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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1093/nar/gkq1270
  • Primary Citation of Related Structures:  

  • 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-RN ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'A,B8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SR
Query on SR

Download SDF File 
Download CCD File 
B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
UFT
Query on UFT
A, B
DNA LINKINGC9 H12 F N2 O8 PDU
AF2
Query on AF2
A, B
DNA LINKINGC10 H13 F N5 O6 PDA
CFZ
Query on CFZ
A, B
DNA LINKINGC9 H13 F N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 40.550α = 90.00
b = 40.550β = 90.00
c = 117.222γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL2Mapmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL2Mapphasing
HKL-2000data scaling
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description