Mapping small molecule-RNA binding sites via Chem-CLIP synergized with capillary electrophoresis and nanopore sequencing.

ABSTRACT: Target validation and identification of binding sites are keys to the development of bioactive small molecules that target RNA. Herein, we describe optimized protocols to profile small molecule-RNA interactions and to define binding sites of the small molecules in RNAs using covalent chemistry. Various reactive modules appended to an RNA-binding small molecule were studied for cross-linking to the RNA target. Electrophilic modules, whether N-chloroethyl aniline or diazirine, have reactive profiles consistent with induced proximity; however, probes with N-chloroethyl aniline were more reactive and more specific than those with a diazirine cross-linking moiety. Depending upon the identity of the cross-linking module, covalent adducts with different nucleotides that are proximal to a small mo

SUBMITTER: Yang X 

PROVIDER: S-EPMC11952968 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature