Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components

Reconfigurable DNA structures DNA origami—nanostructures created by programming the assembly of single-stranded DNA through base pairing—can create intricate structures. However, such structures lack the flexible and reversible interactions more typical of biomolecular recognition. Gerling et al. created three-dimensional DNA nanostructures that assemble though nucleotide base-stacking interactions (see the Perspective by Shih). These structures cycled from open to closed states with changes in salt concentration or temperature. Science, this issue p. 1446; see also p. 1417 Readily reconfigurable DNA structures can be made that do not need detailed strand sequences to connect components. [Also see Perspective by Shih] We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.