Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network

Abstract

The X-ray structure of a partly self-complementary peptide nucleic acid (PNA) decamer (H-GTAGATCACT-L-Lys-NH2) to 2.60 Å resolution is reported. The structure is mainly controlled by the canonical Watson-Crick base pairs formed by the self-complementary stretch of four bases in the middle of the decamer (G4A5T6C7). One right- and one left-handed Watson-Crick duplex are formed. The two PNA units C 9T10 change helical handedness, so that each PNA strand contains both a right- and a left-handed section. The changed handedness in C9T10 allows formation of Hoogsteen hydrogen bonding between C9T10 and G4A5 of a PNA strand in an adjacent Watson-Crick double helix of the same handedness. Thereby, a PNA-PNA-PNA triplex is formed. The PNA unit A3 forms a noncanonical base pair with A8 in a symmetry-related strand of opposite handedness; the base pair is of the A-A reverse Hoogsteen type. The structural diversity of this PNA demonstrates how the PNA backbone is able to adapt to structures governed by the stacking and hydrogen-bonding interactions between the nucleobases. The crystal structure further shows how PNA oligomers containing limited sequence complementarity may form complex hydrogen-bonding networks.