Gel extraction purifies DNA nanostructures based on electrophoretic mobility, not size like PEG purification and ultrafiltration do. This enables gel extraction to selectively purify correctly assembled DNA nanostructures from aggregates, free scaffold, excess staples, and even partially folded nanostructures. To perform gel extraction, researchers run an agarose gel as usual but load the wells with as much sample as possible. After the gel is run, the band corresponding to the origami is excised and then typically a crush-and-squeeze, freeze-and-squeeze, or a hybrid approach is used to elute the nanostructure from the agarose1.
Although this is considered the method that achieves the highest purity, gel extraction suffers from several limitations. The yield is typically much lower than other methods, and scaling to larger amounts of origami is more challenging. In addition, the time required is longer as gels are often run for over 1 hour. In addition, your use of DNA stain can affect the DNA structure2 and it is difficult to fully remove agarose from the final solution containing your origami.
References
- Wagenbauer, K. F. et al. How We Make DNA Origami. ChemBioChem 18, 1873–1885 (2017).
- Lee, J. Y., Kim, Y. & Kim, D.-N. Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies. Nat Commun 15, 6446 (2024).