We synthesized flavin-containing PNA monomer unit 5 from lumiflavin and prepared PNAs containing a flavin moiety (FPNA) by the standard tBoc chemistry. Each PNA oligomer was purified by reversed-phase HPLC and characterized by MALDI-TOF MS and UV spectra. Thermodynamic analyses indicated that the PNA oligomer containing a flavin moiety near the amino terminal considerably stabilized the PNA–DNA hybrids.