Abstract: Fluorescent-labeled substrates are provided for fluorescence polarization says of enzymes. These substrates are proteins labeled with derivatives of BODIPY.RTM., 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene. The BODIPY.RTM. fluorescent tag of the present invention is pH independent, and can be used over a pH range of from about 2 to about 11. Thus one can assay, in real time, enzymes with pH maxima at pH below 7 using fluorescence polarization methodology, which could not be done with fluorescein derivatives. Different enzymes can be compared using the same BODIPY.RTM. conjugate by merely changing the buffer system which changes the pH conditions.Fluorescence polarization assays of enzyme activity can be performed in the presence of whole bacteria and other finely suspended particles, such as might be present in tissue homogenates or cellular material. This is particularly useful for chairside assays on dental plaque or clinical assays on bacteria or tissue or exudates.