Optical imaging of individual biomolecules in densely packed clusters

Recent advances in fluorescence super-resolution microscopy have allowed subcellular features and synthetic nanostructures down to 10-20 nm in size to be imaged. However, the direct optical observation of individual molecular targets (similar to 5 nm) in a densely packed biomolecular cluster remains a challenge. Here, we show that such discrete molecular imaging is possible using DNA-PAINT (points accumulation for imaging in nanoscale topography) a super-resolution fluorescence microscopy technique that exploits programmable transient oligonucleotide hybridization on synthetic DNA nanostructures. We examined the effects of a high photon count, high blinking statistics and an appropriate blinking duty cycle on imaging quality, and developed a software-based drift correction method that achieves <1 nm residual drift (root mean squared) over hours. This allowed us to image a densely packed triangular lattice pattern with similar to 5 nm point-to-point distance and to analyse the DNA origami structural offset with angstrom-level precision (2 A) from single-molecule studies. By combining the approach with multiplexed exchange-PAINT imaging, we further demonstrated an optical nanodisplay with 5 x 5 nm pixel size and three distinct colours with <1 nm cross-channel registration accuracy.