The association of two gramicidin A (gA) peptides via H-bonds in lipid bilayers causes the formation of an ion channel that is selective for monovalent cations only. In this study, two gAs were covalently linked with a dioxolane group (SS dimer). Some functional properties of natural gA channels were compared to that synthetic dimer in Na(+)- or Cs(+)-containing solutions. The SS dimer remained in the open configuration most of the time, while natural gA channels had a relatively brief mean open time. Single channel conductances to Na(+) (g(Na)) or Cs(+) (g(Cs)) in the SS dimer were smaller than in natural gA. However, g(Na) was considerably more attenuated than g(Cs). This probably results from a tight solvation of Na(+) by the dioxolane linker in the SS channel. In Cs(+) solutions, the SS had frequent closures. By contrast, in Na(+) solutions the synthetic dimer remained essentially in the open state. The mean open times of SS channels in different solutions (T(open, Na) > T(open,Cs) > T(open,H)) were inversely proportional to the single channel conductances (g(H) > g(Cs) > g(Na)). This suggests that ion occupancy inside the pore stabilizes the open configuration of the gA dimer. The mean closed time of the SS dimer was longer in Cs(+) than in H(+) solutions. Possible mechanisms for these effects are discussed.