2KWG

Solution structure of a fully modified 2'-F/2'-OMe siRNA construct


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Solution-state structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA construct.

Podbevsek, P.Allerson, C.R.Bhat, B.Plavec, J.

(2010) Nucleic Acids Res. 38: 7298-7307

  • DOI: 10.1093/nar/gkq621

  • PubMed Abstract: 
  • A high-resolution solution structure of a stable 42-nt RNA dimeric construct has been derived based on a high number of NMR observables including nuclear overhauser effects (NOEs), J-coupling constants and residual dipolar couplings (RDCs), which wer ...

    A high-resolution solution structure of a stable 42-nt RNA dimeric construct has been derived based on a high number of NMR observables including nuclear overhauser effects (NOEs), J-coupling constants and residual dipolar couplings (RDCs), which were all obtained with isotopically unlabeled molecules. Two 21-nt siRNA that efficiently hybridize consist of ribose units that were alternately substituted by 2'-fluoro or 2'-methoxy groups. Structure calculations utilized a set of H-F RDC values for all 21 2'-fluoro modified nucleotides under conditions of weak alignment achieved by Pf1 phages. A completely 2'-F/2'-OMe modified dimeric RNA construct adopts an antiparallel double-helical structure consisting of 19 Watson-Crick base pairs with additional 3' UU overhangs and a 5' phosphate group on the antisense strand. NMR data suggest that the stability of individual base pairs is not uniform throughout the construct. While most of the double helical segment exhibits well dispersed imino resonances, the last three base pairs either display uncharacteristic chemical shifts of imino protons or absence of imino resonances even at lower temperatures. Accessibility of imino protons to solvent exchange suggests a difference in stability of duplex ends, which might be of importance for incorporation of the guide siRNA strand into a RISC.


    Organizational Affiliation

    Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*(GF2)P*(OMG)P*(GF2)P*(OMU)P*(AF2)P*(A2M)P*(AF2)P*(OMU)P*(AF2)P*(OMC)P*(AF2)P*(OMU)P*(UFT)P*(OMC)P*(UFT)P*(OMU)P*(CFZ)P*(A2M)P*(UFT)P*(OMU)P*(UFT))-3'A21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(P*(A2M)P*(UFT)P*(OMG)P*(AF2)P*(A2M)P*(GF2)P*(A2M)P*(AF2)P*(OMU)P*(GF2)P*(OMU)P*(AF2)P*(OMU)P*(UFT)P*(OMU)P*(AF2)P*(OMC)P*(CFZ)P*(OMC)P*(UFT)P*(OMU))-3'B21N/A
Small Molecules
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
A, B
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
A, B
RNA LINKINGC10 H15 N2 O9 PU
GF2
Query on GF2
A, B
DNA linkingC10 H13 F N5 O7 PDG
UFT
Query on UFT
A, B
DNA LINKINGC9 H12 F N2 O8 PDU
OMC
Query on OMC
A, B
RNA LINKINGC10 H16 N3 O8 PC
AF2
Query on AF2
A, B
DNA LINKINGC10 H13 F N5 O6 PDA
OMG
Query on OMG
A, B
RNA LINKINGC11 H16 N5 O8 PG
CFZ
Query on CFZ
A, B
DNA LINKINGC9 H13 F N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance