DNA Computing Uses Dendricolloid Scaffolds for Data Storage

For billions of years, living things have relied on lengthy deoxyribonucleic acid molecules, known as DNA, to retain information and tackle problems.

Engineers are now adapting DNA computing for their own purposes, using it to archive data and act as a biological computer. Until recently, however, they had found it difficult to create a synthetic system able to store information and carry out operations simultaneously.

DNA computing with dendricolloid scaffolds

A new study has shown that DNA can be packaged and arranged to do both jobs, delivering a complete set of computing capabilities from nucleic-acid strands. These include storing, reading, deleting, transferring and rewriting data in programmable, repeatable ways, much like a conventional computer.

In laboratory experiments, researchers at North Carolina State University (NC State) and Johns Hopkins University showed that their new nucleic-acid scaffold demonstrates the flexibility of DNA computing and could form the basis of remarkably compact biological machines.

"It's been thought that while DNA data storage may be useful for long-term data storage, it would be difficult or impossible to develop a DNA technology that encompassed the full range of operations found in traditional electronic devices," says NC State molecular biologist Albert Keung.

"We've demonstrated that these DNA-based technologies are viable, because we've made one."

DNA provides the underlying code for organisms, supplying molecular blueprints for biological processes and structures. In principle, though, these chemical strands could encode almost any ordered set of information. For years, scientists have been working on ways to pack many forms of data into freely floating DNA strands.

Storing and editing DNA information

Rather than keeping the molecules in solution, the team placed them on minute, tree-shaped structures called dendricolloids. This approach made it possible not only to store the code, but also to edit it continuously with much greater ease.

Central to the method is the ability to tell apart the DNA information and the dendricolloid nanofibres on which it is held. As a result, the data can be copied into RNA (ribonucleic acid) for processing, or selected sections of DNA can be rewritten, without harming either the original DNA ‘files’ or the storage material.

The branched dendricolloid scaffold also appears to protect DNA information better than polymers in solution. Accelerated ageing analysis indicated that strands kept on dendricolloids at about 4 degrees Celsius (about 39 degrees Fahrenheit) would have a half-life of millennia. At colder temperatures, that could extend to millions of years.

According to Keung, a system of this kind could reliably hold the equivalent of data filling a thousand laptops within an area no larger than a pencil eraser, enabling vast databases to be preserved over the long term.

"It essentially allows us to conduct the full range of DNA data storage and computing functions," says NC State chemical engineer Kevin Lin.

Potential for biological computers

DNA computers remain a considerable distance from widespread practical deployment, but this work establishes that such a system is achievable. The biological machine has already solved straightforward chess and sudoku problems - nowhere near supercomputer territory, but still notable for microscopic molecules.

At present, it is neither especially fast nor especially powerful. The appeal of DNA storage and computing instead lies in fitting immense quantities of information into an extremely small space, using a medium that might potentially survive longer than entire civilisations.

"We wanted to develop something that would inspire the field of molecular computing," says Keung. "And we hope what we've done here is a step in that direction."

The research was published in Nature Nanotechnology.