Fluorescent In Situ Detection of RNA-Protein Interactions in Intact Cells by RNA-PLA

Methods Mol Biol. 2023:2666:165-175. doi: 10.1007/978-1-0716-3191-1_13.


RNA-protein proximity ligation assay (RNA-PLA) enables the detection of specific RNA-protein interactions in fixed cells. In RNA-PLA, bridging and ligation of a circular DNA template occurs if the target RNA and protein are within 40 nanometers of each other. The resulting circular template is amplified by rolling circle amplification and abundantly recognized by fluorescent antisense DNA oligonucleotides. This strategy therefore enables localization of RNA-protein interactions in situ with high specificity and sensitivity. Here, we describe the use of RNA-PLA to detect interactions between a nuclear viral RNA and a host RNA-binding protein in Epstein-Barr virus (EBV)-infected B cells.

Keywords: Fixed cell; In situ hybridization; Proximity ligation assay; RNA–protein interaction; Ribonucleoprotein (RNP).

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA, Circular
  • Epstein-Barr Virus Infections*
  • Herpesvirus 4, Human
  • Humans
  • RNA* / genetics
  • RNA-Binding Proteins / metabolism


  • RNA
  • RNA-Binding Proteins
  • DNA, Circular