Short RNA duplexes guide sequence-dependent cleavage by human Dicer

RNA. 2010 Dec;16(12):2464-73. doi: 10.1261/rna.2346510. Epub 2010 Oct 25.


Dicer is a member of the double-stranded (ds) RNA-specific ribonuclease III (RNase III) family that is required for RNA processing and degradation. Like most members of the RNase III family, Dicer possesses a dsRNA binding domain and cleaves long RNA duplexes in vitro. In this study, Dicer substrate selectivity was examined using bipartite substrates. These experiments revealed that an RNA helix possessing a 2-nucleotide (nt) 3'-overhang may bind and direct sequence-specific Dicer-mediated cleavage in trans at a fixed distance from the 3'-end overhang. Chemical modifications of the substrate indicate that the presence of the ribose 2'-hydroxyl group is not required for Dicer binding, but some located near the scissile bonds are needed for RNA cleavage. This suggests a flexible mechanism for substrate selectivity that recognizes the overall shape of an RNA helix. Examination of the structure of natural pre-microRNAs (pre-miRNAs) suggests that they may form bipartite substrates with complementary mRNA sequences, and thus induce seed-independent Dicer cleavage. Indeed, in vitro, natural pre-miRNA directed sequence-specific Dicer-mediated cleavage in trans by supporting the formation of a substrate mimic.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Base Sequence / physiology*
  • Binding Sites
  • Cells, Cultured
  • DEAD-box RNA Helicases / metabolism*
  • DEAD-box RNA Helicases / physiology
  • Humans
  • MicroRNAs / chemistry
  • MicroRNAs / metabolism
  • Models, Biological
  • Nucleic Acid Conformation
  • Protein Binding
  • RNA Processing, Post-Transcriptional
  • RNA, Double-Stranded / chemistry
  • RNA, Double-Stranded / metabolism*
  • RNA, Guide, Kinetoplastida / chemistry
  • RNA, Guide, Kinetoplastida / metabolism*
  • Ribonuclease III / metabolism*
  • Ribonuclease III / physiology


  • MicroRNAs
  • RNA, Double-Stranded
  • RNA, Guide
  • DICER1 protein, human
  • Ribonuclease III
  • DEAD-box RNA Helicases