A proximity-based programmable DNA nanoscale assembly line

Abstract

Our ability to synthesize nanometre-scale chemical species, such as nanoparticles with desired shapes and compositions, offers the exciting prospect of generating new functional materials and devices by combining them in a controlled fashion into larger structures. Self-assembly can achieve this task efficiently, but may be subject to thermodynamic and kinetic limitations: reactants, intermediates and products may collide with each other throughout the assembly time course to produce non-target species instead of target species. An alternative approach to nanoscale assembly uses information-containing molecules such as DNA to control interactions and thereby minimize unwanted cross-talk between different components. In principle, this method should allow the stepwise and programmed construction of target products by linking individually selected nanoscale components-much as an automobile is built on an assembly line. Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and are attached in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo. As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an 'ON' state, allowing its cargo to be transferred to the walker, and an 'OFF' state, in which no transfer occurs. We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.

Figure 1. The molecular assembly line and its operation

(a) The basic components of the system are the origami tile (shown as a tan outline), programmable 2-state DNA machines inserted in series into the file (shown in blue, purple and green), and the walker (shown as a trigonal arrangement of DNA double helices in red). The cargo of the machines consists of a 5 nm gold particle, a coupled pair of 5 nm particles or a 10 nm particle (indicated by brown dots), with their states labeled as PX (meaning ON or ‘donate’ cargo) and JX₂ (meaning OFF or ‘do not donate’ cargo). In the example shown, the walker collects cargo from each machine. (b) Atomic force micrographs of the system corresponding to the process steps sketched in the right panels (a). AFM was performed by tapping in air; this mode of AFM results in only the nanoparticles and the origami being visible, and the individual nanoparticle components are not resolved from each other. Owing to the washing procedures between steps, the AFM images are not of the same individual assembly line. All scale bars are 50 nm.

Figure 2. Details of the Walker, Movement, and Cargo Transfer

(a) Walker structure: The drawing at left is a stick figure indicating the three hands (H1-H3) and four feet (F1-F4). The image at right shows the strand structure. (b) Movement: Walker reactions are in panels i and ii, and movement on the origami is in panels iii and iv. Figure S5 shows the complete walker transit. (c) Cargo transfer: (i) The PX state brings the arm of cassette 1 close to hand H1. (ii) The brown toehold binds its complement (red). (iii) Branch migration transfers the cargo strand to hand H1.

Figure 3. The Eight Products of the Assembly Line

The small Roman numerals indicate the different pathways illustrated in panels (a), (b) and (c). (a) The eight possible products that can be generated through appropriate programming of the state of the three DNA machines. The walker is shown at the left, without cargo. Each DNA machine is shown twice: in the upper row in the OFF state where no cargo transfer takes place, and in the lower row in the ON state where cargo can be transferred to the walker. The different assembly trajectories are color coded as black, dark blue, rose, brown, yellow, light blue, green, and magenta, giving products i-viii, respectively, shown schematically at right. (b) Schematic of the final state the system reaches for each of the eight assembly pathways. The states of the cassettes and the dispositions of the cargo species (attached to the robot arms or attached to the walker) are visible. (c) TEM images of the products generated in each of the assembly pathways. (Note that TEM resolves the individual gold Nanoparticles.) In each image, several products generated by the given pathway are visible. All scale bars are 50 nm.