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

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Britt Petersson, Bettina Bryde Nielsen, Hanne Rasmussen, Ingrid Kjøller Larsen, Michael Gajhede, Peter E Nielsen, Jette Sandholm Jensen Kastrup

The X-ray structure of a partly self-complementary peptide nucleic acid (PNA) decamer (H-GTAGATCACT-l-Lys-NH(2)) to 2.60 A 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 (G(4)A(5)T(6)C(7)). One right- and one left-handed Watson-Crick duplex are formed. The two PNA units C(9)T(10) change helical handedness, so that each PNA strand contains both a right- and a left-handed section. The changed handedness in C(9)T(10) allows formation of Hoogsteen hydrogen bonding between C(9)T(10) and G(4)A(5) 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 A(3) forms a noncanonical base pair with A(8) 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.
Original languageEnglish
JournalJournal of the American Chemical Society
Volume127
Issue number5
Pages (from-to)1424-30
Number of pages7
ISSN0002-7863
DOIs
Publication statusPublished - 9 Feb 2005

    Research areas

  • Base Pairing, Crystallography, X-Ray, Hydrogen Bonding, Models, Molecular, Peptide Nucleic Acids

ID: 44730035