Introduction: The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions that restricts their applications. To mitigate the requirement of magnesium, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (~134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp).
Materials and
Methods: We characterized DNA nanostructure assembly and quantified the assembly yields in twelve different cations using gel electrophoresis and provide visual confirmation of DNA origami assembly using atomic force microscopy (AFM). We also determined the biostability of these structures against DNase I and in fetal bovine serum (FBS) and show that the choice of cations for DNA nanostructure assembly can play a significant role in their enhanced biostability.
Results, Conclusions, and Discussions: In this study, we have presented new results on DNA nanostructure self-assembly in the presence of different monovalent and divalent cations. For the smaller DX motif, we show that the structure can be assembled in 10 mM Ca2+. For the DNA tetrahedron assembled through sticky end cohesion, we analyzed assembly at 10 mM ion concentrations and did not observe assembly in monovalent ions. To our knowledge, our study is the first to show assembly of a variety of DNA nanostructures in Ba2+, with assembly yields comparable to a Mg2+ - containing buffer for the DX and the three-point-star motif as well as for the larger DNA origami triangle. While our work shows that a variety of DNA nanostructures can be assembled in different cations, the choice of cation would be dependent on the specific design of the structure and the application.
