Design automation for DNA self-assembled nanostructures

DNA self-assembly is an emerging technology with potential as a future replacement of conventional lithographic fabrication. A key challenge is the specification of appropriate DNA sequences that are optimal according to specified metrics and satisfy various design rules. To meet this challenge we developed a thermodynamics-based design automation tool to evaluate the vast DNA sequence space (2.8k base pairs) and select appropriate sequences. We use this tool to design DNA nanostructures that were previously impossible with existing text distance based tools. We also show that for nanoscale structures our approach produces superior results compared to existing tools