Facile syntheses of BODIPY derivatives for fluorescent labeling of the 3′ and 5′ ends of RNAs

As inexpensive and readily available fluorophores for 3′ and 5′ end labeling of RNA molecules, symmetrical BODIPY (boron dipyrromethene: 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) derivatives having a primary amino group were designed, and their facile synthetic route was established. Novel BODIPY derivatives exhibited photophysical properties comparable to commercially available BODIPY FL EDA (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionyl ethylenediamine). To confirm utility of new derivatives, specific labeling of the 3′ and 5′ ends of in vitro transcribed RNAs was carried out. Furthermore, the 3′ end of the 5′ fragment of the bimolecular Tetrahymena ribozyme was labeled, and its catalytic activity was investigated.