Design Automation Software for DNA-Based Nano-Sensor Architectures

A continuing and growing threat to U.S. military personnel and civilians is exposure to toxic chemicals and pathogens. Useful detection systems exist, but it remains imperative to investigate next-generation technologies that have the potential to improve by an order of magnitude the cost, sensitivity and size of sensor devices. A promising technology that may achieve these goals is DNA-based nano-sensors. In order for DNA-based nano-sensors to become commercially viable, the technology needs automated assay design software. Towards this end, Celadon will partner with Dr. David H. Mathews, one of the few internationally recognized experts in the computation of nucleic acid structures. During Phase I, the Celadon/Mathews team will compute databases of optimal helices and loops; develop a heuristic algorithm so as to obviate the need to evaluate an entire, computationally intractable, structure; develop a new algorithm for design of pseudo-knots; develop draft versions of Product Requirements, Software Development and Validation Project Plan, Design Specifications, and Technical Specifications; and demonstrate proof-of-concept design software.