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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.

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Supplementary files

Publication details

The article was received on 29 Oct 2017, accepted on 14 Nov 2017 and first published on 14 Nov 2017


Article type: Paper
DOI: 10.1039/C7OB02654D
Citation: Org. Biomol. Chem., 2017, Accepted Manuscript
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    Controlling miRNA-like Off-target Effects of an siRNA with Nucleobase Modifications

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

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