PAIR Technology: Exon-Specific RNA-Binding Protein Isolation in Live Cells

  • Thomas J. Bell
  • Emelía Eiríksdóttir
  • Ülo Langel
  • James Eberwine
Part of the Methods in Molecular Biology book series (MIMB, volume 683)


RNA-binding proteins (RBPs) are fundamental regulatory proteins for all forms of transcriptional and posttranscriptional control of gene expression. However, isolating RBPs is technically challenging for investigators. Currently, the most widely used techniques to isolate RBPs are in vitro biochemical approaches. Although these approaches have been useful, they have several limitations. One key limitation to using in vitro biochemical approaches is that RBP–RNA interactions are isolated under nonbiological conditions. Here we review a novel experimental approach to identify RBPs called peptide nucleic acid (PNA)-assisted identification of RBPs (PAIR) technology (Zielinski et al., Proc Natl Acad Sci USA 103:1557–1562, 2006). This technology has two significant advantages over traditional approaches. (1) It overcomes the in vitro limitation of biochemical approaches by allowing investigators to isolate RBP–RNA interactions under in vivo conditions. (2) This technology is highly mRNA specific; it isolates RBPs in an exon-specific manner. By selectively targeting alternatively spliced exons with PAIR technology, investigators can isolate splice variant-specific and mRNA region-specific (5-UTR and 3-UTR) RBP complexes for any mRNA of interest.

Key words

RNA-binding proteins Cell-penetrating peptide Post-transcriptional regulation Alternative splicing 



We would like to acknowledge our colleagues who have helped to refine the cell biology of the PAIR technology including Jennifer Zielinski, Tiina Peritz, and Drs. Fanyi Zeng, Peter Buckley, and Kalle Kilk. Also we appreciate funding from the the NIH Institutes on Aging and Mental Health as well as the Swedish Science Foundation and a European Community Grant.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Thomas J. Bell
    • 1
  • Emelía Eiríksdóttir
    • 2
  • Ülo Langel
    • 2
    • 3
  • James Eberwine
    • 1
  1. 1.Department of Pharmacology and PsychiatryUniversity of Pennsylvania Medical CenterPhiladelphiaUSA
  2. 2.Department of NeurochemistryStockholm UniversityStockholmSweden
  3. 3.Laboratory of Molecular Biotechnology, Institute of TechnologyTartu UniversityTartuEstonia

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