New fluorescent dyes based on 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) and functionalized with a free carboxyl group have been conveniently synthesized from pyrroles and dicarboxylic anhydrides in one-pot reactions. Their spectral properties in different solvents showed little effect of solvatochromism (<10 nm). The methyl groups on the BODIPY skeleton benefit the fluorescence quantum yields (Phi(f) up to 0.80 in water) but affect the photostability of the dyes. Photooxidation and photodegradation experiments suggest that dyes 1a and 2a exhibit excellent photostability, especially in water, and several factors were taken into account to elucidate the experimental phenomena. Dyes 1c and 2c, derived from 1a and 2a via the esterification of NHS (N-hydroxysuccinimidyl ester), can be easily acquired in high yields (>90%). Single crystal X-ray structures of dyes 2c and 3a are also obtained and discussed. The fluorescence labeling of BSA and followed prestaining method for gel electrophoresis of BSA demonstrate that the protein can be directly observed by naked eyes at as low as 2 ng level under a normal UV fluorescence electrophorogram gel image system.

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