Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution.
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.
García
A E
AE
Theoretical Division, Los Alamos National Laboratory, NM 87545.
Soumpasis
D M
DM
D000838:Anions; D002414:Cations, Monovalent; D004247:DNA; D004355:Drug Stability; D004563:Electrochemistry; D006860:Hydrogen Bonding; D007700:Kinetics; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009994:Osmolar Concentration; D011089:Polydeoxyribonucleotides; D012965:Sodium Chloride / Q000494:pharmacology; D012996:Solutions; D013816:Thermodynamics; D014732:Vibration
D000838:Anions; D002414:Cations, Monovalent; D011089:Polydeoxyribonucleotides; D012996:Solutions; C019530:poly(dC-dG); D012965:Sodium Chloride; D004247:DNA