1XJ9

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.255 

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This is version 1.2 of the entry. See complete history. 

Literature

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.

(2005) J.Am.Chem.Soc. 127: 1424-1430

  • DOI: 10.1021/ja0458726

  • 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-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.

    Related Citations: 
    • 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

    Organizational Affiliation: 

    Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)A,B11N/A
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
CPN
Query on CPN
A, B
PEPTIDE-LIKEC10 H16 N5 O4

--

TPN
Query on TPN
A, B
PEPTIDE-LIKEC11 H17 N4 O5

--

GPN
Query on GPN
A, B
PEPTIDE-LIKEC11 H16 N7 O4

--

APN
Query on APN
A, B
PEPTIDE-LIKEC11 H16 N7 O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.255 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.600α = 90.00
b = 41.900β = 117.70
c = 30.100γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance