Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Aug 11;22(15):3147–3150. doi: 10.1093/nar/22.15.3147

The effect of sodium ion concentration on intrastrand base-pairing in single-stranded DNA.

A R Wolfe 1, T Meehan 1
PMCID: PMC310288  PMID: 8065928

Abstract

The salt-induced formation of duplex structure (primarily hairpin loops) in denatured calf thymus DNA was monitored by measuring the decrease in absorbance at 260 nm as a function of increasing sodium ion concentration. It was found that this process was noncooperative and could be accurately described by the mass-action expression for the reversible formation of a binary complex: single strand (coil) + free sodium ion <==> hairpin (with associated sodium ion). The equilibrium constant for the transition was found to be 6 (M Na+)-1. The extrapolated absorbance at infinite salt concentration represents 11% hyperchromicity, which is one third of the hyperchromicity of denatured DNA in the absence of salt (36%).

Full text

PDF
3147

Selected References

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

  1. Anderson C. F., Record M. T., Jr The relationship between the poisson-boltzmann model and the condensation hypothesis: an analysis based on the low salt form of the Donnan coefficient. Biophys Chem. 1980 Jun;11(3-4):353–360. doi: 10.1016/0301-4622(80)87008-6. [DOI] [PubMed] [Google Scholar]
  2. Bujalowski W., Lohman T. M. A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions. Biochemistry. 1987 Jun 2;26(11):3099–3106. doi: 10.1021/bi00385a023. [DOI] [PubMed] [Google Scholar]
  3. Cornish-Bowden A., Eisenthal R. Estimation of Michaelis constant and maximum velocity from the direct linear plot. Biochim Biophys Acta. 1978 Mar 14;523(1):268–272. doi: 10.1016/0005-2744(78)90030-x. [DOI] [PubMed] [Google Scholar]
  4. Cornish-Bowden A., Eisenthal R. Statistical considerations in the estimation of enzyme kinetic parameters by the direct linear plot andother methods. Biochem J. 1974 Jun;139(3):721–730. doi: 10.1042/bj1390721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. DOWD J. E., RIGGS D. S. A COMPARISON OF ESTIMATES OF MICHAELIS-MENTEN KINETIC CONSTANTS FROM VARIOUS LINEAR TRANSFORMATIONS. J Biol Chem. 1965 Feb;240:863–869. [PubMed] [Google Scholar]
  6. Eisenthal R., Cornish-Bowden A. The direct linear plot. A new graphical procedure for estimating enzyme kinetic parameters. Biochem J. 1974 Jun;139(3):715–720. doi: 10.1042/bj1390715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. Mascotti D. P., Lohman T. M. Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids. Proc Natl Acad Sci U S A. 1990 Apr;87(8):3142–3146. doi: 10.1073/pnas.87.8.3142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Olmsted M. C., Anderson C. F., Record M. T., Jr Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: a grand canonical Monte Carlo analysis. Biopolymers. 1991 Nov;31(13):1593–1604. doi: 10.1002/bip.360311314. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Record M. T., Jr, Lohman M. L., De Haseth P. Ion effects on ligand-nucleic acid interactions. J Mol Biol. 1976 Oct 25;107(2):145–158. doi: 10.1016/s0022-2836(76)80023-x. [DOI] [PubMed] [Google Scholar]
  12. Record M. T., Jr, Woodbury C. P., Lohman T. M. Na+ effects on transition of DNA and polynucleotides of variable linear charge density. Biopolymers. 1976 May;15(5):893–915. doi: 10.1002/bip.1976.360150507. [DOI] [PubMed] [Google Scholar]
  13. Studier F. W. Conformational changes of single-stranded DNA. J Mol Biol. 1969 Apr;41(2):189–197. doi: 10.1016/0022-2836(69)90384-2. [DOI] [PubMed] [Google Scholar]
  14. Walz F. G., Jr Rapid kinetic studies on the conformation of single-stranded DNA. Biopolymers. 1972;11(11):2365–2379. doi: 10.1002/bip.1972.360111115. [DOI] [PubMed] [Google Scholar]
  15. Wilson W. D., Lopp I. G. Analysis of cooperativity and ion effects in the interaction of quinacrine with DNA. Biopolymers. 1979 Dec;18(12):3025–3041. doi: 10.1002/bip.1979.360181210. [DOI] [PubMed] [Google Scholar]
  16. Wolfe A., Shimer G. H., Jr, Meehan T. Polycyclic aromatic hydrocarbons physically intercalate into duplex regions of denatured DNA. Biochemistry. 1987 Oct 6;26(20):6392–6396. doi: 10.1021/bi00394a013. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES