Some additional information about this SNP assay is available from Molecular Devices. Free floating molecules in solution rotate, that is tumble about in all directions, at a speed proportional to their molecular weight. Thus, a small molecule containing a fluorophore will be spinning around rapidly, and a large molecule containing a fluorophore will be spinning around slowly.
Fluorescent molecules relax shortly after excitation and emit light.
If they are large molecules and rotating slowly then they will emit light in the same plane in which they were excited. If they are small molecules and rotating quickly then they will emit light in essentially every plane. Fluorescence polarization is defined as the ratio of the difference in fluorescence intensity measured between the parallel and perpendicular axes to the total florescence intensity. Large molecules will yield higher fluorescence polarization values than small molecules. A nucleotide covalently bonded to a fluorophore, at 1,000 Daltons, is small on the FP scale.