Design Automation Software for DNA-Based Nano-Sensor Architectures

A continuing and growing threat to US military personnel and civilians is exposure to toxic chemicals and pathogens. Useful detection systems exist, but it remains imperative to investigate new technologies that have the potential to significantly improve the cost, sensitivity, and size of sensor devices. A promising technology that may achieve these goals is DNA-based nono-sensors. In order for this technology to become viable, it needs automated assay design software. To achieve this, Celadon will collaborate with Dr. David Mathews, an expert in the computation of nucleic acid structures; and with Dr. Jason Kahn, an expert in dna structure and topology and nucleic acid thermodynamics. In Phase I, our team computed databates of optimal helices and loops; developed a heuristic algorithm that obviates the need to evaluate an entire structure; developed a new algorithm for design of psuedo knots, among other deliverables. In Phase II, we will nxnxnxnxnxnxnxnxn