Bioorthogonal peptide nucleic acids with five-membered rings

Abstract Nature relies on nucleobase complementation to store and deploy genetic information. Peptide nucleic acids (PNAs) are nucleic acid analogues widely adopted for their high biological stability and robust sequence-specific nucleobase complementation properties. Here, we report a strategy to modify PNAs, affording bioorthogonal analogues that hybridize to one another without binding to complementary nucleic acids under physiological conditions. Chiral cyclopentane and tetrahydrofuran rings are incorporated into the PNA backbone to promote left-handed helical conformations, opposite to the right-handed helix adopted by DNA and RNA. The binding of left-handed PNAs (LH-PNAs) to DNA and RNA is evaluated using melting temperature ( T m ) experiments and circular dichroism (CD) experiments. The binding of LH-PNAs in the presence of right-handed PNA (RH-PNA) and DNA is examined using analytical HPLC. Results suggest that only a few left-handed substitutions at the center of PNA sequences attain bioorthogonal properties. These findings may facilitate the use of LH-PNAs for a range of applications in bioorthogonal chemical space.