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Updated: Jun 5, 2026

Conventional BODIPY Conjugates for Live-Cell Super-Resolution Microscopy and Single-Molecule Tracking
Published on: June 8, 2020
Highly substituted Bodipy dyes with spectroscopic features sensitive to the environment
Thomas Bura1, Pascal Retailleau, Gilles Ulrich
1Laboratoire de Chimie Moléculaire et Spectroscopies Avancées (LCOSA), ECPM, CNRS, 25 rue Becquerel, 67087 Strasbourg Cedex 02, France.
Abstract:
A general method for the synthesis of butterfly-shaped difluoroboradiaza-s-indacenes with different substituents has been developed. The mixed AB dye was produced in two successive Knoevenagel reactions involving first 4-dimethylaminobenzaldehyde and second 4-hydroxybenzaldehyde. Two pathways to A(2)B(2) and ABCD derivatives were investigated starting from a tetramethyl-substituted Bodipy. The pivotal compound is a bis-styryl phenol derivative also produced by a Knoevenagel reaction without the need to protect the phenol functions. Methylation of the phenol functions provides mono- and bis-derivatives which have been used to construct tetrastyryl A(2)B(2) and ABCD derivatives, respectively. Stepwise alkylation of the monomethoxyphenol dye provided a mixed dye that was converted to a tris-substituted compound, isolated as a mixture of regioisomers. The fourth styryl function was introduced by using 4-dimethylaminobenzaldehyde and forcing conditions. These highly colored dyes display outstanding optical properties with absorption wavelengths spanning from 573 to 718 nm and emission wavelengths from 585 to 800 nm. The high quantum yields, nanosecond excited state lifetimes, and weak Stokes shifts are typical of singlet emitters. The presence of both dimethylamino and phenol residues in some of these dyes makes them sensitive to acids and bases, allowing the tuning of the optical properties over a large wavelength range as a function of pH. A unique three-color ratiometric pH sensor based on both absorption and fluorescence has been characterized and studied in detail. The tris- and tetra-substitution of the methyl groups by vinyl residues induces a weaker bathochromic shift than that due to mono- and disubstitution. Consequently, replacing an alkoxy function by a dimethylamino moiety in the tetra-substituted derivatives has little effect on the spectroscopic features.
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