6BGB

Crystal Structure of the 16mer GCAGNCUUAAGUCUGC containing BrPh 7-triazolyl-8-aza-7-deazaadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications.

Suter, S.R.Ball-Jones, A.Mumbleau, M.M.Valenzuela, R.Ibarra-Soza, J.Owens, H.Fisher, A.J.Beal, P.A.

(2017) Org. Biomol. Chem. 15: 10029-10036

  • DOI: 10.1039/c7ob02654d

  • PubMed Abstract: 
  • SiRNAs can cause unintended gene silencing due to miRNA-like effects because of the similarity in function of an siRNA guide strand and a miRNA. Here we evaluate the effect on miRNA-like off targeting of introducing the adenosine derivative 7-EAA and ...

    SiRNAs can cause unintended gene silencing due to miRNA-like effects because of the similarity in function of an siRNA guide strand and a miRNA. Here we evaluate the effect on miRNA-like off targeting of introducing the adenosine derivative 7-EAA and triazoles prepared from 7-EAA at different positions in an siRNA guide strand. We find that a sterically demanding triazole placed in the RNA duplex major groove at position six of the guide strand dramatically reduces miRNA-like off targeting potency. A high-resolution structure of an RNA duplex bearing a novel, major-groove localized triazole is reported, which suggests that modified triazoles could be disrupting the hAgo2-guide-target RNA ternary complex. Five different triazole modifications were tested at the guide strand 6-position for effects on on-target and miRNA-like off target knockdown potency. A 7-EAA triazole bearing a benzylamine substituent displayed on-target knockdown activity as potent as the native siRNA, while having an IC50 against a miRNA-like off target >100-fold higher. Melting temperature studies revealed no obvious correlation between potency in knockdown assays and a modification's effect on duplex stability. These results, along with known structures of hAgo2-guide-target ternary complexes, are used to rationalize the effect of 7-EAA triazoles on miRNA-like off target effects.


    Organizational Affiliation

    Department of Chemistry, University of California, Davis, One Shields Ave, Davis, California, 95616 USA. pabeal@ucdavis.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
(5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')A,B,C16synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A7C
Query on A7C
A, B, C
RNA linkingC18 H20 Br N8 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.640α = 90.00
b = 43.150β = 120.46
c = 48.940γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM080784

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references