Self-Assembly of DNA Nanodonuts via Selective Insertions of Azobenzene Molecules

As DNA-based materials increasingly interface with diverse chemical moieties to create more complex assemblies, a deeper understanding is needed of how the structural properties of diverse components interact to preserve the geometrical precision of intended nanostructures. In this work, we describe and characterize the manipulation of rigid DNA nanotubes using azobenzene, which has been previously used for creating dynamically reconfigurable DNA nanostructures. The steric hindrance of azobenzene, site-specifically embedded within the double helix, enables the controlled modulation of nanotube bending into donut structures with a controlled radius of curvature. Overall, we find that three azobenzene compounds within an 8-nt DNA motif can increase the steric diameter of the DNA duplex. By strategically selecting the quantity and positions of inserted azobenzene molecules, we experimentally demonstrate the bending of DNA nanotubes into DNA donut-shaped nanostructures ranging from 40 to 200 nm. This work provides a promising design principle for heterogeneous DNA-based nanostructures, which may be arranged to synthesize complex nanostructures and nanomechanical components cooperatively.