Tuning the Stability of DNA Tetrahedra with Base Stacking Interactions

DNA nanotechnology uses the programmable assembly of DNA to create nanoscale objects. Recent work from our laboratory suggested that terminal stacking interactions between adjacent strands could be a design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra with sticky ends containing identical base pairing interactions but different stacking interactions. Testing all 16 stacking combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. We also show that a 4 bp sticky end with weak stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to that of a 6 bp sticky end with weak stacking (49.7 ± 2.9 °C). The results likely apply to other DNA nanostructures and suggest that stacking interactions play a role in the formation and stability of DNA nanostructures.