Crystal Structure of a Partly Self-Complementary Peptide Nucleic Acid (PNA) Oligomer Showing a Duplex-Triplex NetworkPetersson, B., Nielsen, B.B., Rasmussen, H., Larsen, I.K., Gajhede, M., Nielsen, P.E., Kastrup, J.S.
(2005) J.Am.Chem.Soc. 127: 1424-1430
- PubMed: 15686374
- DOI: 10.1021/ja0458726
- PubMed Abstract:
- Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution
Rasmussen, H.,Kastrup, J.S.,Nielsen, J.N.,Nielsen, J.M.,Nielsen, P.E.
(1997) Nat.Struct.Mol.Biol. 4: 98
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-compleme ...
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.
Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.