5‐(Pyren‐1‐yl)uracil as a Base‐Discriminating Fluorescent Nucleobase in Pyrrolidinyl Peptide Nucleic Acids

A pyrene‐labeled uridine (U^Py) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2‐aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U^Py base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T_m) experiments. The fluorescence of the U^Py‐containing single‐stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7–41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U^Py and dA, making the U^Py‐modified acpcPNA useful as a hybridization‐responsive fluorescence probe for DNA‐sequence determination.