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

Scott R. Suter, Alexi Ball-Jones, Madeline M. Mumbleau, Rachel Valenzuela, Jose Ibarra-Soza, Hassan Owens, Andrew J Fisher, Peter A. Beal

Research output: Contribution to journalArticle

8 Citations (Scopus)

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 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.

Original languageEnglish (US)
Pages (from-to)10029-10036
Number of pages8
JournalOrganic and Biomolecular Chemistry
Volume15
Issue number47
DOIs
StatePublished - Jan 1 2017

Fingerprint

Triazoles
MicroRNAs
Small Interfering RNA
strands
Bearings (structural)
RNA
grooves
Guide RNA
disrupting
adenosines
Gene Silencing
genes
Adenosine
Freezing
Inhibitory Concentration 50
Melting point
Assays
Genes
melting
Derivatives

ASJC Scopus subject areas

  • Biochemistry
  • Physical and Theoretical Chemistry
  • Organic Chemistry

Cite this

Suter, S. R., Ball-Jones, A., Mumbleau, M. M., Valenzuela, R., Ibarra-Soza, J., Owens, H., ... Beal, P. A. (2017). Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Organic and Biomolecular Chemistry, 15(47), 10029-10036. https://doi.org/10.1039/c7ob02654d

Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. / Suter, Scott R.; Ball-Jones, Alexi; Mumbleau, Madeline M.; Valenzuela, Rachel; Ibarra-Soza, Jose; Owens, Hassan; Fisher, Andrew J; Beal, Peter A.

In: Organic and Biomolecular Chemistry, Vol. 15, No. 47, 01.01.2017, p. 10029-10036.

Research output: Contribution to journalArticle

Suter, SR, Ball-Jones, A, Mumbleau, MM, Valenzuela, R, Ibarra-Soza, J, Owens, H, Fisher, AJ & Beal, PA 2017, 'Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications', Organic and Biomolecular Chemistry, vol. 15, no. 47, pp. 10029-10036. https://doi.org/10.1039/c7ob02654d
Suter SR, Ball-Jones A, Mumbleau MM, Valenzuela R, Ibarra-Soza J, Owens H et al. Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Organic and Biomolecular Chemistry. 2017 Jan 1;15(47):10029-10036. https://doi.org/10.1039/c7ob02654d
Suter, Scott R. ; Ball-Jones, Alexi ; Mumbleau, Madeline M. ; Valenzuela, Rachel ; Ibarra-Soza, Jose ; Owens, Hassan ; Fisher, Andrew J ; Beal, Peter A. / Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. In: Organic and Biomolecular Chemistry. 2017 ; Vol. 15, No. 47. pp. 10029-10036.
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