1XJ9

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

Summary for 1XJ9

• Entry DOI: 10.2210/pdb1xj9/pdb
• Related: 176D 1NR8 1PDT 1PNN 1PUP 1RRU
• Descriptor: peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2) (2 entities in total)
• Functional Keywords: pna, peptide nucleic acid, partly self-complementary, duplex-triplex complex, right-handed, left-handed
• Total number of polymer chains: 2
• Total formula weight: 5607.75

Authors

Petersson, B.,Nielsen, B.B.,Rasmussen, H.,Larsen, I.K.,Gajhede, M.,Nielsen, P.E.,Kastrup, J.S. (deposition date: 2004-09-23, release date: 2005-02-22, Last modification date: 2023-11-15)

Primary citation

Petersson, B.,Nielsen, B.B.,Rasmussen, H.,Larsen, I.K.,Gajhede, M.,Nielsen, P.E.,Kastrup, J.S.
Crystal Structure of a Partly Self-Complementary Peptide Nucleic Acid (PNA) Oligomer Showing a Duplex-Triplex Network
J.Am.Chem.Soc., 127:1424-1430, 2005

PubMed Abstract: 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.

PubMed: 15686374
DOI: 10.1021/ja0458726

Experimental method

X-RAY DIFFRACTION (2.6 Å)