Three-dimensional orientation measurements of symmetric single chromophores using polarization microscopy

A complete understanding of any complex molecular system generally requires a knowledge of the three-dimensional (3D) orientation of its components relative both to each other, and to directional perturbations such as interfaces and electromagnetic fields. Far-field polarization microscopy is a convenient and widespread technique for detecting and measuring the orientation of single chromophores. But because the polarized electromagnetic field that is used to probe the system lacks a significant longitudinal component, it was thought that, in general, only 2D orientation information could be obtained1,2,3. Here we demonstrate that far-field polarization microscopy can yield the 3D orientation of certain highly symmetric single chromophores (CdSe nanocrystal quantum dots in the present case). The key requirement is that the chromophores must have a degenerate transition dipole oriented isotropically in two dimensions, which gives rise to a perpendicular ‘dark axis’ that does not couple to the light field. By measuring the fluorescence intensity from the dipole as a function of polarization angle, it is possible to calculate both the tilt angle between the dark axis and the sample plane, as well as the in-plane orientation, and hence obtain the 3D orientation of the chromophore