A table providing information on several commonly used single molecule probes for super resolution microscopy. Color is the color of light emitted by the fluorescent molecule in the on state, εabs is the extinction coefficient, λex and λem are the excitation and emission coefficients respectively, ηfl (%) is the quantum yield, τfl is the fluorescence lifetime, N is the number of photons detected per molecule per imaging cycle, NA and ND are not applicable and not determined respectively. Used with permission5.
| Color | λ ex (nm) | λ em (nm) | ε abs (M−1 cm−1) | η fl (%) | τ fl (ns) | N | Used for | |
|---|---|---|---|---|---|---|---|---|
| Regular fluorescent dyes | ||||||||
| ATTO532 | Orange | 532 | 553 | 115 000 | 90 | 3.8 | ND | STED |
| Photoswitchers | ||||||||
| Rhodamine B | Red | 530 | 620 | 105 000 | 65 | ND | 750 | PALMIRA |
| Alexa Fluor 647a | Red | 650 | 665 | 240 000 | 33 | 1.0 | 6000 | STORM |
| Cy5a | Red | 649 | 664 | 250 000 | 28 | 1.0 | 6000 | STORM |
| Cy5.5a | Red | 675 | 694 | 190 000 | 23 | 1.0 | 6000 | STORM |
| Cy7a | NearIR | 747 | 767 | 200 000 | 28 | <0.3 | ∼1000 | STORM |
| Photocaged fluorophores | ||||||||
| Caged Q-rhodamine | Red | 545 | 575 | 90 000 | 90 | ND | ND | PALM |
| Caged carboxyfluorescein | Green | 494 | 518 | 29 000b | 93 | 4.6 | ND | FPALM |
a
Photoactivation of these fluorophores is strongly facilitated by the presence of an activator fluorophore, such as Cy2, Cy3 or Alexa Fluor 405, to induce photoswitching.
b
The extinction coefficient is estimated at physiological pH.