 cyanine dyes have been shown to undergo reversible photoswitching , where the fluorophore can be switched between a fluorescent state and a dark state upon illumination at different wavelengths . 
 the photochemical mechanism by which switching occurs has yet to be elucidated . in this study , we have determined the mechanism of photoswitching by characterizing the kinetics of dark state formation and the spectral and structural properties of the dark state . 
 the rate of switching to the dark state depends on the concentration of the primary thiol in the solution and the solution ph in a manner quantitatively consistent with the formation of an encounter complex between the cyanine dye and ionized thiol prior to their conjugation . 
 mass spectrometry suggests that the photoconversion product is a thiolcyanine adduct in which covalent attachment of the thiol to the polymethine bridge disrupts the original conjugated -electron system of the dye . 
Supplementary Material