Coulombic free energy of polymeric nucleic acid: Low- and high-salt analytical approximations for the cylindrical Poisson-Boltzmann model

Journal of Physical Chemistry B

Volumn 114, Issue 33, 2010, Pages 10793-10803

  Shkel, Irina A ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; BOLTZMANN EQUATION; DNA; GENES; IONS; MODEL STRUCTURES; NONLINEAR EQUATIONS; NUCLEIC ACIDS; NUMERICAL ANALYSIS; POISSON EQUATION; POLYMERS; THERMODYNAMICS;

ANALYTICAL APPROXIMATION; ANALYTICAL EXPRESSIONS; ASYMPTOTIC SOLUTIONS; CHARGE SEPARATIONS; COULOMBIC INTERACTIONS; CYLINDER AXIS; CYLINDRICAL MODELS; FURTHER DEVELOPMENT; IONIC CORRELATIONS; NUMERICAL CALCULATION; NUMERICAL COEFFICIENTS; NUMERICAL SOLUTION; POISSON-BOLTZMANN; SALT CONCENTRATION; SALT IONS; SECOND DERIVATIVES; SINGLE-STRANDED (SS) DNA; SPECIFIC EFFECTS; STRUCTURAL MODELS; THERMODYNAMIC QUANTITIES;

FREE ENERGY;

EID: 77955900720     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp908267c     Document Type: Article

References (55)

