Biological systems are complicated. Though DNA may carry a simple sequence of base pairs, once this information is transcribed into RNA and translated into proteins, this simple sequence can give rise to numerous, often unpredictable convolutions. Contending with this unpredictability of RNA and protein structure, synthetic biologists can struggle to design precise biological systems with specific goals. But what if the system was constructed entirely of DNA?
In a study in Journal of Royal Society Interface published online last week, Harish Chandran of Duke University and colleagues use DNA’s simplicity and predictability to propose possible DNA nanostructures that mimic polymerases or restriction enzymes to carry out a variety of biological processes.
“It’s a theoretically neat demonstration that some important reactions could be possible using DNA’s structure,” said Chris Dwyer, a computer engineer at Duke University who designs DNA nanostructures and was not involved with the research.
While DNA “origami”—the construction of precisely folded DNA nanostructures—has already been used to facilitate enzymatic reactions through precise placement of components, Chandran’s work is the first attempt to use DNA as the enzyme in such systems. The models take advantage of the double helix, and DNA’s “desire” to keep twisting. Chandran and his team created computer models of meta-DNA structures using pieces of DNA as the building blocks, or bricks, to build something much bigger that still acts a lot like a strand of DNA. Just as a real base is the primary unit of DNA, the meta-bases (DNA bricks) are the primary units of meta-DNA.
Meta-bases are designed from three strands of normal double-stranded DNA. The ends of each strand complement the other two, and all three will match up in what Chandran describes as a “three-prong star.” These stars can be linked, again through complementary end sequences, with other stars, to form meta-DNA strands.
Creating meta-DNA structures that can act like enzymes, the researchers added, simply involves the combining of two meta-strands of differing length, providing an opening for other single-stranded bit of meta-DNA to bind. Under the right conditions, new meta-bases could start binding to the longer meta-strand, allowing for possible “enzymatic” reactions, like DNA replication (much like PCR reactions, in which shorter primer pieces of DNA extend under the right conditions). Meta-DNA could also be designed to mimic restriction enzyme activity if a strand within one of its meta-bases recognizes a sequence in the meta-DNA strand to be cleaved.
The researchers have yet to build such DNA-based enzyme reactions, but they have begun to build actual meta-DNA structures, and Chandran is confident that with some careful planning, they should be able to put these principles into practice, he said. He imagines someday being able to create entire meta-cells, capable of interacting with living tissue, possibly carrying therapeutic components inside.
A system built entirely of DNA should theoretically eliminate unnecessary unpredictability of RNA and proteins, and should make it easier, in the long run, for synthetic biologists to design unique systems, Chandran said. “We have a strong belief in our group that we can probably create primitive life using just DNA strands.”
Dwyer agreed that enzyme design is a problem “not yet solved,” but pointed to a critical drawback of the DNA-only system. At this point, “it’s only really applicable to other meta-DNA constructs,” Dwyer explained. To become truly useful, meta-DNA will need to be able to interact with proteins. Meta-DNA is also likely to perform reactions (like replication) much more slowly than normal protein enzymes, a point which Chandran acknowledged.
And not everyone sees the need for DNA-only systems in the first place. Though he calls the research “neat,” systems chemist Douglas Philp of the University of St Andrews in Scotland doesn’t feel that enzymes and RNA need replacing. “Proteins do enzymatic work, RNA can carry both information and catalyze reactions, and DNA carries information,” said Philp. “DNA is great for carrying information because it’s so stable,” but it’s the extraordinary complexity of protein structure that helps enzymes work so well. DNA’s monotonous propensity for the double helix could actually limit its applicability, he noted.