The structural integrity, assembly yield, and biostability of DNA nanostructures are influenced by the metal ions used to construct them. Although high (>10 mM) concentrations of divalent ions are often preferred for assembling DNA nanostructures, the range of ion concentrations and the composition of the assembly products vary for different assembly conditions. Here, we examined the unique ability of Ba2+ to retard double crossover DNA motifs by forming a low mobility species, whose mobility on the gel is determined by the concentration ratio of DNA and Ba2+. The formation of this electrophoretically retarded species is promoted by divalent ions such as Mg2+, Ca2+, and Sr2+ when combined with Ba2+ but not on their own, while monovalent ions such as Na+, K+, and Li+ do not have any effect on this phenomenon. Our results highlight the complex interplay between the metal ions and DNA self-assembly and could inform the design of DNA nanostructures for applications that expose them to multiple ions at high concentrations.
Keywords: DNA nanostructures; barium; electrophoresis; gel mobility; metal ions; self-assembly.