Synthesis of peptide nucleic acid FRET probes via an orthogonally protected building block for post-synthetic labeling of peptide nucleic acids at the 5-position of uracil

We report the design and synthesis of an orthogonally protected peptide nucleic acid (PNA) building block, Fmoc-PNA-U′-(Dde)-OH, and its use in the construction of PNA FRET probes. This building block allows for the post-synthetic attachment of reporter groups to the amino group attached to the 5-position of uracil (U) following selective deprotection of the Dde group. We illustrate the use of this building block for the synthesis of a series of FAM Cy5 donor acceptor pairs and their ability to detect a target DNA sequence.