Software for Design and Validation of DNA Nanostructure Surface Patterning

A continuing threat to U.S. military personnel and civilians is exposure to toxic chemicals and pathogens. While there exist methods and systems for vaccine development, agent detection, and assessment of exposure and immune response, it remains imperative to investigate next-generation technologies that have the potential to improve by an order of magnitude their cost, sensitivity, specificity, and speed. A promising technology is the self-assembly of charge-patterned DNA nanostructures on a flat surface. In order for patterned DNA nanostructures to become commercially viable, the technology needs investigation of the thermodynamics of self-assembly, both with and without charged pendants; development of predictive algorithms that take into account pendant thermodynamics and modified nucleic acids; and automated design software. Towards this end, Celadon will partner with Dr. Jason Kahn and Dr. David H. Mathews, both internationally recognized experts in nucleic acid chemistry and computation. During Phase I, the Celadon/Kahn/Mathews team will assemble origami surface with patterned hydrophilic and hydrophobic patches on ~5 nm scale; confirm with atomic force microscopy and fluorescence; conduct temperature-dependence studies and develop thermodynamic algorithms to predict assembly in presence of pendant groups; construct Phase II plan to develop predictive algorithm and software; and demonstrate prototype browser-based and Cloud-enabled user interface.