Selection of Chemical Modifications in the siRNA Seed Region That Repress Off-Target Effect

Methods Mol Biol. 2021:2282:17-30. doi: 10.1007/978-1-0716-1298-9_2.

Abstract

RNA interference mediated by small interfering RNA (siRNA) has been widely used as a procedure to knock down the expression of an intended target gene with perfect sequence complementarity. However, siRNA often exhibits off-target effects on genes with partial sequence complementarities. Such off-target effect is an undesirable adverse effect for knocking down a target gene specifically. Here we describe the powerful strategy to avoid off-target effects without affecting the RNAi activity by the introduction of DNA or 2'-O-methyl modifications in the siRNA seed region. These two types of chemical modifications repress off-target effects through different molecular mechanisms.

Keywords: 2′-OMe; Off-target effect; RNAi; Seed region; siRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Methylation*
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • HeLa Cells
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • RNA Interference*
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / genetics*
  • RNA, Small Interfering / metabolism
  • Research Design
  • Vimentin / genetics*
  • Vimentin / metabolism
  • Workflow

Substances

  • RNA, Small Interfering
  • VIM protein, human
  • Vimentin
  • Green Fluorescent Proteins