The metal binding properties of the dinucleotide duplex, dCG(.)dCG, were analyzed in the gas phase with ion mobility mass spectrometry. Both MALDI and ESI were used to generate [M(dCG(.)dCG)](+) complexes. The collision cross section of each complex was measured in helium using ion mobility based methods and compared to calculated cross sections of theoretical structures. When metal cations classified as hard acids were combined with dCG(.)dCG, the [M(dCG(.)dCG)](+) complex organized into a globular structure. However, when soft acid metal cations were examined, a structure was observed where the two C-G base pairs were Watson-Crick bound.