1. Record, M. T.; Zhang, W. T.; 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, 281353
2. Ballin, J. D.; Shkel, I. A.; Record, M. T. Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt Nucleic Acids Res. 2004, 32, 3271-3281
3. Meulen, K. A. V.; Saecker, R. M.; Record, M. T. Formation of a wrapped DNA-protein interface: Experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H'DNA J. Mol. Biol. 2008, 377, 9-27
4. Frank, D. E.; Saecker, R. M.; Bond, J. P.; Capp, M. W.; Tsodikov, O. V.; Melcher, S. E.; Levandoski, M. M.; Record, M. T. Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: Effects of converting a consensus site to a non-specific site J. Mol. Biol. 1997, 267, 1186-1206
5. Record, M. T.; Ha, J. H.; Fisher, M. A. Analysis of equilibrium and kinetic measurements to determine thermodynaics origns of stability and specificity and mechanism of formationof site-specific complexes between protein and helical DNA Methods Enzymol. 1991, 208, 291-343
6. Blake, R. D.; Haydock, P. V. Effect of sodium-ion on the high-resolution melting of Lambda DNA Biopolymers 1979, 18, 3089-3109
7. Hamaguchi, K.; Geiduschek, E. P. The effect of electrolytes on the stability of the deoxyribonucleate helix J. Am. Chem. Soc. 1962, 84, 1329-1338
8. Pegram, L. M.; Wendorff, T.; Erdmann, R.; Shkel, I.; Bellissimo, D.; Felitsky, D. J.; Record, M. T., Jr. Why Hofmeister effects of many salts favor protein folding but not DNA helix formation Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 7716-7721
9. Lebret, M.; Zimm, B. H. Distribution of counterions around a cylindrical poly-electrolyte and manning condensation theory Biopolymers 1984, 23, 287-312
10. Mills, P.; Anderson, C. F.; Record, M. T. Monte-Carlo studies of counterion DNA interactions-comparison of the radial-distribution of counterions with predictions of other poly-electrolyte theories J. Phys. Chem. 1985, 89, 3984-3994
11. Olmsted, M. C.; Bond, J. P.; Anderson, C. F.; Record, M. T. Grand-canonical Monte-Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation (L(8+)) to the center of DNA oligomers Biophys. J. 1995, 68, 634-647
12. Olmsted, M. C.; Anderson, C. F.; Record, M. T. Monte-Carlo description of oligoelectrolyte properties of DNA oligomers-range of the end effect and the approach of molecular and thermodynamic properties to the poly-electrolyte limits Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 7766-7770
13. Mills, P.; Anderson, C. F.; Record, M. T. Grand canonical Monte-Carlo calculations of thermodynamic coefficients for a primitive model of DNA salt-solutions J. Phys. Chem. 1986, 90, 6541-6548
14. Ni, H. H.; Anderson, C. F.; Record, M. T. Quantifying the thermodynamic consequences of cation (M2+, M+) accumulation and anion (X-) exclusion in mixed salt solutions of polyanionic DNA using Monte Carlo and Poisson-Boltzmann calculations of ion-polyion preferential interaction coefficients J. Phys. Chem. B 1999, 103, 3489-3504
15. Jayaram, B.; Beveridge, D. L. Grand canonical Monte-Carlo simulations on aqueous-solutions of NaCl and NaDNA-excess chemical-potential and sourses of nonideality in electrolyte and polyelectrolyte solutions J. Phys. Chem. 1991, 95, 2506-2516
16. Manning, G. S. Molecular theory of polyelectrolyte solutions with applications to electrostatic properties of polynucleotides Q. Rev. Biophys. 1978, 11, 179-246
17. Tan, Z. J.; Chen, S. J. Nucleic acid helix stability: Effects of salt concentration, cation valence and size, and chain length Biophys. J. 2006, 90, 1175-1190
18. Gavryushov, S. Electrostatics of B-DNA in NaCl and CaCl2 solutions: Ion size, interionic correlation, and solvent dielectric saturation effects J. Phys. Chem. B 2008, 112, 8955-8965
19. Record, M. T.; Lohman, T. M.; Dehaseth, P. Ion effects on ligand-nucleic acid interactions J. Mol. Biol. 1976, 107, 145-158
20. Zhang, W.; Bond, J. P.; Anderson, C. F.; Lohman, T. M.; Record, M. T. Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 2511-2516
21. Misra, V. K.; Draper, D. E. The interpretation of Mg2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory J. Mol. Biol. 1999, 294, 1135-1147
22. Misra, V. K.; Draper, D. E. Mg2+ binding to tRNA revisited: The nonlinear Poisson-Boltzmann model J. Mol. Biol. 2000, 299, 813-825
23. Korolev, N.; Lyubartsev, A. P.; Nordenskiold, L. Application of polyelectrolyte theories for analysis of DNA melting in the presence of Na+ and Mg2+ ions Biophys. J. 1998, 75, 3041-3056
24. Korolev, N.; Lyubartsev, A. P.; Nordenskiold, L. Application of the Poisson Boltzmann polyelectrolyte model for analysis of equilibria between single-, double-, and triple-stranded polynucleotides in the presence of K+, Na+, and Mg2+ ions J. Biomol. Struct. Dyn. 2002, 20, 275-290
25. Korolev, N.; Lyubartsev, A. P.; Nordenskiold, L. Application of the Poisson Boltzmann polyelectrolyte model for analysis of thermal denaturation of DNA in the presence of Na+ and polyamine cations Biophys. Chem. 2003, 104, 55-66
