Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq

Methods. 2022 Sep;205:83-88. doi: 10.1016/j.ymeth.2022.06.009. Epub 2022 Jun 25.


In the development of therapeutics, it is important to establish engagement of a compound to its intended target and identify other targets it binds to. Methods for demonstrating target engagement in the growing field of RNA-targeted therapeutics are therefore needed. We present a detailed protocol for Photoaffinity Evaluation of RNA Ligation-Sequencing (PEARL-seq), a platform for determining interactions between small molecule ligands and their target RNA(s). PEARL-seq allows detection of binding and crosslinking events with single nucleotide resolution and allows measurement of enrichment of the target RNA relative to all other RNAs. PEARL-seq is a valuable tool in the effort to verify bona fide RNA-ligand interactions.

Keywords: Chemical biology; RNA structure; RNA therapeutics; Target engagement.

MeSH terms

  • Base Sequence
  • High-Throughput Nucleotide Sequencing* / methods
  • Ligands
  • RNA* / genetics
  • RNA* / metabolism
  • Sequence Analysis, RNA / methods


  • Ligands
  • RNA