Structural Contributions to Hydrodynamic Diameter for Quantum Dots Optimized for Live-Cell Single-Molecule Tracking

Quantum dots are fluorescent nanoparticles with narrow-band, size-tunable, and long-lasting emission. Typical formulations used for imaging proteins in cells are hydrodynamically much larger than the protein targets, so it is critical to assess the impact of steric effects deriving from hydrodynamic size. This report analyzes a new class of quantum dots that have been engineered for minimized size specifically for imaging receptors in narrow synaptic junctions between neurons. We use fluorescence correlation spectroscopy and transmission electron microscopy to calculate the contributions of the crystalline core, organic coating, and targeting proteins (streptavidin) to the total hydrodynamic diameter of the probe, using a wide range of core materials with emission spanning 545-705 nm. We find the contributing thickness of standard commercial amphiphilic polymers to be ~8 to ~14 nm, whereas coatings based on the compact ligand HS-(CH₂)₁₁ ^- (OCH₂CH₂)₄-OH contribute ~6 to ~9 nm, reducing the diameter by ~2 to ~5 nm, depending on core size. When the number of streptavidins for protein targeting is minimized, the total diameter can be further reduced by ~5 to ~11 nm, yielding a diameter of 13.8-18.4 nm. These findings explain why access to the narrow synapse derive primarily from the protein functionalization of commercial variants, rather than the organic coating layers. They also explain why those quantum dots with size around 14 nm with only a few streptavidins can access narrow cellular structures for neuronal labeling, whereas those >27 nm and a large number of streptavidins, cannot.