Recycling DNA origami nanostructures

DNA origami is a technique that creates precisely shaped nanostructures. Methods for recycling the DNA strands that are used to build these structures could help this form of nanoscale engineering become more cost effective as it scales up toward commercial applications (Nano Lett. 2024, DOI: 10.1021/acs.nanolett.4c02695).

To assemble these minuscule structures, researchers first create a scaffold: a long piece of single-stranded DNA with a carefully designed sequence of bases. Then they add hundreds of shorter DNA chunks that each bind to specific sections of the scaffold, acting as staples that help to fold the long strand into a predetermined 3D shape.

To drive folding to completion, researchers typically use 10 times as many staples as actually get incorporated in the finished structure and then discard the excess. “I’ve thrown away staples for almost a decade now,” says Wolfgang G. Pfeifer at the Ohio State University, part of the team behind the work.

DNA origami is being developed for applications including biosensors, drug delivery platforms, templates for optical materials, nanomachines, and even traps for viruses. The Ohio State team says the DNA needed for 1 mg of nanostructures typically costs around $100–$150, but specially modified staples that carry antibodies or drug molecules can be much more expensive. As applications mature, larger-scale production could drive those costs up significantly and could generate a lot more waste.

So the researchers have developed two methods to recycle staples and scaffolding strands. “Cost is our number one limitation, so this is a big deal,” says Fei Zhang, who works on DNA nanotechnology at Rutgers University and was not involved in the research.

The first method uses ethanol and magnesium chloride to precipitate excess staples from solution after they have been used in making new nanostructures. The staples are then centrifuged to create a solid pellet. These recovered staples are just as good as fresh DNA for stitching together new structures. Zhang has already tried this method in her own laboratory and is delighted with the results. “It’s really great!” she says. “The procedure is so simple and straightforward.”

The second recycling method involves reprogramming an existing DNA origami nanostructure by swapping its original staples for a fresh batch so that the scaffold folds into a completely new shape.

As a proof of principle for the second method, the team started with a nanostructure shaped like the G clef musical symbol and heated it to 95 °C for a few minutes to separate the scaffold from its staples. Then the researchers added a 20-fold excess of new staples, which refolded the scaffold into a springlike structure called NuSpring. They repeated the method to convert the scaffold into a shape known as a Hilbert structure, and finally they transformed it back into a G clef. Each transformation happened in 80–90% yields.

Team leader Carlos E. Castro at the Ohio State University says it might be possible to exploit this reprogramming in other ways. If the DNA structures were to form part of a biosensor, for example, sections of the structures could be remodeled so that they sense different molecules. “If you want to change from sensing molecule A to molecule B, you could probably use something similar to this reprogramming,” Castro says.