Peptide Nucleic Acid (PNA)-Assisted Identification of RNA Binding Proteins

PAIR uses PNAs to capture RBPs in vivo (Zielinski et al., 2006) (Zeng et al., 2006). The PNAs are coupled to a cell membrane-penetrating peptide (CPP) to deliver PNAs efficiently into living cells, as well as a photoactivatable compound, p-benzoylphenylalanine (Bpa). The cells are illuminated with UV light, activating the Bpa on the PNA to form covalent bonds with the RBP. Next, the cells are lysed, and the RNA complexes are captured on magnetic beads. The proteins can be reverse-crosslinked and visualized by denaturing gel electrophoresis, while the RNA strands are sequenced.


  • Identifies RNA-protein interactions in vivo
  • Commercial PNAs can be purchased, eliminating the need for PNA design


  • Custom PNA design can cause problems with low protein yield
  • Not yet adopted widely by the scientific community


Illumina Library prep and Array Kit Selector


Jazurek M., Ciesiolka A., Starega-Roslan J., Bilinska K. and Krzyzosiak W. J. Identifying proteins that bind to specific RNAs – focus on simple repeat expansion diseases. Nucleic Acids Res. 2016;44:9050-9070

McHugh C. A., Russell P. and Guttman M. Methods for comprehensive experimental identification of RNA-protein interactions. Genome Biol. 2014;15:203


Zielinski J., Kilk K., Peritz T., et al. In vivo identification of ribonucleoprotein-RNA interactions. Proc Natl Acad Sci U S A. 2006;103:1557-1562