3P4C

Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-R32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.

Pallan, P.S.Greene, E.M.Jicman, P.A.Pandey, R.K.Manoharan, M.Rozners, E.Egli, M.

(2011) Nucleic Acids Res 39: 3482-3495

  • DOI: https://doi.org/10.1093/nar/gkq1270
  • Primary Citation of Related Structures:  
    3P4A, 3P4B, 3P4C, 3P4D

  • PubMed Abstract: 

    Various chemical modifications are currently being evaluated for improving the efficacy of short interfering RNA (siRNA) duplexes as antisense agents for gene silencing in vivo. Among the 2'-ribose modifications assessed to date, 2'deoxy-2'-fluoro-RNA (2'-F-RNA) has unique properties for RNA interference (RNAi) applications. Thus, 2'-F-modified nucleotides are well tolerated in the guide (antisense) and passenger (sense) siRNA strands and the corresponding duplexes lack immunostimulatory effects, enhance nuclease resistance and display improved efficacy in vitro and in vivo compared with unmodified siRNAs. To identify potential origins of the distinct behaviors of RNA and 2'-F-RNA we carried out thermodynamic and X-ray crystallographic analyses of fully and partially 2'-F-modified RNAs. Surprisingly, we found that the increased pairing affinity of 2'-F-RNA relative to RNA is not, as commonly assumed, the result of a favorable entropic contribution ('conformational preorganization'), but instead primarily based on enthalpy. Crystal structures at high resolution and osmotic stress demonstrate that the 2'-F-RNA duplex is less hydrated than the RNA duplex. The enthalpy-driven, higher stability of the former hints at the possibility that the 2'-substituent, in addition to its important function in sculpting RNA conformation, plays an underappreciated role in modulating Watson-Crick base pairing strength and potentially π-π stacking interactions.


  • Organizational Affiliation

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


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
A, B
8synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.55α = 90
b = 40.55β = 90
c = 117.222γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL2Mapmodel building
SHELXLrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2020-06-24
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations