Sorting molecules with DNA robots
Single-stranded DNA robots can move over the surface of a DNA origami sheet and sort molecular cargoes. Thubagere et al. developed a simple algorithm for recognizing two types of molecular cargoes and their drop-off destinations on the surface (see the Perspective by Reif). The DNA robot, which has three modular functional domains, repeatedly picks up the two types of molecules and then places them at their target destinations. No additional power is required because the DNA robot does this by random walking across the origami surface.
Science, this issue p. eaan6558; see also p. 1095
Since the 1980s, the design and synthesis of molecular machines has been identified as a grand challenge for molecular engineering. Robots are an important type of molecular machine that automatically carry out complex nanomechanical tasks. DNA molecules are excellent materials for building molecular robots, because their geometric, thermodynamic, and kinetic properties are well understood and highly programmable. So far, the development of DNA robots has been limited to simple functions. Most DNA robots were designed to perform a single function: walking in a controlled direction. A few demonstrations included a second function combined with walking (for example, picking up nanoparticles or choosing a path at a junction). However, these relatively more complex functions were also more difficult to control, and the complexity of the tasks was limited to what the robot can perform within 3 to 12 steps. In addition, each robot design was tailored for a specific task, complicating efforts to develop new robots that perform new tasks by combining functions and mechanisms.
The design and synthesis of molecular robots presents two critical challenges, those of modularity and algorithm simplicity, which have been transformative in other areas of molecular engineering. For example, simple and modular building blocks have been used for scaling up molecular information processing with DNA circuits. As in DNA circuits, simple building blocks for DNA robots could enable more complex nanomechanical tasks, whereas modularity could allow diverse new functions performed by robots using the same set of building blocks.
We demonstrate a DNA robot that performs a nanomechanical task substantially more sophisticated than previous work. We developed a simple algorithm and three modular building blocks for a DNA robot that performs autonomous cargo sorting. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers each type to a specified destination until all cargo molecules are sorted into two distinct piles. The robot is designed to perform a random walk without any energy supply. Exploiting this feature, a single robot can repeatedly sort multiple cargos. Localization on DNA origami allows for distinct cargo-sorting tasks to take place simultaneously in one test tube or for multiple robots to collectively perform the same task. On average, our robot performed approximately 300 steps while sorting the cargos. The number of steps is one to two magnitudes larger than the previously demonstrated DNA robots performing additional tasks while walking. Using exactly the same robot design, the system could be generalized to multiple types of cargos with arbitrary initial distributions, and to many instances of distinct tasks in parallel, whereas each task can be assigned a distinct number of robots depending on the difficulty of the task.
Using aptamers, antibodies, or direct conjugation, small chemicals, metal nanoparticles, and proteins could be transported as cargo molecules so that the cargo-sorting DNA robots could have potential applications in autonomous chemical synthesis, in manufacturing responsive molecular devices, and in programmable therapeutics. The building blocks developed in this work could also be used for diverse functions other than cargo sorting. For example, inspired by ant foraging, adding a new building block for leaving pheromone-like signals on a path, DNA robots could be programmed to find the shortest path and efficiently transport cargo molecules. With simple communication between the robots, they could perform even more sophisticated tasks. With more effort in developing modular and collective molecular robots, and with simple and systematic approaches, molecular robots could eventually be easily programmed like macroscopic robots, but working in microscopic environments.