Nitroazole universal bases in peptide nucleic acids

[formula: see text] The syntheses of PNA oligomers containing potential ambiguous nucleobase analogues, namely 3-nitropyrrole and 5-nitroindole, have been accomplished. Hybridization properties of these PNAs with complementary oligodeoxynucleotides were evaluated by thermal denaturation experiments. Both novel residues exhibited little variation in Tm (< or = 1.5 degrees C) when positioned against any of the four nucleoside bases. The capability to incorporate degenerate sites should further expand the utility of PNA in applications where precise sequence information is not available.