Laser-induced fluorescence quenching of red fluorescent dyes with green excitation: avoiding artifacts in PIE-FRET and FCCS analysis

Multicolor excitation is at the core of many fluorescence spectroscopy techniques such as PIE-FRET, ALEX-FRET, or FCCS. However, the influence of the multiple laser excitations on the dye photophysics is often overlooked. Here, we show that green laser pulses can surprisingly quench the fluorescence of common red dyes Alexa Fluor 647 and Atto 647N, even when the conditions leading to photobleaching are avoided. The physical origin of this phenomenon is discussed via a long-lived dark state and/or photorefractive effects. These observations are important to avoid measurement artifacts as both the fluorophore concentration and the fluorescence brightness are affected.