The Interaction of Monovalent Cations with a Model DNA Hairpin

Abstract

Capillary electrophoresis was used to study the interactions of monovalent cations with DNA hairpins, using as a model the 16 residue oligonucleotide ATCCTATTTTTAGGAT, which is known to form a stable hairpin with a 6 base pair stem and a 4 base loop. The unstructured 14 base oligonucleotide ACCTGATCACGTTA served as a reference analyte. All measurements were performed in the absence of Mg2+ at pH 7.3 using diethylmalonate as the buffering anion. Increasing the concentration of Na+ in the buffer increased the melting temperature of the hairpin, as predicted by the mFOLD algorithm. Isothermal measurements at 20° indicate that Na+ forms a saturable complex with the hairpin, with a KD of about 100 mM, but does not form a complex with the unstructured reference oligonucleotide. These measurements suggest that the increase in the melting temperature of the hairpin with increasing Na+ is due to the preferential binding of Na+ ions to the hairpin conformation. The cations Li+, K+, Tris+ and tetramethylammonium+ (TMA+) bind equally well to the model hairpin and affect its melting temperature similarly. The tetraethylammonium+ (TEA+) ion also binds equally well to the hairpin, but only to the extent of ∼50% saturation. The tetrapropylammonium+ (TPA+) and tetrabultylammonium+ (TBA+) ions bind to the hairpin very weakly if at all. Surprisingly, the melting temperature of the hairpin is systematically diminished as TMA+ is replaced in turn by TEA+, TPA+ or TBA+, suggesting that the larger tetraalkylammonium ions may destabilize the hairpin conformation by a through-solvent mechanism.