Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate

Abstract

The aim of nanotechnology is to put specific atomic and molecular species where we want them, when we want them there. Achieving such dynamic and functional control could lead to programmable chemical synthesis and nanoscale systems that are responsive to their environments. Structural DNA nanotechnology offers a powerful route to this goal by combining stable branched DNA motifs with cohesive ends to produce programmed nanomechanical devices and fixed or modified patterned lattices. Here, we demonstrate a dynamic form of patterning in which a pattern component is captured between two independently programmed DNA devices. A simple and robust error-correction protocol has been developed that yields programmed targets in all cases. This capture system can lead to dynamic control either on patterns or on programmed elements; this capability enables computation or a change of structural state as a function of information in the surroundings of the system.

Figure 1

Schematic Drawings of the Four Different Capture Molecules. In each of the four cases, two PX-JX₂ cassettes that face each other are shown anchored in a blue origami array beneath them by two green domains. The sticky ends are indicated as A and B (left), or C and D (right). Their relative positions are established by the state (PX or JX₂) of the cassettes. The four different capture molecules are shown to have sticky ends with primed labels that are complementary to the pairs of sticky ends on the cassettes. The pattern is established by the top domain of the capture molecules. This view, along the direction of origami plane, is perpendicular to the views available in the other figures.

Figure 2

Schematics (a) and Atomic Force Micrographs (b) of the Origami Arrays and Capture Molecules. Panel i of (a) illustrates the origami array containing slots for the cassettes and a notch to enable recognition of orientation; the slots and notches are visible in the AFM in (b). Panels ii show the cassettes in place; the color coding in (a) used throughout the schematics is green for the PX state and violet for the JX₂ state; the presence of the cassettes is evident in the AFM image in (b). Panels iii illustrate the PX-PX state which captures a triangle pointing towards the notch in the schematic (a) and in the AFM image (b). Panels iv illustrate the PX-JX₂ state (a), containing a triangle that points away from the notch, which is evident in the AFM image (b). Panels v illustrate the JX₂- PX state which captures a diamond-shaped molecule (a); its shape is visible in the AFM image (b). Panels vi show the linear molecule captured by the JX₂-JX₂ state, both schematically (a) and in the AFM image (b).

Figure 3

Atomic Force Micrographs of the Correction Procedure for the Diamond-Shaped Capture Molecule. The identity of captured molecules is color-coded by arrows pointing at the origami tiles. The key used here and in the Supporting Online Material is: Diamond -- Black; Line -- Red; Triangle pointing away from the notch -- Blue (none in these images); Triangle pointing towards the notch -- Magenta; Damaged Unit -- White. (a) A mixture of the four capture molecules has been applied to the origami. (b) The linear molecule has been applied, using the binding correction protocol described in the text. (c) The triangle pointing to the notch has been applied to the material in (b) and the correction protocol has been applied. (d) The diamond has been applied to the material in (c) and the correction protocol has been applied. (e) The triangle away from the notch has been applied to the material in (d), and the correction protocol has been applied. Only diamonds are visible in (d) and (e). Panels (f), (g), (h) and (i) show the same procedure, but in a different order: The triangle pointing to the notch, the triangle pointing away from the notch, the linear element and the diamond have been applied, respectively. Again, only diamonds are visible in Panel (i). The other three systems are shown in the Supplementary Data (Figures S8-S10).