Mar 20, 2019
(Nanowerk News) Computer scientists at University of California, Davis, Maynooth University in Ireland and the California Institute of Technology have created DNA molecules that can self-assemble into patterns essentially by running their own program. The work is published in the journal Nature ("Diverse and robust molecular algorithms using reprogrammable DNA self-assembly").
"The ultimate goal is to use computation to grow structures and enable more sophisticated molecular engineering," said David Doty, assistant professor of computer science at UC Davis and co-first author on the paper.
The system is analogous to a computer, but instead of using transistors and diodes, it uses molecules to represent a six-bit binary number (for example, 011001). The team developed a variety of algorithms that can be computed by the molecules.
Computer scientists have created DNA molecules that can self-assemble by carrying out a Boolean logic computation. Highlighted in green is the “circuit diagram” made up of DNA tiles that fit together according to inputs and outputs. Below is an atomic force microscope image of a self-assembled DNA ribbon that carried out the same computation. In the background are other ribbons, with different barcode labels, that carried out different computations. (Image: Demin Liu and Damien Woods)
"We were surprised by the versatility of algorithms we were able to design, despite being limited to six-bit inputs," Doty said. The researchers were able to design and run 21 algorithms over the course of the experiments, demonstrating the potential of the system, he said.
Working initially as postdoctoral scholars with Professor Erik Winfree at Caltech, Doty and co-lead author Damien Woods, now at Maynooth University, designed a library of short pieces, or tiles, of DNA. Each DNA tile consists of 42 bases (A, C, G or T) arranged in four domains of 10-11 bases. Each domain can represent a 1 or 0 and can stick to some of the domains on other tiles. No two tiles are a complete match.