Abstract
Capillary electrophoresis has been used to examine the effect of cation size on DNA thermal stability, using hairpins with 6 base pair-stems and 4 nucleotide-loops as the reporter system. The midpoint melting temperatures observed in solutions containing the tetrabutylammonium ion (TBA+) are consistently 16°C lower than observed in solutions containing the same concentration of Na+, even though no preferential interaction with either cation is observed. The thermal melting temperatures decrease progressively with increasing cation size, due primarily to the effect of cation size on solution viscosity. We postulate that the viscosity of the solution affects the hairpin ↔ coil equilibrium because of through-solvent effects on hairpin renaturation, as observed in other studies. The mobilities of the various hairpins are independent of sequence in Na+ but depend on sequence in TBA+ solutions. In particular, the observed mobilities increase with the increasing number of thymine bases in the loop, possibly because of the partial ionization of thymine in TBA+ which would increase the effective net charge of the hairpin.
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