Minor-groove-modulating adenosine replacements control protein binding and RNAi activity in siRNAs

Hayden Peacock, Erik Fostvedt, Peter A. Beal

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Short-interfering RNAs (siRNAs) are common tools in molecular biology; however, the development of RNAi-based therapeutics is limited by immunostimulatory and nonspecific effects mediated by off-target RNA-binding proteins. The RNA-dependent protein kinase (PKR) and adenosine deaminase that acts on RNA 1 (ADAR1) are two proteins implicated in RNAi off-target effects and share a common means of interaction with siRNAs through double-stranded RNA binding motifs (dsRBMs). Here we report the site-specific introduction of N 2-propargyl 2-aminopurine into siRNAs and subsequent conversion to two bulky products via copper-catalyzed azide alkyne cycloaddition (CuAAC) with either N-azidoacetyl-mannosamine azide or N-ethylpiperidine azide. We observed position-specific effects on RNAi activity for modifications made to both the passenger and guide strands. These findings are rationalized in light of recent structural studies of components of the RNA-induced silencing complex (RISC) and RISC-loading complex (RLC). The most active siRNAs were assayed for binding affinity to PKR and ADAR1. PKR binding was significantly reduced by multiple modifications, regardless of size, and ADAR1 binding was reduced in a position- and size-sensitive manner. Our findings present a strategy for designing siRNAs that reduce off-target dsRBM-protein binding while retaining native RNAi activity.

Original languageEnglish (US)
Pages (from-to)1115-1124
Number of pages10
JournalACS Chemical Biology
Volume5
Issue number12
DOIs
StatePublished - Dec 17 2010

Fingerprint

RNA Interference
Protein Binding
Adenosine
Small Interfering RNA
Adenosine Deaminase
Azides
RNA-Induced Silencing Complex
eIF-2 Kinase
RNA
2-Aminopurine
Molecular biology
RNA-Binding Proteins
Alkynes
Double-Stranded RNA
Cycloaddition
Cycloaddition Reaction
Copper
Molecular Biology
Proteins
Double-Stranded RNA Binding Motif

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine

Cite this

Minor-groove-modulating adenosine replacements control protein binding and RNAi activity in siRNAs. / Peacock, Hayden; Fostvedt, Erik; Beal, Peter A.

In: ACS Chemical Biology, Vol. 5, No. 12, 17.12.2010, p. 1115-1124.

Research output: Contribution to journalArticle

Peacock, Hayden ; Fostvedt, Erik ; Beal, Peter A. / Minor-groove-modulating adenosine replacements control protein binding and RNAi activity in siRNAs. In: ACS Chemical Biology. 2010 ; Vol. 5, No. 12. pp. 1115-1124.
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