The interactions between tetranucleotides or heptanucleotides and inorganic cations have been measured by affinity CZE. The variation in migration behavior with increasing concentrations of divalent cations (Ca2+, Mg2+ and Ni2+) in the running buffer was investigated and quantified by the calculation of binding constants for mononuclear and multinuclear interactions. In addition to these fundamental studies of binding equilibria, the effect of sequence and the position of the guanine transition metal-binding site in the oligonucleotide have been investigated.