Harmonic Vibrations and Thermodynamic Stability of a DNA Oligomer in Monovalent Salt Solution

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1989 May 1

PMID 2717613

Citations 10

Authors

A E Garcia

D M Soumpasis

Affiliations

Soon will be listed here.

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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