Single-molecule high-resolution colocalization of single probes

Colocalization of fluorescent probes is commonly used in cell biology to discern the proximity of two proteins in the cell. Considering that the resolution limit of optical microscopy is on the order of 250 nm, there has not been a need for high-resolution colocalization techniques. However, with the advent of higher resolution techniques for cell biology and single-molecule biophysics, colocalization must also improve. For diffraction-limited applications, a geometric transformation (i.e., translation, scaling, and rotation) is typically applied to one color channel to align it with the other; however, to achieve high-resolution colocalization, this is not sufficient. Single-molecule high-resolution colocalization (SHREC) of single probes uses the local weighted mean transformation to achieve a colocalization resolution of at least 10 nm. This protocol describes the acquisition of registration data and the analysis required to obtain a high-resolution mapping between imaging channels. The total internal reflection fluorescence microscope (TIRFM) system described is designed to excite and image the fluorescent probes Cy3 and Cy5. Modifications may be required depending on the requirements of the individual study.