I measure the intensity and polarization of light emitted from a blood sample that contains excited fluorescein (experiment known as fluorescence polarization assay). The excitation is done, as usual, with vertically polarized light.
In case the sample has certain macromolecules of interest (an antibody, in this case), the fluorescein links to the much-larger macromolecules, yielding a higher polarization factor, giving a positive- or "sick"- result. Alternatively, if there is no antibody, the excited fluorescein randomly rotates and then emits light, and the polarization factor is smaller giving a negative-or "healthy"- result.
I find that the light intensity (in both vertical and perpendicular polarizations) decreases for the positive case. Why is that so? Could it be that a non-radiative process like FRET acts stronger for fluorescein linked to macromolecules than for free fluorescein?
EDIT 1: I have used two different intensity detection systems, PMTs and SiPMs, and got similar behaviours.