ISDA

Deposition Date 2004-09-23

Release Date 2005-02-22

Last Version Date 2023-11-15

Entry Detail

PDB ID:

1XJ9

Keywords:

PEPTIDE NUCLEIC ACID

Title:

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

Biological Source:

Source Organism:

(Taxon ID: ) (Taxon ID: )

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.60 Å

R-Value Free:

0.27

R-Value Work:

0.25

Space Group:

C 1 2 1

Download Validation Report

Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)
Chain IDs:A, B
Chain Length:11
Number of Molecules:2
Biological Source:

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
APN	A	DA	?
CPN	A	DC	?
GPN	A	DG	?
TPN	A	DT	?

Primary Citation

Crystal Structure of a Partly Self-Complementary Peptide Nucleic Acid (PNA) Oligomer Showing a Duplex-Triplex Network

Petersson, B, Nielsen, B.B, Rasmussen, H, Larsen, I.K, Gajhede, M, Nielsen, P.E, Kastrup, J.S, Rasmussen, H, Kastrup, J.S, Nielsen, J.N, Nielsen, J.M, Nielsen, P.E.Show

J.Am.Chem.Soc. 127 1424 1430 (2005)

PMID: 15686374 DOI: 10.1021/ja0458726

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures