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. 1989 May;86(9):3160–3164. doi: 10.1073/pnas.86.9.3160

Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution.

A E García 1, D M Soumpasis 1
PMCID: PMC287086  PMID: 2717613

Abstract

We compute the full harmonic vibrational spectrum and eigenmodes of a DNA oligomer, d(C-G)3, in optimized B and Z conformations in various ionic environments (0.01-5.0 M NaCl). The statistical interactions of DNA with the diffuse ionic cloud surrounding it in solution are approximately represented within the potential of mean force framework. The lowest eigenfrequency of the B conformation is found to drastically decrease with increased NaCl concentration. This suggests that a soft mode mechanism may be a precursor for the B-to-Z conversion. The free energy balance governing the B-Z isomerization of d(C-G)3 is dominated by the solvent-averaged effective phosphate-phosphate interactions due to substantial cancelations between the much larger intramolecular energy contributions.

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Selected References

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

  1. Arnott S., Hukins D. W. Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504–1509. doi: 10.1016/0006-291X(72)90243-4. [DOI] [PubMed] [Google Scholar]
  2. Borah B., Cohen J. S., Howard F. B., Miles H. T. Poly(d2NH2A-dT): two-dimensional NMR shows a B to A conversion in high salt. Biochemistry. 1985 Dec 3;24(25):7456–7462. doi: 10.1021/bi00346a064. [DOI] [PubMed] [Google Scholar]
  3. Eyster J. M., Prohofsky E. W. On the B to A conformation change of the double helix. Biopolymers. 1977 May;16(5):965–982. doi: 10.1002/bip.1977.360160503. [DOI] [PubMed] [Google Scholar]
  4. Garcia AE, Krumhansl JA. Role of the Coulomb interaction in the low-frequency density of states of DNA double helices. Phys Rev A Gen Phys. 1988 Jun 15;37(12):4875–4878. doi: 10.1103/physreva.37.4875. [DOI] [PubMed] [Google Scholar]
  5. Irikura K. K., Tidor B., Brooks B. R., Karplus M. Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference. Science. 1985 Aug 9;229(4713):571–572. doi: 10.1126/science.3839596. [DOI] [PubMed] [Google Scholar]
  6. Kopka M. L., Fratini A. V., Drew H. R., Dickerson R. E. Ordered water structure around a B-DNA dodecamer. A quantitative study. J Mol Biol. 1983 Jan 5;163(1):129–146. doi: 10.1016/0022-2836(83)90033-5. [DOI] [PubMed] [Google Scholar]
  7. Lindsay S. M., Lee S. A., Powell J. W., Weidlich T., DeMarco C., Lewen G. D., Tao N. J., Rupprecht A. The origin of the A to B transition in DNA fibers and films. Biopolymers. 1988 Jun;27(6):1015–1043. doi: 10.1002/bip.360270610. [DOI] [PubMed] [Google Scholar]
  8. Pohl F. M. Thermodynamics of the helix-coil transition of (dG-dC) oligomers. Eur J Biochem. 1974 Mar 1;42(2):495–504. doi: 10.1111/j.1432-1033.1974.tb03364.x. [DOI] [PubMed] [Google Scholar]
  9. Seibel G. L., Singh U. C., Kollman P. A. A molecular dynamics simulation of double-helical B-DNA including counterions and water. Proc Natl Acad Sci U S A. 1985 Oct;82(19):6537–6540. doi: 10.1073/pnas.82.19.6537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Singh U. C., Weiner S. J., Kollman P. Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions. Proc Natl Acad Sci U S A. 1985 Feb;82(3):755–759. doi: 10.1073/pnas.82.3.755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Soumpasis D. M., Robert-Nicoud M., Jovin T. M. B-Z DNA conformational transition in 1:1 electrolytes: dependence upon counterion size. FEBS Lett. 1987 Mar 23;213(2):341–344. doi: 10.1016/0014-5793(87)81519-3. [DOI] [PubMed] [Google Scholar]
  12. Soumpasis D. M. Statistical mechanics of the B----Z transition of DNA: contribution of diffuse ionic interactions. Proc Natl Acad Sci U S A. 1984 Aug;81(16):5116–5120. doi: 10.1073/pnas.81.16.5116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Soumpasis D. M., Wiechen J., Jovin T. M. Relative stabilities and transitions of DNA conformations in 1:1 electrolytes: a theoretical study. J Biomol Struct Dyn. 1987 Feb;4(4):535–552. doi: 10.1080/07391102.1987.10507658. [DOI] [PubMed] [Google Scholar]
  14. Tidor B., Irikura K. K., Brooks B. R., Karplus M. Dynamics of DNA oligomers. J Biomol Struct Dyn. 1983 Oct;1(1):231–252. doi: 10.1080/07391102.1983.10507437. [DOI] [PubMed] [Google Scholar]
  15. Trifonov E. N. Sequence-dependent variations of B-DNA structure and protein-DNA recognition. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):271–278. doi: 10.1101/sqb.1983.047.01.032. [DOI] [PubMed] [Google Scholar]
  16. Urabe H., Tominaga Y. Low-lying collective modes of DNA double helix by Raman spectroscopy. Biopolymers. 1982 Dec;21(12):2477–2481. doi: 10.1002/bip.360211212. [DOI] [PubMed] [Google Scholar]
  17. Van Gunsteren W. F., Berendsen H. J., Geurtsen R. G., Zwinderman H. R. A molecular dynamics computer simulation of an eight-base-pair DNA fragment in aqueous solution: comparison with experimental two-dimensional NMR data. Ann N Y Acad Sci. 1986;482:287–303. doi: 10.1111/j.1749-6632.1986.tb20962.x. [DOI] [PubMed] [Google Scholar]
  18. Wang A. J., Quigley G. J., Kolpak F. J., van der Marel G., van Boom J. H., Rich A. Left-handed double helical DNA: variations in the backbone conformation. Science. 1981 Jan 9;211(4478):171–176. doi: 10.1126/science.7444458. [DOI] [PubMed] [Google Scholar]
  19. Weber G. Energetics of ligand binding to proteins. Adv Protein Chem. 1975;29:1–83. doi: 10.1016/s0065-3233(08)60410-6. [DOI] [PubMed] [Google Scholar]

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