They have a lipophilic tail at one end and a highly hydrophilic, cationic head group at the other end. They are virtually non-fluorescent in solution, but when added to cells, insertion of the lipophilic tails into the plasma membrane causes the dyes to become intensely fluorescent.

These dyes can be used to label membranes and vesicles in many cell types, but they are commonly called nerve terminal dyes or synaptic vesicle dyes due totheir utility for dynamic tracking of synaptic vesicles in cultured neurons and tissue preparations). When applied to neurons, the dyes are incorporated into synaptic vesicles by endocytosis (termed the “on-rate”). After extracellular dye is quenched or washed away, the fluorescent vesicles can be imaged over time. During exocytosis and neurotransmitter release, the dyes also are released from the vesicles, causing a decrease in fluorescence signal (or “off-rate”).

C18 and AM3-25 are high molecular weight dyes that cannot pass through ion channels that have been used as controls to distinguish mechanisms of dye uptake.