The association of three monomeric cyanine dyes with double-stranded DNA was investigated. The oxazole yellow dye (YO-PRO-1) and the two thiazole orange dyes (TO-PRO-I and TO) are structurally similar, differing only in their charge and in the heteroatom in their benzothiazole and benzoxazole rings. On the basis of changes in the UV-visible absorption spectra of the dyes when bound to DNA, equilibrium constants were measured to investigate the factors that influence their intercalative association with DNA. When these positively charged dyes associate with DNA, the number of condensed Na+ ions that are released from the DNA backbone is correlated with the structural change of the dye. A comparison of the equilibrium constants demonstrates that the charge and structure of the dye influences the strength of its interaction with DNA. As evident from larger equilibrium constants in buffers containing tetramethylammonium cations as opposed to sodium cations, the identity of the cations also influences the stability of the dye-DNA complex. Finally, equilibrium constants measured using DNA with different AT/GC contents indicate that the cyanine dyes interact nonspecifically with double-stranded DNA.