Issue 47, 2017

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

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.

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

Supplementary files

Article information

Article type
Paper
Submitted
29 Okt. 2017
Accepted
14 Nov. 2017
First published
14 Nov. 2017

Org. Biomol. Chem., 2017,15, 10029-10036

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

S. R. Suter, A. Ball-Jones, M. M. Mumbleau, R. Valenzuela, J. Ibarra-Soza, H. Owens, A. J. Fisher and P. A. Beal, Org. Biomol. Chem., 2017, 15, 10029 DOI: 10.1039/C7OB02654D

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