BODIPY-modified uridines as potential fluorescent probes for nucleic acids that are recognized by DNA-polymerases

Abstract

A new type of BODIPY-modified uridines that contain the fluorophore attached to the 5-position of uridine via a short phenylene bridge have been prepared and characterized by methods of the optical spectroscopy and electrochemistry. The spectroscopic and redox properties can be manipulated by substituent and ligand exchange. After synthetic incorporation into DNA via phosphoramidite chemistry the canonical base pairing is maintained due to the rigid phenylene bridge. Moreover, primer extension experiments show that BODIPY-modified uridines are still recognized as thymidine derivatives by DNA-polymerases and adenine is inserted as the correct counter base.