] [PubMed] [Google Scholar]
  14. 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]

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