Quantifying the strength of miRNA-target interactions

Methods. 2015 Sep 1:85:90-99. doi: 10.1016/j.ymeth.2015.04.012. Epub 2015 Apr 16.


We quantify the strength of miRNA-target interactions with MIRZA, a recently introduced biophysical model. We show that computationally predicted energies of interaction correlate strongly with the energies of interaction estimated from biochemical measurements of Michaelis-Menten constants. We further show that the accuracy of the MIRZA model can be improved taking into account recently emerged experimental data types. In particular, we use chimeric miRNA-mRNA sequences to infer a MIRZA-CHIMERA model and we provide a framework for inferring a similar model from measurements of rate constants of miRNA-mRNA interaction in the context of Argonaute proteins. Finally, based on a simple model of miRNA-based regulation, we discuss the importance of interaction energy and its variability between targets for the modulation of miRNA target expression in vivo.

Keywords: CLASH; CLIP; MIRZA; Non-canonical miRNA binding; miRNA; miRNA target prediction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / physiology
  • Gene Targeting / methods*
  • Humans
  • MicroRNAs / chemistry*
  • MicroRNAs / metabolism*
  • Models, Molecular*
  • Protein Structure, Secondary


  • MicroRNAs