title: Detecting RNA-RNA interactions using psoralen derivatives.
abstract: Psoralens are tricyclic compounds that intercalate into double-stranded DNA or RNA and, on irradiation with long-wavelength (365-nm) UV light, covalently link pyrimidines on adjacent strands. More rarely, psoralen cross-links can be observed at the ends of helices (i.e., double-stranded-single-stranded boundaries). Although psoralens can, in some instances, cross-link protein to RNA, their primary application is to detect RNA-RNA base-pairing interactions. The most useful psoralen derivative is 4'-aminomethyl trioxsalen (AMT), which is soluble in H2O. This protocol describes the use of AMT to detect RNA-RNA interactions in tissue culture cells or in extracts. Cross-linked RNAs are detectable by their reduced mobility in polyacrylamide gels. Cross-links can be reversed by exposure to short-wavelength (254 nm) UV light.
authors.forename: Timothy W
authors.initials: TW
authors.lastname: Nilsen
mesh_terms: D002467:Cell Nucleus / Q000187:drug effects / Q000378:metabolism; D003432:Cross-Linking Reagents / Q000494:pharmacology*; D004247:DNA / Q000187:drug effects; D006367:HeLa Cells; D006801:Humans; D012313:RNA / Q000187:drug effects* / Q000378:metabolism*; D014307:Trioxsalen / Q000494:pharmacology*
chemical_list: D003432:Cross-Linking Reagents; D012313:RNA; D004247:DNA; D014307:Trioxsalen