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. 1999 Feb;76(2):1008–1017. doi: 10.1016/S0006-3495(99)77265-6

The importance of coulombic end effects: experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (L8+) binding to single-stranded DNA oligomers.

W Zhang 1, H Ni 1, M W Capp 1, C F Anderson 1, T M Lohman 1, M T Record Jr 1
PMCID: PMC1300050  PMID: 9916032

Abstract

Binding constants Kobs, expressed per site and evaluated in the limit of zero binding density, are quantified as functions of salt (sodium acetate) concentration for the interactions of the oligopeptide ligand KWK6NH2 (designated L8+, with ZL = 8 charges) with three single-stranded DNA oligomers (ss dT-mers, with |ZD| = 15, 39, and 69 charges). These results provide the first systematic experimental information about the effect of changing |ZD| on the strength and salt dependence of oligocation-oligonucleotide binding interactions. In a comparative study of L8+ binding to poly dT and to a short dT oligomer (|ZD| = 10),. Proc. Natl. Acad. Sci. USA. 93:2511-2516) demonstrated the profound thermodynamic effects of phosphate charges that flank isolated nonspecific L8+ binding sites on DNA. Here we find that both Kobs and the magnitude of its power dependence on salt activity (|SaKobs|) increase monotonically with increasing |ZD|. The dependences of Kobs and SaKobs on |ZD| are interpreted by introducing a simple two-state thermodynamic model for Coulombic end effects, which accounts for our finding that when L8+ binds to sufficiently long dT-mers, both DeltaGobso = -RT ln Kobs and SaKobs approach the values characteristic of binding to poly-dT as linear functions of the reciprocal of the number of potential oligocation binding sites on the DNA lattice. Analysis of our L8+-dT-mer binding data in terms of this model indicates that the axial range of the Coulombic end effect for ss DNA extends over approximately 10 phosphate charges. We conclude that Coulombic interactions cause an oligocation (with ZL < |ZD|) to bind preferentially to interior rather than terminal binding sites on oligoanionic or polyanionic DNA, and we quantify the strong increase of this preference with decreasing salt concentration. Coulombic end effects must be considered when oligonucleotides are used as models for polyanionic DNA in thermodynamic studies of the binding of charged ligands, including proteins.

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Selected References

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  1. Anderson C. F., Record M. T., Jr Salt-nucleic acid interactions. Annu Rev Phys Chem. 1995;46:657–700. doi: 10.1146/annurev.pc.46.100195.003301. [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. Edelhoch H. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry. 1967 Jul;6(7):1948–1954. doi: 10.1021/bi00859a010. [DOI] [PubMed] [Google Scholar]
  4. Epstein I. R. Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions. Biophys Chem. 1978 Sep;8(4):327–339. doi: 10.1016/0301-4622(78)80015-5. [DOI] [PubMed] [Google Scholar]
  5. Ferrari M. E., Lohman T. M. Apparent heat capacity change accompanying a nonspecific protein-DNA interaction. Escherichia coli SSB tetramer binding to oligodeoxyadenylates. Biochemistry. 1994 Nov 1;33(43):12896–12910. doi: 10.1021/bi00209a022. [DOI] [PubMed] [Google Scholar]
  6. Latt S. A., Sober H. A. Protein-nucleic acid interactions. II. Oligopeptide-polyribonucleotide binding studies. Biochemistry. 1967 Oct;6(10):3293–3306. doi: 10.1021/bi00862a040. [DOI] [PubMed] [Google Scholar]
  7. Lohman T. M., Mascotti D. P. Nonspecific ligand-DNA equilibrium binding parameters determined by fluorescence methods. Methods Enzymol. 1992;212:424–458. doi: 10.1016/0076-6879(92)12027-n. [DOI] [PubMed] [Google Scholar]
  8. Lohman T. M., deHaseth P. L., Record M. T., Jr Pentalysine-deoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic acids. Biochemistry. 1980 Jul 22;19(15):3522–3530. doi: 10.1021/bi00556a017. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Mascotti D. P., Lohman T. M. Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition. Biochemistry. 1993 Oct 12;32(40):10568–10579. doi: 10.1021/bi00091a006. [DOI] [PubMed] [Google Scholar]
  11. Mascotti D. P., Lohman T. M. Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan. Biochemistry. 1992 Sep 22;31(37):8932–8946. doi: 10.1021/bi00152a033. [DOI] [PubMed] [Google Scholar]
  12. McGhee J. D., von Hippel P. H. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J Mol Biol. 1974 Jun 25;86(2):469–489. doi: 10.1016/0022-2836(74)90031-x. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Olmsted M. C., Anderson C. F., Record M. T., Jr Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7766–7770. doi: 10.1073/pnas.86.20.7766. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Olmsted M. C., Bond J. P., Anderson C. F., Record M. T., Jr Grand canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation (L8+) to the center of DNA oligomers. Biophys J. 1995 Feb;68(2):634–647. doi: 10.1016/S0006-3495(95)80224-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Padmanabhan S., Zhang W., Capp M. W., Anderson C. F., Record M. T., Jr Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: thermodynamic analysis of effects of coulombic interactions and alpha-helix induction. Biochemistry. 1997 Apr 29;36(17):5193–5206. doi: 10.1021/bi962927a. [DOI] [PubMed] [Google Scholar]
  17. Ray J., Manning G. S. Theory of delocalized ionic binding to polynucleotides: structural and excluded-volume effects. Biopolymers. 1992 May;32(5):541–549. doi: 10.1002/bip.360320510. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. 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]
  20. Record M. T., Jr, Zhang W., Anderson C. F. Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv Protein Chem. 1998;51:281–353. doi: 10.1016/s0065-3233(08)60655-5. [DOI] [PubMed] [Google Scholar]
  21. Rouzina I., Bloomfield V. A. Competitive electrostatic binding of charged ligands to polyelectrolytes: practical approach using the non-linear Poisson-Boltzmann equation. Biophys Chem. 1997 Feb 28;64(1-3):139–155. doi: 10.1016/s0301-4622(96)02231-4. [DOI] [PubMed] [Google Scholar]
  22. Stein V. M., Bond J. P., Capp M. W., Anderson C. F., Record M. T., Jr Importance of coulombic end effects on cation accumulation near oligoelectrolyte B-DNA: a demonstration using 23Na NMR. Biophys J. 1995 Mar;68(3):1063–1072. doi: 10.1016/S0006-3495(95)80281-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Stigter D., Dill K. A. Binding of ionic ligands to polyelectrolytes. Biophys J. 1996 Oct;71(4):2064–2074. doi: 10.1016/S0006-3495(96)79405-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Zhang W., Bond J. P., Anderson C. F., Lohman T. M., Record M. T., Jr Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA. Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2511–2516. doi: 10.1073/pnas.93.6.2511. [DOI] [PMC free article] [PubMed] [Google Scholar]

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