Functionalization of the meso-phenyl ring of rhodamine dyes through SNAr with sulfur nucleophiles: Synthesis, biophysical characterizations, and comprehensive NMR analysis
Authors: Mitronova GY, Polyakova S, Wurm CA, Kolmakov K, Wolfram T, Meineke DN, Belov VN, John M, Hell SW
CellNetworks People: Hell Stefan
Journal: European Journal of Organic Chemistry, 2015(2), 337-349. doi: 10.1002/ejoc.201403269

Aromatic nucleophilic substitution (SNAr) of fluorine in 9-(3′-carboxy-4′,5′,6′,7′-tetrafluorophenyl) groups of xanthene dyes constitutes a powerful tool in dye design. Thiols and amines regioselectively replace F-6′. This approach enables additional hydrophilic residues or functional groups required for bioconjugation to be introduced. By using this methodology, a "bright" and photostable dye for two-color superresolution microscopy was synthesized (with absorption and emission maxima at 604 and 627 nm, respectively). In the case of red-emitting rhodamine dyes with 3′-carboxy-4′,5′,7′-trifluorophenyl residues, two-dimensional NMR techniques and a chemical transformation were used to prove the precise position of the additional substituent - a carboxylic acid group linked through the S-atom at C-6′. Furthermore, simple 1H NMR spectra reliably permit the position of the additional carboxy substituent in the 3′-carboxyphenyl ring (at C-5′ or C-6′) to be established. Information on the exact position of this substituent is significant for the design of molecular probes and for the prediction of the properties of their bioconjugates.