Super-Resolution Imaging of Fluorophore-Labeled DNA Bound to Gold Nanoparticles: A Single-Molecule, Single-Particle Approach

We use a triplet-state-mediated super-resolution technique to map the location of individual fluorescently labeled double-stranded DNA (dsDNA) bound to the surface of gold nanorods. By calculating the emission center position for each fluorescent tag on the nanoparticle surface, we successfully reconstruct the orientation and shape of the underlying gold nanorods but fail to reconstruct the expected size of the nanorods. We have tested several experimental strategies to address the size mismatch issue, including using a more rigorous model to fit the contribution of the gold nanorod luminescence to the overall signal, tuning fluorophore coverage density and fluorophore identity, and increasing the spacing between the gold nanorod and the fluorescent tag. Although each experiment provided additional insight into the system, the size mismatch issue has not been resolved. However, in all experiments, we observe differences in the apparent locations of where the dsDNA is bound to gold nanorods, an observation that is not attainable with ensemble studies, indicating the power of super-resolution fluorescence imaging for understanding surface binding heterogeneity.