The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR.

TitleThe selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR.
Publication TypeJournal Article
Year of Publication1996
AuthorsHud, NV, Smith, FW, Anet, FA, Feigon, J
JournalBiochemistry
Volume35
Issue48
Pagination15383-90
Date Published1996 Dec 3
ISSN0006-2960
KeywordsDNA, Magnetic Resonance Spectroscopy, Models, Chemical, Potassium, Potassium Chloride, Sodium, Sodium Chloride, Thermodynamics
Abstract

We have studied the competition between Na+ and K+ for coordination by G quartets using the oligonucleotide d(G3T4G3) as a model system. d(G3T4G3) forms a dimeric foldback structure containing three G quartets in the presence of either NaCl or KCl. Proton chemical shifts, which are particular to the species of coordinated ion, have been used to monitor the conversion between the sodium and potassium forms under equilibrium conditions. Analysis of titration experiments indicates that at least two K+ are coordinated by the three quartets of the dimeric molecule, and perfect fits of the data are obtained for two Na+ being displaced by two K+. Our results also indicate that the conversion of [d(G3T4G3)]2 from the sodium to the potassium form is associated with a net free energy change (delta G degrees) of -1.7 +/- 0.15 kcal/mol. It has long been suggested that the greater thermal stability of DNA quadruplex structures in the presence of K+ is primarily a result of the optimal fit of this ion in the coordination sites formed by G quartets. However, a consideration of the relatively small change in free energy associated with the conversion from the sodium to the potassium form and the relatively large difference between the free energy of hydration for Na+ and K+ indicates that this cannot be correct. Rather, the preferred coordination of K+ over Na+ is actually driven by the greater energetic cost of Na+ dehydration with respect to K+ dehydration.

DOI10.1021/bi9620565
Alternate JournalBiochemistry
PubMed ID8952490
Grant ListGM17652 / GM / NIGMS NIH HHS / United States
GM48123 / GM / NIGMS NIH HHS / United States