Abstract
Numerical calculations, using Poisson-Boltzmann (PB) and counterion condensation (CC) polyelectrolyte theories, of the electrostatic free energy difference, DeltaGel, between single-stranded (coil) and double-helical DNA have been performed for solutions of NaDNA + NaCl with and without added MgCl2. Calculations have been made for conditions relevant to systems where experimental values of helix coil transition temperature (Tm) and other thermodynamic quantities have been measured. Comparison with experimental data has been possible by invoking values of Tm for solutions containing NaCl salt only. Resulting theoretical values of enthalpy, entropy, and heat capacity (for NaCl salt-containing solutions) and of Tm as a function of NaCl concentration in NaCl + MgCl2 solutions have thus been obtained. Qualitative and, to a large extent, quantitative reproduction of the experimental Tm, DeltaHm, DeltaSm, and DeltaCp values have been found from the results of polyelectrolyte theories. However, the quantitative resemblance of experimental data is considerably better for PB theory as compared to the CC model. Furthermore, some rather implausible qualitative conclusions are obtained within the CC results for DNA melting in NaCl + MgCl2 solutions. Our results argue in favor of the Poisson-Boltzmann theory, as compared to the counterion condensation theory.
Full Text
The Full Text of this article is available as a PDF (183.4 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Anderson C. F., Record M. T., Jr Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. Annu Rev Biophys Biophys Chem. 1990;19:423–465. doi: 10.1146/annurev.bb.19.060190.002231. [DOI] [PubMed] [Google Scholar]
- Bond J. P., Anderson C. F., Record M. T., Jr Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients. Biophys J. 1994 Aug;67(2):825–836. doi: 10.1016/S0006-3495(94)80542-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Braunlin W. H., Drakenberg T., Nordenskiöld L. Ca2+ binding environments on natural and synthetic polymeric DNA's. J Biomol Struct Dyn. 1992 Oct;10(2):333–343. doi: 10.1080/07391102.1992.10508651. [DOI] [PubMed] [Google Scholar]
- Braunlin W. H., Nordenskiöld L., Drakenberg T. A reexamination of 25Mg2+ NMR in DNA solution: site heterogeneity and cation competition effects. Biopolymers. 1991 Oct;31(11):1343–1346. doi: 10.1002/bip.360311111. [DOI] [PubMed] [Google Scholar]
- Braunlin W. H., Nordenskiöld L., Drakenberg T. The interaction of calcium (II) with DNA probed by 43Ca-NMR is not influenced by terminal phosphate groups at ends and nicks. Biopolymers. 1989 Jul;28(7):1339–1342. doi: 10.1002/bip.360280713. [DOI] [PubMed] [Google Scholar]
- Breslauer K. J. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods Enzymol. 1995;259:221–242. doi: 10.1016/0076-6879(95)59046-3. [DOI] [PubMed] [Google Scholar]
- Duguid J. G., Bloomfield V. A., Benevides J. M., Thomas G. J., Jr Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+. Biophys J. 1995 Dec;69(6):2623–2641. doi: 10.1016/S0006-3495(95)80133-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Duguid J. G., Bloomfield V. A. Electrostatic effects on the stability of condensed DNA in the presence of divalent cations. Biophys J. 1996 Jun;70(6):2838–2846. doi: 10.1016/S0006-3495(96)79853-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eichhorn G. L., Shin Y. A. Interaction of metal ions with polynucleotides and related compounds. XII. The relative effect of various metal ions on DNA helicity. J Am Chem Soc. 1968 Dec 18;90(26):7323–7328. doi: 10.1021/ja01028a024. [DOI] [PubMed] [Google Scholar]
- Filimonov V. V., Privalov P. L. Thermodynamics of base interaction in (A)n and (A.U)n. J Mol Biol. 1978 Jul 15;122(4):465–470. doi: 10.1016/0022-2836(78)90422-9. [DOI] [PubMed] [Google Scholar]
- Galindo CE, Sokoloff JB. Uncoiling transition for DNA in solution. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Jul;54(1):691–705. doi: 10.1103/physreve.54.691. [DOI] [PubMed] [Google Scholar]
- Gruenwedel D. W. Salt effects on the denaturation of DNA. 3. A calorimetric investigation of the transition enthalpy of calf thymus DNA in Na2SO4 solutions of varying ionic strength. Biochim Biophys Acta. 1974 Feb 27;340(1):16–30. doi: 10.1016/0005-2787(74)90170-1. [DOI] [PubMed] [Google Scholar]
- Heinecke M., Bode D., Schernau U. Calorimetric investigation of the helix-coil conversion of polyuridylic acid. Biopolymers. 1974 Jan;13(1):227–235. doi: 10.1002/bip.1974.360130116. [DOI] [PubMed] [Google Scholar]
