Title :
Design automation for DNA self-assembled nanostructures
Author :
Pistol, Constantin ; Lebeck, Alvin R. ; Dwyer, Chris
Author_Institution :
Dept. of Comput. Sci., Duke Univ., Durham, NC
Abstract :
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
Keywords :
DNA; biocomputing; electronic design automation; thermodynamics; DNA self assembled nanostructures; DNA sequences; nanoscale structures; thermodynamics-based design automation tool; Algorithm design and analysis; Assembly; Computer science; DNA; Design automation; Design optimization; Fabrication; Nanostructures; Self-assembly; Sequences; Algorithms; DNA self-assembly; Design; Experimentation; Theory; nanostructure design; optimized self-assembly;
Conference_Titel :
Design Automation Conference, 2006 43rd ACM/IEEE
Conference_Location :
San Francisco, CA
Print_ISBN :
1-59593-381-6
DOI :
10.1109/DAC.2006.229413
