Complex cooperativity in DNA origami revealed via design-dependent defectivity

DNA origami has become a ubiquitous platform because it enables straightforward design of nanostructures that self-assemble with high yield. The interactions between the cooperative effects involved in its assembly are currently not well understood. Fortunately, the nearly infinite number of choices available to the origami designer provides a rich environment in which to explore cooperativity. The DNA domains comprising origami have predictable energetics, and the sources of cooperativity are conceptually straightforward, and the difficulty in predicting assembly comes from their large number of cooperative interactions. We are able to probe cooperativity by using design variations and measuring their effect on assembly yield. We employ an accelerated assembly protocol that increases the sensitivity of structural perfection, or lack thereof, to design variation, and apply this approach to survey a broad set of design features. Using the resulting dataset, we develop metrics to correlate thermal stability, beneficial cooperativity from short folds, and detrimental cooperativity from long folds, with defectivity. Surprisingly, these metrics can be combined to create a single parameter with a clear correlation to yield, which serves as a useful starting place for a predictive understanding of the interplay between cooperativity and design. In doing so, we also identify qualitative trends that provide useful insight into design best practice.