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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 3.

Example affinity stain probes used in SMLM.

Target Basis of Affinity Recognition Mechanism Examples used in SMLM
Mitochondria Positive charge of dye and/or ligand Mitochondria negative potential in live cells attracts cationic, membrane permeable dyes MitoTracker Orange,216 MitoTracker Red,216,338 MitoTracker Deep Red,216 Rhodamine 123,338 TMRE338, RhoB-HMSiR339
Plasma Membrane Appended hydrophobic group (e.g., octadecane) Hydrophobic group partitions dye to plasma membrane; uptake may follow DiI/DiD/DiR216, DiI-C6-HMSiR339
Endoplasmic Reticulum (ER) Lipophilic framework or glibenclamide (containing sulfonylurea group) Lipophilic affinity or binding between sulfonylurea and its potassium channel receptor enriched on ER ER-Tracker Red,216 Nile Red338,340, Cer-HMSiR339
Golgi Appended ceramide or sphingomyelin group Interaction with endogenous lipids and cholesterol Cer-HMSiR339
Lysosomes Appended weakly basic amine linker Protonation-induced accumulation in acidic environment of lysosomes LysoTracker Red,216 LysoTracker Green338
DNA Polycyclic, aromatic, and planar Intercalation, π- π stacking Picogreen,120,341 YOYO-1120,342
Filamentous actin Appended phalloidin group Phalloidin binds interface of polymerized actin subunits Phalloidin-Alexa Fluor 647343