Synthesis of 3′-BODIPY-Labeled Active Esters of Nucleotides and a Chemical Primer Extension Assay on Beads

A solution-phase synthesis of active esters of 3'-fluorophore-labeled deoxynucleoside 5'-monophosphates was developed for thymine and cytosine as nucleobases by using two different BODIPY dyes. Starting from the respective 2'-amino-2',3'-dideoxynucleoside-5'-monophosphate, the fluorescent oxyazabenzotriazolides can be prepared in one-pot procedures involving labeling and activation. Screening of a range of supports led to a chemical primer extension assay on beads with in situ detection of nucleobases in target DNA through optical read-out.