26. Shkel, I. A.; Record, M. T. Effect of the number of nucleic acid oligomer charges on the salt dependence of stability (Delta G degrees(37)) and melting temperature (T-m): NLPB analysis of experimental data Biochemistry 2004, 43, 7090-7101
27. Shkel, I. A.; Ballin, J. D.; Record, M. T. Interactions of cationic ligands and proteins with small nucleic acids: Analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration Biochemistry 2006, 45, 8411-8426
28. Misra, V. K.; Hecht, J. L.; Sharp, K. A.; Friedman, R. A.; Honig, B. Salt effects on protein-DNA interactions-the lambda-ci repressor and ecori endoneclease J. Mol. Biol. 1994, 238, 264-280
29. Honig, B.; Nicholls, A. Classical electrostatics in biologu and chemistry Science 1995, 268, 1144-1149
30. Fogolari, F.; Elcock, A. H.; Esposito, G.; Viglino, P.; Briggs, J. M.; McCammon, J. A. Electrostatic effects in homeodomain-DNA interactions J. Mol. Biol. 1997, 267, 368-381
31. Garcia-Garcia, C.; Draper, D. E. Electrostatic interactions in a peptide-RNA complex J. Mol. Biol. 2003, 331, 75-88
32. Sharp, K. A.; Friedman, R. A.; Misra, V.; Hecht, J.; Honig, B. Salt effects on polyelctrolyte-ligand binding-comparison of Poisson-Boltzmann and limitimg law counterion binding models Biopolymers 1995, 36, 245-262
33. Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Electrostatics of nanosystems: Application to microtubules and the ribosome Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037-10041
34. Boschitsch, A. H.; Fenley, M. O. Hybrid boundary element and finite difference method for solving the nonlinear poisson-boltzmann equation J. Comput. Chem. 2004, 25, 935-955
35. Shkel, I. A.; Tsodikov, O. V.; Record, M. T. Asymptotic solution of the cylindrical nonlinear Poisson-Boltzmann equation at low salt concentration: Analytic expressions for surface potential and preferential interaction coefficient Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2597-2602
36. Shkel, I. A.; Tsodikov, O. V.; Record, M. T. Complete asymptotic solution of cylindrical and spherical Poisson-Boltzmann equations at experimental salt concentrations J. Phys. Chem. B 2000, 104, 5161-5170
37. Bond, J. P.; Anderson, C. F.; Record, M. T. Conformational transitions of duplex and tripler nucleic-acid helices-thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients Biophys. J. 1994, 67, 825-836
38. Vervey, E. J W.; Overbeek, J. T. G. Theory of stability of lyophobic colloids; Elsevier: Amsterdam, The Netherlands, 1948.
39. Sharp, K. A.; Honig, B. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation J. Phys. Chem. 1990, 94, 7684-7692
40. Vanaken, G. A.; Lekkerkerker, H. N. W.; Overbeek, J. T. G.; Debruyn, P. L. Adsorption of monovalent ions in thin spherical and cylindrical diffuse double-layers J. Phys. Chem. 1990, 94, 8468-8472
41. Klein, B. K.; Anderson, C. F.; Record, M. T. Comparison of Poisson-Boltzmann and Condesation model expressions for the colligative properties of cylindrical polyions Biopolymers 1981, 20, 2263-2280
42. Tellez, G.; Trizac, E. Nonlinear screening of spherical and cylindrical colloids: The case of 1: 2 and 2: 1 electrolytes Phys. Rev. E 2004, 70, 9-18
43. Owczarzy, R.; You, Y.; Moreira, B. G.; Manthey, J. A.; Huang, L. Y.; Behlke, M. A.; Walder, J. A. Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures Biochemistry 2004, 43, 3537-3554
44. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
45. Chen, C. S. Y.; White, A.; Love, J.; Murphy, J. R.; Ringe, D. Methyl groups of thymine bases are important for nucleic acid recognition by DtxR Biochemistry 2000, 39, 10397-10407
46. Garvie, C. W.; Pufall, M. A.; Graves, B. J.; Wolberger, C. Structural analysis of the autoinhibition of Ets-1 and its role in protein partnerships J. Biol. Chem. 2002, 277, 45529-45536
47. Kalodimos, C. G.; Biris, N.; Bonvin, A.; Levandoski, M. M.; Guennuegues, M.; Boelens, R.; Kaptein, R. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes Science 2004, 305, 386-389
48. Baker, N. A. Poisson-Boltzmann methods for biomolecular electrostatics Methods Enzymol. 2004, 383, 94-118
49. 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, 2, 103-178
50. Privalov, P. L.; Ptitsyn, O. B.; Birshtein, T. M. Determination of stability of DNA double helix in aqueous medium Biopolymers 1969, 8, 559-571
51. Debye, P.; Hückel, E. Zur Theorie der Elektrolyte I. Gefrierpunktserniedrigung und verwandte Eurscheinungen Phys. Z. 1923, 24, 185-206
52. McCoy, B. M.; Tracy, C. A.; Wu, T. T. Painlevé functions of 3rd kind J. Math. Phys. 1977, 18, 1058-1092
53. Tellez, G.; Trizac, E. Exact asymptotic expansions for the cylindrical Poisson-Boltzmann equation J. Stat. Mech.: Theory Exp. 2006, 31, P06018
54. Trizac, E.; Tellez, G. Preferential interaction coefficient for nucleic acids and other cylindrical polyions Macromolecules 2007, 40, 1305-1310
55. Manning, G. S. Electrostatic free energies of spheres, cylinders, and planes in counterion condensation theory with some applications Macromolecules 2007, 40, 8071-8081