Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution.
AUTOR(ES)
García, A E
RESUMO
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.
ACESSO AO ARTIGO
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=287086Documentos Relacionados
- Conformational stability of alternating d (CG) oligomers in high salt solution.
- Conformation and dynamics of Z-DNA oligomer duplex of d[(CG)3TATA(CG)3] in solution.
- Structure of A-DNA in solution.
- Structural features and stability of an RNA triple helix in solution.
- Thermotropic phase behavior and stability of monosialoganglioside micelles in aqueous solution.
