Table 1.

Comparison of genetic tags for CLEM

Genetic tag	MW (kDa)	FQY	1O2 QY	Advantages	Disadvantages	References
GFP	26.9	0.6	< 0.004	Bright fluorescence, well established technology	Poor photooxidizer, Very low reactive oxygen yield.	(Grabenbauer et al., 2005)
Tetracysteine/ ReAsH (present 4C or 4N generation).	2.22	0.42–0.47 *	0.024	Small size, versatility of ligands especially for pulse chase labeling at LM and EM levels	Low reactive oxygen yield, Limited diffusion and non-specific background of ligands	(Griffin et al., 1998a, Gaietta et al., 2002, Martin et al., 2005, Gaietta et al., 2006)
miniSOG/ FMN	15.4	0.37	0.47	Medium size between GFP an tetracysteine Very good singlet oxygen generator; FMN is an endogenous ligand. Strong EM signal after photooxidation.	Weak fluorescence, bleaches rapidly	(Shu et al., 2011)
HRP	34	NA	NA	Enzymatic reaction. Labeling limited to expressing cells. No photooxidation necessary. High sensitivity.	Needs to be combined with fluorescent protein (GFP) for LM Does not work in oxidized environments, limited so far to plasma membrane or ER targeting.	(Schikorski et al., 2007, Li et al., 2010, Schikorski, 2010)
Metallothionein (MTH)	6	NA	NA	When gold atoms bind, delivers high contrast. High spatial resolution. Relatively small tag size.	Needs to be combined with fluorescent protein (GFP) for LM Difficult to get gold atoms into cells, toxic.	(Mercogliano and DeRosier, 2006, 2007, Nishino et al., 2007, Diestra et al., 2009a, Diestra et al., 2009b)
Ferritin	19.4 †	NA	NA	Iron less toxic. Strong signal from iron cores. High spatial resolution.	Needs to be combined with fluorescent protein (GFP) for LM. Large size of label when oligomerized. Need to get exogenous iron atoms into cells for labeling.	(Wang et al., 2011)

FQY = fluorescence quantum yield; ¹O₂ QY = singlet oxygen quantum yield; NA = not applicable

^*Measurements done using FRET based emission of GFP-TC proteins

^†monomer size.