Purification of the DNA origami

After annealing, 1 μM Cy3-tagged single-stranded DNA (Integrated DNA Technologies; DNA sequence: 5′ Cy3-AAAAAAAAAAAAAAAAAAAA 3′, purification: high-performance liquid chromatography) was added to the DNA origami and incubated for at least 20 min at room temperature. Then, the DNA origami was separated from excess staple strands by spin filtration in a Biofuge Fresco microlitre centrifuge (Heraeus 75005521) using 100 kDa cut-off filters from Amicon (Amicon Ultra-15, PLHK Ultracel-PL Membran, UFC910008) at 4°C. The filter was placed in a clean microtube and centrifuged with 500 μL 1× TAE and 5 mM MgCl₂ for 5 min at 13,000 × g. Subsequently, 50 μL DNA origami topped up with 450 μL 1× TAE and 5 mM MgCl₂ were added, and the centrifugation step was repeated twice. Finally, the DNA origami-containing filters were centrifuged upside down for two minutes at 1,000 × g into a fresh microtube. The MgCl₂ concentration was adjusted back to 20 mM. To measure the DNA origami concentration, a NanoDrop ND-1000 Spectrophotometer (PEQLAB Biotechnologie, Erlangen, Germany) was used; typical concentrations were around 10 nM.