3UKB

(R)-cEt-BNA decamer structure

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2011-11-09 Released: 2012-06-20 
  • Deposition Author(s): Pallan, P.S., Egli, M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


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


Literature

Structure and nuclease resistance of 2',4'-constrained 2'-O-methoxyethyl (cMOE) and 2'-O-ethyl (cEt) modified DNAs.

Pallan, P.S., Allerson, C.R., Berdeja, A., Seth, P.P., Swayze, E.E., Prakash, T.P., Egli, M.

(2012) Chem Commun (Camb) 48: 8195-8197

  • DOI: https://doi.org/10.1039/c2cc32286b
  • Primary Citation of Related Structures:  
    3UKB, 3UKC, 3UKE

  • PubMed Abstract: 

    Combining the structural elements of the second generation 2'-O-methoxyethyl (MOE) and locked nucleic acid (LNA) antisense oligonucleotide (AON) modifications yielded the highly nuclease resistant 2',4'-constrained MOE and ethyl bicyclic nucleic acids (cMOE and cEt BNA, respectively). Crystal structures of DNAs with cMOE or cEt BNA residues reveal their conformational preferences. Comparisons with MOE and LNA structures allow insights into their favourable properties for AON applications.

    • Organizational Affiliation: 

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*GP*TP*AP*(RCE)P*AP*CP*GP*C)-3')
A, B
10N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.022α = 90
b = 44.897β = 90
c = 44.911γ = 90
Software Package:
Software NamePurpose
MD2data collection
CCP4model building
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description