Agarose gel electrophoresis is commonly used to characterize DNA origami and DNA nanostructures on the MDa scale1. Agarose gels of DNA origami can be used to characterize if and how well a DNA origami structure has formed.
To determine whether a DNA origami structure has formed, it is important to run at least three wells. One well should consist of a DNA ladder to maintain consistency and comparability between runs. Another well should consist of only the DNA origami scaffold. Another well should be your synthesized DNA origami. The DNA origami well should have one clear band and it should migrate differently from your scaffold strand alone. Whether it migrates more or less than the scaffold depends on the shape of your origami. When staples are added in excess, they are present in the gel as a diffuse band at low molecular weights migrating further than scaffold and origami.
References
- Castro, C. E. et al. A primer to scaffolded DNA origami. Nat Methods 8, 221–229 (2011).