DNA nanostructure yield varies significantly by the class of structure chosen as well as the design. Typically scaffolded methods can achieve higher yield because staples can be added in excess, reducing concentration-dependent issues. Modifying staple routing, scaffold routing, and lattice arrangement all impact stability1. For a structure, modifying the staple and scaffold design can result in vast improvements of nanostructure yield. For a given design, experimental synthesis conditions also drastically affect the folding yield. Modifying the annealing protocol, cation concentration, and staple:scaffold ratio all can improve or hurt your yield.
To determine the yield, three methods are commonly used. Gel electrophoresis is used to pseudo-quantify folding yield by determining the ratio of intensity within the band corresponding to well-formed structure to the total intensity within the gel lane. Particle counting in atomic force microscopy (AFM) is a more quantitative, but more tedious, method for yield determination of 2D structures. Particle counting with transmission electron microscopy (TEM) is also a quantitative, but again tedious, method for yield determination of 3D structures.
References
- Aksel, T., J. Navarro, E., Fong, N. & Douglas, S. M. Design principles for accurate folding of DNA origami. Proceedings of the National Academy of Sciences 121, e2406769121 (2024).