A team of researchers in the School of Engineering and Applied Science at the University of Pennsylvania, Philadelphia, attached short sequences of single-stranded DNA to nanoscale building blocks, which, they say, has allowed them to design structures that can effectively build themselves. Only the building blocks meant to connect have complementary DNA sequences on their surfaces, which ensures only the correct pieces bind together while suspended in a test tube.
While earlier work assumed that the liquid medium in which the pieces float could be treated as a vacuum, the Penn team has demonstrated that fluid dynamics plays a critically important role in the kind and quality of the structures that can be created this way.
As the DNA-coated pieces rearrange themselves and bind, they create slipstreams into which other pieces can flow. This phenomenon makes some patterns within the structures more likely to form than others, they said.
The Penn team’s discovery started with an unusual observation about a previous study, which dealt with a reconfigurable crystalline structure the team had made using DNA-coated plastic spheres, each 400 nanometers wide. These structures assemble into floppy crystals with square-shaped patterns, but can be coaxed into more stable, triangular configurations. Surprisingly, the structures they were making in the lab were better than the ones their computer simulations predicted would result. The simulated crystals were full of defects, places where the crystalline pattern of the spheres was disrupted, but the experimentally grown crystals were all perfectly aligned.
By process of elimination, they discovered that hydrodynamic effects, essentially, the interplay between the particles and the fluid in which they are suspended while growing, was the key. The simulation of a system’s hydrodynamics is critical when the fluid is flowing, such as how rocks are shaped by a rushing river, but has been considered irrelevant when the fluid is still, as it was in the researchers’ experiments. While the particles’ jostling perturbs the medium, the system remains in equilibrium, suggesting the overall effect is negligible.
Particle systems like ones made by these self-assembling DNA-coated spheres typically rearrange themselves until they reach the lowest energy state. An unusual feature of the researchers’ system is that there are thousands of final configurations, with most containing defects just as energetically favorable as the perfect one they produced in the experiment. (See Figure 1)
The researchers’ breakthrough came when they realized that while hydrodynamic effects would not make any one final configuration more energy-favorable than another, the different ways particles would need to rearrange themselves to get to those states were not all equally easy. Critically, it is easier for a particle to make a certain rearrangement if it’s following in the wake of another particle making the same moves.
The researchers believe that this finding will lay the foundation for future work with these DNA-coated building blocks, but the principle discovered in their study will likely hold up in other situations where microscopic particles are suspended in a liquid medium.