Figure 3. Gel and TEM analysis of folding conditions for three-dimensional DNA origami.

a, Cylinder models of shapes: monolith, stacked cross, railed bridge, and two versions of genie bottle, with corresponding scaffold sequences. b, Shapes were folded using different thermal-annealing ramps (1.2 h: 95°C to 20°C at 1.6 min/°C; 3 h, 6 h, 12 h, 18 h, 37 h, 74 h, 173 h: 80°C to 60°C at 4 min/°C, followed by 60°C to 24°C at 5, 10, 20, 30, 60, 120, or 280 min/°C, respectively) in 5 mM Tris, 1 mM EDTA, and 16 mM MgCl₂ and analyzed by gel electrophoresis (2% agarose, 0.5 × TBE, 11 mM MgCl₂). c–e, TEM and gel analysis of influence of MgCl₂ concentration on folding quality. c, The fastest-migrating bands in the 4 mM MgCl₂ lanes were purified and imaged, revealing gross folding defects. d, Shapes were folded with a 173 h ramp in 5 mM Tris, 1 mM EDTA, and MgCl₂ concentrations varying from 0 to 30 mM. e, As in c, leading bands were purified from the 16 mM MgCl₂ lanes and found to exhibit higher-quality folding when analyzed by TEM. f, Excess NaCl inhibits proper folding. Shapes were folded with 173 h ramp in 5 mM Tris, 1 mM EDTA, 16 mM MgCl₂, and varying NaCl concentrations.