Sequence-specific binding of single-stranded RNA: is there a code for recognition?

Nucleic Acids Res. 2006;34(17):4943-59. doi: 10.1093/nar/gkl620. Epub 2006 Sep 18.

Abstract

A code predicting the RNA sequence that will be bound by a certain protein based on its amino acid sequence or its structure would provide a useful tool for the design of RNA binders with desired sequence-specificity. Such de novo designed RNA binders could be of extraordinary use in both medical and basic research applications. Furthermore, a code could help to predict the cellular functions of RNA-binding proteins that have not yet been extensively studied. A comparative analysis of Pumilio homology domains, zinc-containing RNA binders, hnRNP K homology domains and RNA recognition motifs is performed in this review. Based on this, a set of binding rules is proposed that hints towards a code for RNA recognition by these domains. Furthermore, we discuss the intermolecular interactions that are important for RNA binding and summarize their importance in providing affinity and specificity.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Base Sequence
  • Binding Sites
  • Models, Molecular
  • Protein Binding
  • Protein Engineering
  • Protein Structure, Tertiary
  • RNA / chemistry*
  • RNA / metabolism
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism

Substances

  • RNA-Binding Proteins
  • RNA