Design Software for DNA-Based Sensing Nano-Architectures

Beginning from an advanced stage of development, this Phase I SBIR project will produce design automation software for creating DNA nanostructures for a wide variety of applications, remedying a deficit that has stymied advancement in this promising field. Building atop an established grid computing platform, the software will combine a robust, easy-to-use, CAD (computer-aided design) interface, which allows for the specification of complex DNA-based nano-sensor architectures, with a grid-powered sequence optimization engine that computes the sequence-sets required for reliable self-assembly of specified designs. The research plan calls for the integration of a nearest neighbor thermodynamics model with an opportunistic evolutionary search algorithm to effect sequence optimization across a large-scale computational grid. These new capabilities will reduce defects and increase the manufacturing yield of designed nanostructures, and provide designers with novel control over the order of DNA self-assembly, which in turn will lead to products with enhanced functionality. To test the resultant software, a prototype nano-scale molecular capture system will be designed and its formation experimentally validated in Phase I. A capture and reporter bio-sensor system will be developed and demonstrated in Phase II.