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Excess DNA tiles support lifespan of nanotubes

By Stephen Riffle August 14, 2019
DNA tiles
Although DNA nanotubes degrade rapidly in a serum-supplemented medium at 37°C, when DNA tiles (green) that make up the DNA nanotubes are also present, these monomers can repair damaged nanotubes, extending nanotube lifetimes. Credit: Nano Letters

With its highly specific base pairing and sequence-independent structure, DNA represents a versatile material that can be easily manipulated to form a myriad of nanoscale structures, including spring-loaded boxes and nanotubes. Such structures may find application in targeted drug delivery, medical diagnostics, and synthetic biology so long as researchers are able to find a way to protect them from the rapid degradation that occurs in harsh environments, such as the human body. One way to do this, according to two biomolecular engineers at The Johns Hopkins University, Yi Li and Rebecca Schulman, is to facilitate DNA self-healing.

Engineering nanoscale structures is a difficult task which is made easier by materials that are capable of self-assembly. A DNA helix is an ideal material for this type of engineering because the properties governing hybridization (the joining of DNA strands), as well as the availability of technology that allows researchers to easily generate custom DNA sequences, enables engineers to design precise structures through self-assembly.

Schulman’s group is exploring the potential use of DNA nanotubes as self-assembling molecular bridges, capable of connecting two distant objects (such as cells or drug delivery vehicles). Unlike other materials, DNA nanotubes have the ability to grow across non-static distances, meaning that as two objects move in space, DNA nanotubes may be able to adjust through self-assembly. Schulman and Li, therefore, need not know the precise distance between two landmarks to build a nanotube bridge between them.

However, to use such bridges for targeted drug delivery, Schulman says that they needed to prevent nanotube degradation. “In particular, we need to prevent nanotubes from getting ‘holes’ that would cause fluid [containing the drug] to leak out of the tubes before it got to its destination,” she says.

Li, a postdoctoral researcher in Schulman’s laboratory, reasoned that the addition of polyethylene glycol (PEG) to nanotubes may help. PEG is commonly used in biotechnology and has been shown to prolong nanoparticle circulation time in vivo. PEG-coated nanotubes were put to the test in vitro by growing them in a solution containing DNA-degrading enzymes (nucleases). To Li’s surprise, PEG-coating did not help. “The method for conjugating PEG to DNA strands worked beautifully and PEGylated nanotubes grew just as expected....I was soon very surprised [that] PEG-coating provided no help with the nanotube lifetime,” Li says.

During these experiments, however, Li noticed that the DNA tiles—free-floating, short strands of DNA—that are used to build the nanotubes appeared to integrate with the decaying structures despite the ongoing degradation. This prompted Li and Schulman to consider the potential utility of self-healing, in which excess DNA tiles repair damage that would otherwise lead to degradation.

Through methods involving fluorescently tagged DNA tiles, Li and Schulman showed that, in the presence of nucleases, DNA nanotubes were completely degraded and lost within 24 hours. If the research team included an excess of DNA tiles, however, nanotubes survived much longer, retaining approximately 40% of their original length after 96 hours. Further examination revealed that DNA tiles were added to damaged nanotubes and also served as molecular fodder for nucleases, resulting in a slower rate of nanotube degradation.

Taken together, these results suggest that DNA nanotube lifetime could be dramatically affected by altering the balance between degradation rate and repair rate. This was underscored by modeling developed by Li and Schulman which predicts that increasing self repair—through the inclusion of DNA tiles—has the potential to outpace nanotube degradation and to cause an exponential increase in nanotube lifetimes.

Results like these are far removed from medical applications, but they offer a tantalizing new path forward. Shawn Douglas, a University of California at San Francisco researcher with a focus on DNA nanotechnology, says these results contribute to the broader field of biomolecular engineering, “[I]t’s suggestive of a future engineering approach that may be useful (or even indispensable) as we [build] devices and machines from biomolecules. In nanoscale manufacturing, we should think of our products as continually falling apart...but you can imagine some cases where you want the device to last a bit longer.”

Douglas says that, while the feasibility of adding excess DNA tiles to in vivo systems is unknown, it may be very easy to extend nanotechnology lifecycles in vitro by “spiking in an excess of building blocks.”

To that end, Li and Schulman will use these learnings to continue their work on developing nanotube bridges.

Read the abstract in Nano Letters.