Supplementary Figure 4: Example of how antibody-bearing microscopy images differ as a function of the geometry of target protein complexes and the size of probes.

See Supplementary Note 3 for related results text. (a) Cross section of a rectangular protein complex of interest, with an end-to-end length of 25 nm, and immunolabeled at the two lateral ends. (b) Cross section of a cylindrical protein complex of interest with a diameter of 25 nm, labeled from all sides. (c) Cross section of the same protein complex as in a, but labeled with a DNA-conjugated secondary antibody. Panel a and c show examples in which primary antibodies (green) bind only to the left and right surfaces of the protein complex. In panel a, fluorophore (yellow star)-labeled secondary antibodies (orange) are used. In panel c, DNA (purple line)-conjugated secondary antibodies (orange) are used. (d) The resulting fluorescence signal profiles (modeled by convolving the patterns of panels a-c with a FWHM of 22.8 nm, the point-spread function (PSF) of iExM excluding the label size (Supplementary Fig. 6b)) approximate how a small object might look when labeled with conventional antibodies (panel a and b) or DNA-conjugated antibodies (panel c) imaged via a super-resolution technique with a resolution of 22.8 nm (such as iExM).