DNA Computing Could Store and Process Data on Dendricolloids

For billions of years, living organisms have relied on long molecules of deoxyribonucleic acid, or DNA, to retain information and resolve problems.

Today, engineers are adapting DNA computing both to archive data and to function as biological computers. Until now, however, they have found it difficult to create a synthetic system capable of storing information and carrying out operations simultaneously.

DNA computing with dendricolloid scaffolds

Fresh research has shown that DNA can be packaged and arranged to do both jobs, delivering a complete range of computing capabilities from nucleic-acid strands. These include storing, reading, deleting, transferring and rewriting data, with each operation performed in programmable, repeatable ways much like those of an ordinary 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 enable exceptionally 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."

Storing and editing DNA data

DNA provides the codebase of living organisms, supplying molecular blueprints for biological structures and processes. In principle, though, these chemical strands could encode virtually any sequence of information. For years, scientists have been developing techniques to pack many types of data into freely floating DNA strands.

Rather than leaving the molecules free in solution, the team stored them on minute, tree-like structures known as dendricolloids. This allowed the code not only to be stored, but also to be edited continuously with much greater ease.

The system depends on being able to distinguish DNA information from the dendricolloid nanofibres that hold it. As a result, data can be copied into RNA (ribonucleic acid) for processing, or selected regions of DNA can be rewritten, without harming the original DNA 'files' or their storage material.

Long-term storage in a microscopic space

The branched dendricolloid scaffold also appears to protect stored DNA information more effectively than polymers in solution. Accelerated ageing analysis indicated that strands kept on dendricolloids at roughly 4 degrees Celsius would have a half-life of millennia. At colder temperatures, that lifespan might extend to millions of years.

Keung says a system of this kind could reliably hold the data equivalent of a thousand laptops in a space no larger than a pencil eraser, making it suitable for preserving enormous databases 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.

DNA computers remain far from widespread deployment, but the work demonstrates that such a system is achievable. The biological machine has already solved basic chess and sudoku problems – nowhere near supercomputer territory, but still an impressive result for microscopic molecules.

It is currently neither especially powerful nor especially fast. Nevertheless, DNA storage and computing offer the prospect of fitting immense quantities of information into an extraordinarily small area, using a medium that might outlast 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 has been published in Nature Nanotechnology.