Extended Data Fig. 4: RESI in 3D DNA origami.
a, DNA origami design featuring one pair of orthogonal docking strands (red R1, blue R3) as well as six alignment docking strands (green R4). Docking strands extend from both the top and bottom surface of the DNA origami (insert). b, The design ensures that all but the R1/R3 docking strand pair are spaced sufficiently to be resolved by DNA-PAINT. c, 3D DNA-PAINT imaging resolves R4 alignment sites, barely resolves R1/R3 axially and does not resolve R1/R3 laterally. d, Sequential 3D DNA-PAINT imaging with R4 sites used for alignment. e, RESI resolves R1/R3 both axially and laterally. f, An overlay of 88 DNA origami reveals overall good alignment despite structural heterogeneity. g, Average of 88 DNA origamis. h, The particle average recovers the structure with an alignment uncertainty of 0.7 nm CI = [0, 1.6] nm, showing a distance between the average R1/R3 positions of 11.6 ± 0.8 nm (xy-distance: 2.5 ± 0.4 nm, z-distance: 11.3 ± 0.8 nm), matching the designed distances20. Same scale applies to all magnification panels. CI describes 68% confidence interval.
