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

Biophysical Journal

Volumn 76, Issue 2, 1999, Pages 1008-1017

  Zhang, Wentao ^a   Ni, Haihong ^a   Capp, Michael W ^a   Anderson, Charles F ^a   Lohman, Timothy M ^b   Record Jr , M Thomas ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; DNA; OLIGONUCLEOTIDE; POLYCATION;

ARTICLE; BINDING AFFINITY; BINDING SITE; IONIC STRENGTH; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; THERMODYNAMICS;

EID: 0033064802     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77265-6     Document Type: Article

References (34)

1. Allison, S. A. 1994. End effects in electrostatic potentials of cylinders -models for DNA fragments. J. Phys. Chem. 98:12091-12096.
2. Anderson, C. F., and M. T. Record, Jr. 1993. The salt-dependence o oligoion-polyion binding: a thermodynamic description based on pref erential interaction coefficients. J. Phys. Chem. 97:7116-7126.
3. Anderson, C. F., and M. T. Record, Jr. 1995. Salt-nucleic acid interactions Annu. Rev. Phys. Chem. 46:657-700.
4. Bujalowski, W., and T. M. Lohman. 1987. A general method of analysis o 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. 26:3099-3106.
5. Chen, S. W., and B. Honig. 1997. Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poission-Boltzmann equation: application to DNA binding reactions. J. Phys. Chem. B. 101:9113-9118.
6. Edelhoch. H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry. 6:1948-1954.
7. Epstein, I. R. 1978. Cooperative and noncooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions. Biophys. Chem. 8:327-339.
8. Fasman, G. D. 1975. CRC Handbook of Biochemistry and Molecular Biology, 3rd Ed. CRC Press, Boca Raton, FL. 589.
9. Ferrari, M. E., and T. M. Lohman. 1994. Apparent heat capacity change accompanying a non-specific protein-DNA interaction. E. coli SSB tetramer binding to oligodeoxyadenylates. Biochemistry. 33: 12896-12910.
10. Fogolari, F., G. Manzini, and F. Quadrifoglio. 1992. Polyelectrolytes in mixed salts: Scatchard plots obtained by means of Poisson-Boltzmann calculations. Biophys. Chem. 43:213-219.
11. Johnson, M. L., and S. G. Frasier. 1985. Nonlinear least squares analysis. Methods Enzymol. 117:301-342.
12. Latt, S. A., and H. A. Sober. 1967. Protein-nucleic acid interactions. II. Oligopeptide-polyribonucleotide binding studies. Biochemistry. 6:3293-3306.
13. Lohman, T. M., P. L. deHaseth, and M. T. Record, Jr. 1980. Pentalysinedeoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic acids. Biochemistry. 19:3522-3530.
14. Lohman, T. M., and D. P. Mascotti. 1992. Nonspecific ligand-DNA equilibrium binding parameters determined by fluorescence methods. Methods Enzymol. 212:424-458.
15. Manning, G. S., and U. Mohanty. 1997. Counterion condensation on ionic oligomers. Physica A. 247:196-204.
16. Mascotti, D. P., and T. M. Lohman. 1990. Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids. Proc. Natl. Acad. Sci. USA. 87:3142-3146.
17. Mascotti, D. P., and T. M. Lohman. 1992. Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan. Biochemistry. 31:8932-8946.
18. Mascotti, D. P., and T. M. Lohman. 1993. Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan: effects of base composition. Biochemistry. 32: 10568-10579.
19. McGhee, J. D., and P. H. von Hippel. 1974. 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. 86: 469-489.
20. Olmsted, M. C. 1991. Grand canonical Monte Carlo analysis of the thermodynamics of processes involving oligomeric and polymeric DNA. Ph.D. thesis. University of Wisconsin, Madison, WI.
21. Olmsted, M. C., C. F. Anderson, and M. T. Record, Jr. 1989. 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. Nail. Acad. Sci. USA. 86: 7766-7770.
22. Olmsted, M. C., C. F. Anderson, and M. T. Record, Jr. 1991. Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: a grand canonical Monte Carlo analysis. Biopolymers. 31:1593-1604.
23. 8+) to the center of DNA oligomers. Biophys. J. 68:634-647.
24. Padmanabhan, S., W. Zhang, M. W. Capp, C. F. Anderson, and M. T. Record Jr. 1997. Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: thermodynamic analysis of effects of coulombic interactions and α-helix induction. Biochemistry. 31:5193-5206.
25. Ray, J., and G. S. Manning. 1992. Theory of delocalized ionic binding to polynucleotides - structural and excluded-volume effects. Biopolymers. 32:541-549.
26. Record, M. T., Jr., C. F. Anderson, and T. M. Lohman. 1978. 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. 11:103-178.
27. Record, M. T., Jr., and T. M. Lohman. 1978. A semiempirical extension of polyelectrolyte theory to the treatment of oligoelectrolytes: application to oligonucleotide helix-coil transitions. Biopolymers. 17:159-166.
28. Record, M. T., Jr., T. M. Lohman, and P. de Haseth. 1976. Ion effects on ligand-nucleic acid interactions. J. Mol. Biol. 107:145-158.
29. Record, M. T., Jr., W. Zhang, and C. F. Anderson. 1998. 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. 51:281-353.
30. Rouzina, J., and V. Bloomfield. 1997. Competitive electrostatic binding of charged ligands to polyelectrolytes: practical approach using the nonlinear Poisson-Boltzmann equation. Biophys. Chem. 64:139-155.
31. 23Na NMR. Biophys. J. 68:1063-1072.
32. Stigter, D., and K. A. Dill. 1996. Binding of ionic ligands to polyelectrolytes. Biophys. J. 71:2064-2074.
33. Zhang, W. 1996. Thermodynamic characterizations of coulombic end effects and coupled folding effects on binding of cationic oligopeptides to nucleic acids. Two-domain analysis of preferential solute-protein interactions. Ph.D. thesis. University of Wisconsin, Madison, Wisconsin.
34. Zhang, W., J. P. Bond, C. F. Anderson, T. M. Lohman, and M. T. Record, Jr. 1996. Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA. Proc. Natl. Acad. Sci. USA. 93:2511-2516.