3.

Hollow DNA origami box separation is sensitive to centrifugal force. (A) Agarose gel showing the lack of staples when the assemblies are purified at 5000 g for 20 min compared to 20,000 g for 5 min. (B) DNA origami and (C) normalized staple band fluorescence intensities for closed box assemblies (red), one-lid-open box assemblies (light blue), and two-lids-open box assemblies (dark blue) shown in (A). DNA origami and staple intensities were normalized by dividing the intensity of a particular band by the sum of all band intensities for a particular sample in one lane. (D) In solution AFM images of the origami structures obtained after purification at each of the two centrifugal forces (3 μM DNA origami). Solid white boxes show DNA origami structures within the expected size. Dashed white boxes show particles too small to be DNA origami structures. The scale bar represents 200 nm. (E) Quantification of number of DNA origami boxes vs small box fragments. Counting was performed on one AFM image from a single gradient-temperature assembly experiment per condition.