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.
Caltech scientists have developed an autonomous molecular machine that can perform similar tasks—at the nanoscale. This “robot,” made of a single strand of DNA, can autonomously “walk” around a surface, pick up certain molecules and drop them off in designated locations.
How to Build a Molecular Robot
Led by former graduate student Anupama Thubagere (PhD ’17), the researchers constructed three basic building blocks that could be used to assemble a DNA robot: a “leg” with two “feet” for walking, an “arm” and “hand” for picking up cargo, and a segment that can recognize a specific drop-off point and signal to the hand to release its cargo. Each of these components is made of just a few nucleotides within a single strand of DNA.
In principle, these modular building blocks could be assembled in many different ways to complete different tasks—a DNA robot with several hands and arms, for example, could be used to carry multiple molecules simultaneously.
In the work described in the Science paper, the Qian group built a robot that could explore a molecular surface, pick up two different molecules—a fluorescent yellow dye and a fluorescent pink dye—and then distribute them to two distinct regions on the surface. Using fluorescent molecules enabled the researchers to see if the molecules ended up in their intended locations. The robot successfully sorted six scattered molecules, three pink and three yellow, into their correct places in 24 hours. Adding more robots to the surface shortened the time it took to complete the task.
“Though we demonstrated a robot for this specific task, the same system design can be generalized to work with dozens of types of cargos at any arbitrary initial location on the surface,” says Thubagere. “One could also have multiple robots performing diverse sorting tasks in parallel.”
Design through DNA
The key to designing DNA machines is the fact that DNA has unique chemical and physical properties that are known and programmable. A single strand of DNA is made up of four different molecules called nucleotides—abbreviated A, G, C, and T—and arranged in a string called a sequence. These nucleotides bond in specific pairs: A with T, and G with C. When a single strand encounters a so-called reverse complementary strand—for example, CGATT and AATCG—the two strands zip together in the classic double helix shape.
A single strand containing the right nucleotides can force two partially zipped strands to unzip from each other. How quickly each zipping and unzipping event happens and how much energy it consumes can be estimated for any given DNA sequence, allowing researchers to control how fast the robot moves and how much energy it uses to perform a task. Additionally, the length of a single strand or two zipped strands can be calculated. Thus, the leg and foot of a DNA robot can be designed for a desired step size—in this case, 6 nanometers, which is about a hundred millionth of a human’s step size.
Using these chemical and physical principles, researchers can design not only robots but also “playgrounds,” such as molecular pegboards, to test them on. In the current work, the DNA robot moves around on a 58-nanometer-by-58-nanometer pegboard on which the pegs are made of single strands of DNA complementary to the robot’s leg and foot. The robot binds to a peg with its leg and one of its feet—the other foot floats freely. When random molecular fluctuations cause this free foot to encounter a nearby peg, it pulls the robot to the new peg and its other foot is freed. This process continues with the robot moving in a random direction at each step.
It may take a day for a robot to explore the entire board. Along the way, as the robot encounters cargo molecules tethered to pegs, it grabs them with its “hand” components and carries them around until it detects the signal of the drop-off point. The process is slow, but it allows for a very simple robot design that utilizes very little chemical energy.
“We don’t develop DNA robots for any specific applications. Our lab focuses on discovering the engineering principles that enable the development of general-purpose DNA robots,” says Qian. “However, it is my hope that other researchers could use these principles for exciting applications, such as using a DNA robot for synthesizing a therapeutic chemical from its constituent parts in an artificial molecular factory, delivering a drug only when a specific signal is given in bloodstreams or cells, or sorting molecular components in trash for recycling.”
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.
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. 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.
Conceptual illustration of two DNA robots. The robots are collectively performing a cargo-sorting task on a DNA origami surface, transporting fluorescent molecules with different colors from initially unordered locations to separated destinations. Considerable artistic license has been taken. ILLUSTRATION: DEMIN LIU (WWW.MOLGRAPHICS.COM)/i>
Researchers 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.