6CY0

RNA octamer containing 2'-F, 4'-Cbeta-OMe U.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.398 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity.

Harp, J.M.Guenther, D.C.Bisbe, A.Perkins, L.Matsuda, S.Bommineni, G.R.Zlatev, I.Foster, D.J.Taneja, N.Charisse, K.Maier, M.A.Rajeev, K.G.Manoharan, M.Egli, M.

(2018) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gky703
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chemical modification is a prerequisite of oligonucleotide therapeutics for improved metabolic stability, uptake and activity, irrespective of their mode of action, i.e. antisense, RNAi or aptamer. Phosphate moiety and ribose C2'/O2' atoms are the mo ...

    Chemical modification is a prerequisite of oligonucleotide therapeutics for improved metabolic stability, uptake and activity, irrespective of their mode of action, i.e. antisense, RNAi or aptamer. Phosphate moiety and ribose C2'/O2' atoms are the most common sites for modification. Compared to 2'-O-substituents, ribose 4'-C-substituents lie in proximity of both the 3'- and 5'-adjacent phosphates. To investigate potentially beneficial effects on nuclease resistance we combined 2'-F and 2'-OMe with 4'-Cα- and 4'-Cβ-OMe, and 2'-F with 4'-Cα-methyl modification. The α- and β-epimers of 4'-C-OMe-uridine and the α-epimer of 4'-C-Me-uridine monomers were synthesized and incorporated into siRNAs. The 4'α-epimers affect thermal stability only minimally and show increased nuclease stability irrespective of the 2'-substituent (H, F, OMe). The 4'β-epimers are strongly destabilizing, but afford complete resistance against an exonuclease with the phosphate or phosphorothioate backbones. Crystal structures of RNA octamers containing 2'-F,4'-Cα-OMe-U, 2'-F,4'-Cβ-OMe-U, 2'-OMe,4'-Cα-OMe-U, 2'-OMe,4'-Cβ-OMe-U or 2'-F,4'-Cα-Me-U help rationalize these observations and point to steric and electrostatic origins of the unprecedented nuclease resistance seen with the chain-inverted 4'β-U epimer. We used structural models of human Argonaute 2 in complex with guide siRNA featuring 2'-F,4'-Cα-OMe-U or 2'-F,4'-Cβ-OMe-U at various sites in the seed region to interpret in vitro activities of siRNAs with the corresponding 2'-/4'-C-modifications.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')A,B,C,D,E,F,G,H8synthetic construct
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UFB
Query on UFB
A, B, C, D, E, F, G, H
RNA linkingC10 H14 F N2 O9 P

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CBV
Query on CBV
A, B, C, D, E, F, G, H
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.398 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.012α = 90.00
b = 47.631β = 90.00
c = 100.744γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PHENIXrefinement
SHELXDEphasing
PDB_EXTRACTdata extraction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-04-04 
  • Released Date: 2018-08-29 
  • Deposition Author(s): Harp, J.M., Egli, M.

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release