siRNA has greatly elevated mismatch tolerance at 3'-UTR sites

PLoS One. 2012;7(11):e49309. doi: 10.1371/journal.pone.0049309. Epub 2012 Nov 8.


It has been noted that target sites located in the coding region or the 3'-untranslated region (3'-UTR) can be silenced to significantly different levels by the same siRNA, but little is known about at what specificity the silencing was achieved. In an exploration of positional effects on siRNA specificity by luciferase reporter system, we surprisingly discovered that siRNA had greatly elevated tolerance towards mismatches in target sites in the 3'-UTR of the mRNA compared with the same target sites cloned in the coding region. Assessment of changes in protein and mRNA levels suggested that the differential mismatch tolerance might have resulted from location-specific translational repression in the 3'-UTR. Ablation of argonaute proteins by AGO-specific siRNAs revealed that the AGO2 had major impact on siRNA silencing activity against sites in both coding region and 3'-UTR, while the silencing of nonnucleolytic AGO proteins (AGO1, AGO3 and AGO4) did not significantly affect silencing of sites in either region. This paper revealed the discovery that the specificity of an siRNA can be affected by the location of its target site.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions*
  • Argonaute Proteins / chemistry
  • Argonaute Proteins / genetics*
  • Base Pair Mismatch*
  • Binding Sites
  • Humans
  • RNA Interference / physiology*
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / physiology*


  • 3' Untranslated Regions
  • Argonaute Proteins
  • RNA, Small Interfering

Grant support

This work was supported by the National Natural Science Foundation of China, 30871385 and 30873187; Beijing Natural Science Foundation, 5092011; the National Basic Research Program of China, 2011CBA01102; a grant from Shanghai Science and Technology Committee, 10411969100; and the Department of Education of China, 20090001110052 and 200800010019. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.