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. Author manuscript; available in PMC: 2019 Sep 26.
Published in final edited form as: Chem Rev. 2018 Sep 17;118(18):9412–9454. doi: 10.1021/acs.chemrev.7b00767

Table 1.

Switching properties of selected organic fluorophores for SR-imaging by SMLM.

Organic dye λex/ (nm) λem (nm) λon/off (nm) ε (M−1cm−1) QY Duty cycle # Photons # Cycles Refs
Alexa Fluor 647a,f 650 665 405/647 239,000 0.33 1.2×10−3 5,202 26 128
Alexa Fluor 647c,f 650 665 405/647 239,000 0.33 1.3×10−4 ~2400 NR 135
Alexa Fluor 750a,f 749 775 405/750 240,000 0.12 1×10−4 703 6 128
Alexa Fluor 750c,f 749 775 405/750 240,000 0.12 4×10−4 2800 NR 135
ATTO 488a,f 501 523 405/488 90,000 0.8 2.2×10−3 1,110 49 128
ATTO 488b,g 501 523 405/488 90,000 0.8 2×10−3 ~104 ~1 128,136
BODIPY FLa,g 503 512 405/488 80,000 0.97 1.8×10−2 756 3.4 214,215
Cy3Ba,f 559 570 405/561 130,000 0.67 4×10−4 2,057 5 128
Cy3Bb,g 559 570 405/561 130,000 0.67 3×10−3 ~105 ~1 128,136
Amino-DCDHFe,i 594 613 407 54,100 0.39 NR 2.3×106 1 212
DTE (4-Et)e,f 488 582 488 37,300 0.45 4×10−4 200-300 14 204
Dyomics 654a,f 654 675 405/647 220,000 NR 1.8×10−3 3,014 19 128
DyLight 750a,f 752 778 405/750 220,000 NR 2×10−4 749 6 128
ER-Tracker Reda,h 587 615 405/561 64, 300 NR 3×10−4 820 28 216
HMSiRe,g 650 672 NR 100,000 0.39 NR 2,600 ≥20 164
PA-JF549d,h 561 571 405 101,000 0.88 1×10−5 1.9×104 1 156,168
PA-JF646d,h 637 664 405 152,000 0.54 1.6×10−6 NR 1 156,168
OA-1 (open)e,j 532 650 355/532 83,000 0.02 NR 222 NR 189
SiRa,h 645 662 NR/640 100,000 0.39 NR 630 NR 154
SP (open)e,j 532 665 UV/532 52,000 0.17 NR 1.8×105 NR 112,217

Note: λex (excitation wavelength); λem (emission wavelength); λon/off (wavelengths for switching the fluorescence on and off, respectively); ε (extinction coefficient); QY (fluorescence quantum yield); duty cycle (fraction of time spent in the on state prior to photobleaching); # Photons (number of detected photons per localization event); # cycles (number of switching cycles); Refs (journal references for published data).

‘a’, ‘b’, ‘c’, ‘d’, and ‘e’

indicate the composition of the imaging cocktail: a) deoxygenated + thiol; b) deoxygenated + MVAA (methyl viologen and ascorbic acid) where fluorophores had been previously reduced with NaBH4; c) deoxygenated + TCEP + MVAA; d) deoxygenated; and e) no additives to the aqueous buffer.

‘f’, ‘g’, ‘h’, ‘i’ and ‘j’,

indicate the specimen used for fluorophore characterizations: f) fixed cells; g) antibody adsorbed to coverglass; h) live cells; i) fluorophores immobilized in PMMA (for quantum yield measurements) or gelatin (for other measurements); j) fluorophores on nanoparticles. ‘N.R.’ indicates the parameter was not reported.