3KNC

Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC).

Ovaere, M.Herdewijn, P.Van Meervelt, L.

(2011) Chemistry 17: 7823-7830

  • DOI: 10.1002/chem.201003594

  • PubMed Abstract: 
  • Cyclohexenyl nucleic acids (CeNA) are characterised by the carbon-carbon double bond replacing the O4'-oxygen atom of the natural D-2'-deoxyribose sugar ring in DNA. CeNAs exhibit a high conformational flexibility, are stable against nuclease activit ...

    Cyclohexenyl nucleic acids (CeNA) are characterised by the carbon-carbon double bond replacing the O4'-oxygen atom of the natural D-2'-deoxyribose sugar ring in DNA. CeNAs exhibit a high conformational flexibility, are stable against nuclease activity and their hybridisation is RNA selective. Additionally, CeNA has been shown to induce an enhanced biological activity when incorporated in siRNA. This makes CeNA a good candidate for siRNA and synthetic aptamer applications. The crystal structure of the synthetic CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC) has been solved with a resolution of 2.50 Å. The CeNA:RNA duplex adopts an anti-parallel, right-handed double helix with standard Watson-Crick base pairing. Analyses of the helical parameters revealed the octamer to form an A-like double helix. The cyclohexenyl rings mainly adopt the (3)H(2) conformation, which resembles the C3'-endo conformation of RNA ribose ring. This C3'-endo ring puckering was found in most of the RNA residues and is typical for A-family helices. The crystal structure is stabilised by the presence of hexahydrated magnesium ions. The fact that the CeNA:RNA hybrid adopts an A-type double helical conformation confirms the high potential of CeNAs for the construction of efficient siRNAs which can be used for therapeutical applications.


    Organizational Affiliation

    Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F-box 2404, 3001 Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR)P*(XGR)P*(XGR))-3'A9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'B8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
XAR
Query on XAR
A
DNA LINKINGC12 H16 N5 O5 P

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XTR
Query on XTR
A
DNA linkingC12 H17 N2 O7 PDT
XGR
Query on XGR
A
DNA LINKINGC12 H16 N5 O6 PDG
XCR
Query on XCR
A
DNA LINKINGC11 H16 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 41.919α = 90.00
b = 41.919β = 90.00
c = 68.444γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
MAR345data collection
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-01
    Type: Other
  • Version 1.3: 2017-11-01
    Type: Refinement description