- KOTIN L. ON THE EFFECT OF IONIC STRENGTH ON THE MELTING TEMPERATURE OF DNA. J Mol Biol. 1963 Sep;7:309–311. doi: 10.1016/s0022-2836(63)80009-1. [DOI] [PubMed] [Google Scholar]
- Korolev N. I., Vlasov A. P., Kuznetsov I. A. Thermal denaturation of Na- and Li-DNA in salt-free solutions. Biopolymers. 1994 Sep;34(9):1275–1290. doi: 10.1002/bip.360340915. [DOI] [PubMed] [Google Scholar]
- Krakauer H. A thermodynamic analysis of the influence of simple mono-and divalent cations on the conformational transitions of polynucleotide complexes. Biochemistry. 1974 Jun 4;13(12):2579–2589. doi: 10.1021/bi00709a017. [DOI] [PubMed] [Google Scholar]
- LUZZATI V., MATHIS A., MASSON F., WITZ J. SUTURE TRANSITIONS OBSERVED IN DNA AND POLY A IN SOLUTION AS A FUNCTION OF TEMPERATURE AND PH. J Mol Biol. 1964 Oct;10:28–41. doi: 10.1016/s0022-2836(64)80025-5. [DOI] [PubMed] [Google Scholar]
- Lohman T. M., Ferrari M. E. Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu Rev Biochem. 1994;63:527–570. doi: 10.1146/annurev.bi.63.070194.002523. [DOI] [PubMed] [Google Scholar]
- Manning G. S. On the application of polyelectrolyte "limiting laws" to the helix-coil transition of DNA. I. Excess univalent cations. Biopolymers. 1972;11(5):937–949. doi: 10.1002/bip.1972.360110502. [DOI] [PubMed] [Google Scholar]
- Manning G. S. On the application of polyelectrolyte "limiting laws" to the helix-coil transition of DNA. II. The effect of Mg++ counterions. Biopolymers. 1972;11(5):951–955. doi: 10.1002/bip.1972.360110503. [DOI] [PubMed] [Google Scholar]
- Manning G. S. The application of polyelectrolyte limiting laws to the helix-coil transition of DNA. VI. The numerical value of the axial phosphate spacing for the coil form. Biopolymers. 1976 Dec;15(12NA-NA-770103-770104):2385–2390. doi: 10.1002/bip.1976.360151206. [DOI] [PubMed] [Google Scholar]
- 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]
- Massoulié J. Thermodynamique des associations de poly A et poly U en milieu neutre et alcalin. Eur J Biochem. 1968 Feb;3(4):428–438. doi: 10.1111/j.1432-1033.1967.tb19549.x. [DOI] [PubMed] [Google Scholar]
- McGhee J. D. Theoretical calculations of the helix-coil transition of DNA in the presence of large, cooperatively binding ligands. Biopolymers. 1976 Jul;15(7):1345–1375. doi: 10.1002/bip.1976.360150710. [DOI] [PubMed] [Google Scholar]
- Mrevlishvili G. M., Mdzinarashvili T. D., Metreveli N. O., Kakabadze G. R. Teploemkost' DNK v nativnom i denaturirovannom sostoianiiakh. Biofizika. 1992 Sep-Oct;37(5):859–860. [PubMed] [Google Scholar]
- Nagasawa M., Muroga Y. The effect of charges on the melting of DNA. Biopolymers. 1972 Feb;11(2):461–474. doi: 10.1002/bip.1972.360110211. [DOI] [PubMed] [Google Scholar]
- Painter P. C., Koenig J. L. Raman spectroscopic study of the structure of antibodies. Biopolymers. 1975 Mar;14(3):457–468. doi: 10.1002/bip.1975.360140303. [DOI] [PubMed] [Google Scholar]
- Privalov P. L., Potekhin S. A. Scanning microcalorimetry in studying temperature-induced changes in proteins. Methods Enzymol. 1986;131:4–51. doi: 10.1016/0076-6879(86)31033-4. [DOI] [PubMed] [Google Scholar]
- 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]
- 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]
- 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]
- Schildkraut C. Dependence of the melting temperature of DNA on salt concentration. Biopolymers. 1965;3(2):195–208. doi: 10.1002/bip.360030207. [DOI] [PubMed] [Google Scholar]
- Shiao D. D., Sturtevant J. M. Heats of thermally induced helix-coil transitions of DNA in aqueous solution. Biopolymers. 1973;12(8):1829–1836. doi: 10.1002/bip.1973.360120810. [DOI] [PubMed] [Google Scholar]
- Stigter D. Evaluation of the counterion condensation theory of polyelectrolytes. Biophys J. 1995 Aug;69(2):380–388. doi: 10.1016/S0006-3495(95)79910-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vesnaver G., Breslauer K. J. The contribution of DNA single-stranded order to the thermodynamics of duplex formation. Proc Natl Acad Sci U S A. 1991 May 1;88(9):3569–3573. doi: 10.1073/pnas.88.9.3569. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vorontsov-Velyaminov P. N., Lyubartsev A. P. Monte-Carlo-self consistent field method in the polyelectrolyte theory. J Biomol Struct Dyn. 1989 Dec;7(3):739–747. doi: 10.1080/07391102.1989.10508517. [DOI] [PubMed] [Google Scholar]
- Wada A., Yabuki S., Husimi Y. Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies. CRC Crit Rev Biochem. 1980;9(2):87–144. doi: 10.3109/10409238009105432. [DOI] [PubMed] [Google Scholar]