Increased siRNA duplex stability correlates with reduced off-target and elevated on-target effects

RNA. 2011 Apr;17(4):737-49. doi: 10.1261/rna.2348111. Epub 2011 Mar 2.

Abstract

Argonaute (Ago) proteins form the core of RNA-induced silencing complexes (RISCs) and mediate small RNA-guided gene silencing. In RNAi, short interfering RNAs (siRNAs) guide RISCs to complementary target RNAs, leading to cleavage by the endonuclease Ago2. Noncatalytic Ago proteins, however, contribute to RNAi as well but cannot cleave target RNA and often generate off-target effects. Here we show that synthetic siRNA duplexes interact with all Ago proteins, but a functional RISC rapidly assembles only around Ago2. By stabilizing the siRNA duplex, we show that the noncatalytic Ago proteins Ago1, -3, and -4 can be selectively blocked and do not form functional RISCs. In addition, stabilized siRNAs form an Ago2-RISC more efficiently, leading to increased silencing activity. Our data suggest novel parameters for the design of siRNAs with selective activation of the endonuclease Ago2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Argonaute Proteins
  • Eukaryotic Initiation Factor-2 / genetics
  • Eukaryotic Initiation Factor-2 / metabolism*
  • Eukaryotic Initiation Factors / genetics
  • Eukaryotic Initiation Factors / metabolism
  • HEK293 Cells
  • Humans
  • RNA Stability*
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / metabolism*
  • RNA-Induced Silencing Complex / chemistry
  • RNA-Induced Silencing Complex / metabolism*

Substances

  • AGO1 protein, human
  • AGO2 protein, human
  • AGO3 protein, human
  • AGO4 protein, human
  • Argonaute Proteins
  • Eukaryotic Initiation Factor-2
  • Eukaryotic Initiation Factors
  • RNA, Small Interfering
  • RNA-Induced Silencing Complex