These two dyes have slightly different chemical structure, which results to higher brightness, better contrast and photo stability for FM4-64 compared to FM1-43.

OK, I was just wondering if there was much of a difference besides its excitation/emission spectra. Thank You

Hi Matthew,

                      One of the striking differences between FM1-43 and FM4-64 to monitor endocytosis and exocytosis in neurons is their different hydrophobic properties. FM4-64 is slightly more hydophobic compared to FM1-43 and this can some times result in stronger binding of the dye to the plasma membrane and affect unloading of the dye when one follows the exocytosis (KCL stimulation). On the contrary one advantage of using FM4-64 is that this can be coupled with another functional signaling such as calcium influx (with Fluo-4 dye) or over expressing a GFP tagged protein of interest in neurons to study its function in endocytosis/exocytosis.

http://www2.cbm.uam.es/confocal/Manuales/FM4-64.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225589/

Thank you so much Karthik! Greatly appreciated.