Single molecule spectroscopy allows to investigate heterogeneous behaviours on photochemical and structural grounds. We report on studies of the effect of the excitation intensity on the internal photodynamics of simple dyes immobilized on chemically etched glass slides. The use of the excitation intensity needed for two-photon excitation induces local heating, structural changes and transitions to dark states. Similar behaviour is found on single green fluorescent proteins immobilized on glass slides or embedded in silica gels upon single-photon excitation. However, by sampling the images with sufficiently low frequency, we are able to follow relevant biological events, such as the unfolding kinetics. We find that the glass slides are preferable in terms of the signal-to-noise ratio but the protein is not preserved in its native state, while evidence for the native conformation of the single proteins in the silica gels is found in the uniformity of the fluorescence emission.

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