Coupling RNA annealing and strand displacement: a FRET-based microplate reader assay for RNA chaperone activity

Biotechniques. 2007 Sep;43(3):304, 306, 308 passim. doi: 10.2144/000112530.

Abstract

Proteins with RNA chaperone activity help RNAs to obtain their native conformations, and many of them are active in the two basic reactions-RNA annealing and strand displacement. Therefore, we developed a time-saving in vitro assay that detects protein-facilitated annealing and strand displacement of fluorophore-labeled oligoribonucleotides in a microplate reader The two reactions are followed byfluorescence resonance energy transfer (FRET) in real-time, and the effect of the proteins on the reaction constants can be quantified. The high-throughput property of the fluorescence microplate reader the kinetic characterization, and the material-saving aspect of this assay enables a fast and convenient classification of proteins according to their RNA chaperone activity in annealing and strand displacement.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Biological Assay / methods
  • Computer Systems
  • Fluorescence Resonance Energy Transfer / instrumentation*
  • Fluorescence Resonance Energy Transfer / methods
  • Molecular Chaperones / chemistry*
  • Molecular Chaperones / genetics
  • Molecular Chaperones / metabolism*
  • Protein Binding
  • RNA / chemistry*
  • RNA / genetics
  • RNA / metabolism*
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Reproducibility of Results
  • Sensitivity and Specificity

Substances

  • Molecular Chaperones
  • RNA-Binding Proteins
  • RNA