Complex cooperativity in DNA origami revealed via design dependent defectivity

Abstract

DNA origami has become a ubiquitous platform for nanostructure fabrication because it enables straightforward design of structures 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 provide a rich environment in which to explore cooperativity in a complex system. The DNA domains comprising origami have predictable energetics and the sources of cooperativity are conceptually straightforward. While the assembly of these systems is difficult to predict because of the large number of cooperative interactions, it can be measured. We are thus 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 that 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.