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Journal Article

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

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Soumpasis,  D.M.
Department of Molecular Biology, MPI for biophysical chemistry, Max Planck Society;

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Citation

Garcia, A. E., & Soumpasis, D. (1989). Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proceedings of the National Academy of Sciences of the United States of America, 86(9), 3160-3164.


Cite as: http://hdl.handle.net/11858/00-001M-0000-002C-49CC-3
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.