Overcoming compound interference in fluorescence polarization-based kinase assays using far-red tracers

Kinase-mediated phosphorylation of proteins is critical to the regulation of many biological processes, including cell growth, apoptosis, and differentiation. Because of the central role that kinases play in processes that can lead to disease states, the targeting of kinases with small-molecule inhibitors is a validated strategy for therapeutic intervention. Classic methods for assaying kinases include nonhomogenous enzyme-linked immunosorbent assays or scintillation-based formats using [gamma-(32)P]ATP. However, homogenous fluorescence-based assays have gained in popularity in recent years due to decreased costs in reagent usage through miniaturization, increased throughput, and avoidance of regulatory costs associated with the use of radiation. Whereas the readout signal from a nonhomogenous or radioactive assay is largely impervious to interferences from matrix components (such as library compounds), all homogenous fluorescent assay formats are subject to such interferences. Interference from intrinsically fluorescent compounds or from scattered light due to precipitated compounds can interfere with assays that depend on a fluorescence intensity (or fluorescence quenching), fluorescence resonance energy transfer, or fluorescence polarization-based readout. Because these interfering factors show a greater effect at lower wavelengths, one strategy to overcome such interferences is to develop fluorescent assays using longer wavelength (red-shifted) fluorescent probes. In this article, we describe the PanVera PolarScreen far-red fluorescence polarization assay format, which mitigates assay interference from autofluorescent compounds or scattered light through the use of a far-red tracer. The tracer shows substantially less interference from light scatter or autofluorescent library compounds than do fluorescein-based tracers, and gives rise to a larger assay window than the popular far-red fluorophore Cy5.