3OK2

Crystal structure of the ANA:RNA decamer without lattice translocation defects


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.963 Å
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex.

Ovaere, M.Sponer, J.Sponer, J.E.Herdewijn, P.Van Meervelt, L.

(2012) Nucleic Acids Res. 40: 7573-7583

  • DOI: 10.1093/nar/gks470

  • PubMed Abstract: 
  • Altritol nucleic acids (ANAs) are a promising new tool in the development of artificial small interfering ribonucleic acids (siRNAs) for therapeutical applications. To mimic the siRNA:messenger RNA (mRNA) interactions, the crystal structure of the AN ...

    Altritol nucleic acids (ANAs) are a promising new tool in the development of artificial small interfering ribonucleic acids (siRNAs) for therapeutical applications. To mimic the siRNA:messenger RNA (mRNA) interactions, the crystal structure of the ANA:RNA construct a(CCGUAAUGCC-P):r(GGCAUUACGG) was determined to 1.96 Å resolution which revealed the hybrid to form an A-type helix. As this A-form is a major requirement in the RNAi process, this crystal structure confirms the potential of altritol-modified siRNAs. Moreover, in the ANA strands, a new type of intrastrand interactions was found between the O2' hydroxyl group of one residue and the sugar ring O4' atom of the next residue. These interactions were further investigated by quantum chemical methods. Besides hydration effects, these intrastrand hydrogen bonds may also contribute to the stability of ANA:RNA duplexes.


    Organizational Affiliation

    Department of Chemistry, Katholieke Universiteit Leuven, Biomolecular Architecture and BioMacS, Celestijnenlaan 200F, B-3001 Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
(A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)A,C,E11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
GGCAUUACGGB,D,F10N/A
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
PO4
Query on PO4
A, C, E
NON-POLYMERO4 P

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A6C
Query on A6C
A, C, E
RNA linkingC10 H16 N3 O8 PC
A6G
Query on A6G
A, C, E
RNA linkingC11 H16 N5 O8 PG
A6A
Query on A6A
A, C, E
RNA linkingC11 H16 N5 O7 PA
A6U
Query on A6U
A, C, E
RNA linkingC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.963 Å
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 26.070α = 90.00
b = 42.510β = 90.00
c = 157.790γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2014-11-19
    Type: Database references