In a paper titled ‘Diverse and robust molecular algorithms using reprogrammable DNA self-assembly’, the international team designed DNA molecules that can carry out reprogrammable computations, for the first time creating so-called algorithmic self-assembly in which the same hardware can be configured to run different software.
Prof Damien Woods is joint lead author of the study whose leadership also includes Prof Erik Winfree of Caltech and Prof David Doty of University of California Davis. Co-authors of the paper include Cameron Myhrvold, Joy Hui and Peng Yin of Harvard University, and Felix Zhou of the University of Oxford.
Funding to support this research came from the National Science Foundation and NASA. Woods’ ongoing work is being supported by the European Research Council, Science Foundation Ireland and Maynooth University.
The era of nano apps is here
“Think of them as nano apps,” said Woods. “The ability to run any type of software program without having to change the hardware is what allowed computers to become so useful. We are implementing that idea in molecules, essentially embedding an algorithm within chemistry to control chemical processes.”
While silicon computers use electricity flowing through circuits to carry out tasks, the molecular computers attach strands of DNA together to make larger objects that execute a program effectively, in computer terminology, manipulating ‘bits’.
According to the research, 21 different DNA programs have been developed; for example, determining whether 6-bit inputs such as 011001 contain an odd or even number of ones, or are palindromes (which read the same backwards as they do forward). Another generates random numbers.
The end result is a test tube filled with billions of completed algorithms, each one resembling a knitted scarf of DNA, representing a readout of the computation.
The pattern on the ‘scarf’ gives the solution to the algorithm that was run. The system can be reprogrammed to run a different algorithm by simply selecting a different subset of strands from the roughly 700 that constitute the system.
The algorithms have been able to carry out a variety of tasks, including drawing repeating and random patterns, counting to 63, and performing equality checks.
“We were surprised by the versatility of programs we were able to design, despite being limited to 6-bit inputs,” said Woods, who also carried out some of his research while based at the French national institute for computer science, Inria.
“When we began experiments, we had only designed three programs,” Doty added. “But once we started using the system, we realised just how much potential it has. It was the same excitement we felt the first time we programmed a computer, and we became intensely curious about what else these strands could do. By the end, we had designed and run a total of 21 circuits.”
Although DNA computers have the potential to perform more complex computations than the ones featured in the Nature paper, Winfree cautioned that one should not expect them to start replacing the standard silicon microchip computers. Nor would Woods be drawn on potential applications in obvious areas such as medicine and biotechnology.
“That is not the point of our work. We are showing what can be done and it will be up to others to apply it to the real world. No one would have foreseen the iPhone back in Turing’s day, for example. We are proving what can be done at a molecular level, which opens up a whole world of possibilities.”
The breakthrough was welcomed by Maynooth University vice-president for research and innovation, Prof Ray O’Neill.
“The work of Damien and his colleagues is truly groundbreaking and gives a genuinely exciting sense of what is possible in the new world of molecular computing. Our students will undoubtedly be beneficiaries of this. We are delighted to have welcomed Damien back home to Maynooth and look forward to future developments of this research.”
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