Monovalent cation binding in the minor groove of DNA A-tracts

The binding of five different monovalent cations to DNA oligomers containing A-tracts, runs of four or more contiguous adenine residues, has been assessed by capillary electrophoresis, using the Replacement Ion method. In this method, a nonbinding cation in the background electrolyte is gradually replaced by a binding cation, keeping the ionic strength of the solution constant. Monovalent cation binding reduces the effective charge of an A-tract-containing oligomer, decreasing its free solution mobility. The cations bind in the A-tract minor groove, because the binding site can be blocked by the minor groove binding drug netropsin. Li(+), NH(4)(+), and Tris(+) ions bind to A-tracts with similar affinities; the binding of Na(+) ions is weaker, and K(+) ion binding is highly variable. Each A-tract appears to bind one monovalent cation upon saturation of the binding site(s). For a given cation, the apparent dissociation constants depend on A-tract sequence and orientation, but not on the phasing of the A-tracts with respect to the helix repeat. Differences in the cooperativity of binding of the various cations to A-tracts with different sequences suggest that monovalent cation binding may be coupled with a conformational transition leading to the formation of the characteristic narrow minor groove A-tract structure.