FREMSA: A Method That Provides Direct Evidence of the Interaction between microRNA and mRNA

Methods Mol Biol. 2020;2102:557-566. doi: 10.1007/978-1-0716-0223-2_30.


microRNAs (miRNAs) modulate the expression of enzymes responsible for activation or detoxification of xenobiotics and toxicants. miRNAs are dysregulated in response to environmental exposure and have been implicated in toxicological events. Many in vivo and in vitro experimental approaches have been employed to delineate the mechanisms by which miRNAs regulate target genes; however, all these methods provide only indirect evidence for the interaction between miRNAs and their counterpart mRNA molecules. In this chapter, we describe a novel approach-a fluorescent-based RNA electrophoretic mobility shift assay (FREMSA) that is a sensitive and time-saving method, with a high specificity, to visualize the interactions among miRNAs, mRNAs, and proteins, as direct evidence of mRNA/miRNA complex formation.

Keywords: Fluorescent-based RNA electrophoretic mobility shift assay; miRNA target prediction; miRNA–RNA interaction.

MeSH terms

  • Cell Line
  • Electrophoresis, Polyacrylamide Gel
  • Electrophoretic Mobility Shift Assay / instrumentation
  • Electrophoretic Mobility Shift Assay / methods*
  • Fluorescence
  • Humans
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Oligonucleotides / chemistry
  • Oligonucleotides / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Workflow


  • MicroRNAs
  • Oligonucleotides
  • RNA, Messenger