1NR8

The crystal structure of a D-Lysine-based chiral PNA-DNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights into peptide nucleic acid (PNA) structural features: The crystal structure of a D-lysine-based chiral PNA-DNA duplex

Menchise, V.De Simone, G.Tedeschi, T.Corradini, R.Sforza, S.Marchelli, R.Capasso, D.Saviano, M.Pedone, C.

(2003) Proc.Natl.Acad.Sci.USA 100: 12021-12026

  • DOI: 10.1073/pnas.2034746100

  • PubMed Abstract: 
  • Peptide nucleic acids (PNAs) are oligonucleotide analogues in which the sugar-phosphate backbone has been replaced by a pseudopeptide skeleton. They bind DNA and RNA with high specificity and selectivity, leading to PNA-RNA and PNA-DNA hybrids more s ...

    Peptide nucleic acids (PNAs) are oligonucleotide analogues in which the sugar-phosphate backbone has been replaced by a pseudopeptide skeleton. They bind DNA and RNA with high specificity and selectivity, leading to PNA-RNA and PNA-DNA hybrids more stable than the corresponding nucleic acid complexes. The binding affinity and selectivity of PNAs for nucleic acids can be modified by the introduction of stereogenic centers (such as D-Lys-based units) into the PNA backbone. To investigate the structural features of chiral PNAs, the structure of a PNA decamer containing three D-Lys-based monomers (namely H-GpnTpnApnGpnAdlTdlCdlApnCpnTpn-NH2, in which pn represents a pseudopeptide link and dl represents a D-Lys analogue) hybridized with its complementary antiparallel DNA has been solved at a 1.66-A resolution by means of a single-wavelength anomalous diffraction experiment on a brominated derivative. The D-Lys-based chiral PNA-DNA (LPD) heteroduplex adopts the so-called P-helix conformation. From the substantial similarity between the PNA conformation in LPD and the conformations observed in other PNA structures, it can be concluded that PNAs possess intrinsic conformational preferences for the P-helix, and that their flexibility is rather restricted. The conformational rigidity of PNAs is enhanced by the presence of the chiral centers, limiting the ability of PNA strands to adopt other conformations and, ultimately, increasing the selectivity in molecular recognition.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction studies of a D-Lysine-based chiral PNA-DNA duplex
      Menchise, V.,De Simone, G.,Corradini, R.,Sforza, S.,Sorrentino, S.,Romanelli, A.,Saviano, M.,Pedone, C.
      (2002) Acta Crystallogr.,Sect.D 58: 553


    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 6, I-80134 Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*AP*GP*TP*GP*AP*TP*CP*TP*AP*C)-3'A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
H-((GPN)*(TPN)*(APN)*(GPN)*(A66)*(T66)*(C66)*(APN)*(CPN)*(TPN))-NH2B11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

--

CPN
Query on CPN
B
PEPTIDE-LIKEC10 H16 N5 O4

--

T66
Query on T66
B
L-PEPTIDE LINKINGC15 H25 N5 O5

--

A66
Query on A66
B
L-PEPTIDE LINKINGC15 H24 N8 O3

--

TPN
Query on TPN
B
PEPTIDE-LIKEC11 H17 N4 O5

--

GPN
Query on GPN
B
PEPTIDE-LIKEC11 H16 N7 O4

--

APN
Query on APN
B
PEPTIDE-LIKEC11 H16 N7 O3

--

C66
Query on C66
B
L-PEPTIDE LINKINGC14 H24 N6 O4

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 34.940α = 90.00
b = 34.940β = 90.00
c = 35.800γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance