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Nat Chem Biol DOI:10.1038/nchembio.1655

Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling.

Publication TypeJournal Article
Year of Publication2014
AuthorsMcDonald, RI, Guilinger, JP, Mukherji, S, Curtis, EA, Lee, WI, Liu, DR
JournalNat Chem Biol
Date Published2014 Dec
KeywordsAlkylation, Archaea, Base Sequence, Cell Extracts, Epoxy Compounds, Guanosine, HEK293 Cells, Humans, Molecular Sequence Data, Repressor Proteins, RNA Probes, RNA, Catalytic, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, SELEX Aptamer Technique, Staining and Labeling

Probes that form covalent bonds with RNA molecules on the basis of their chemical reactivity would advance our ability to study the transcriptome. We developed a set of electrophilic activity-based RNA probes designed to react with unusually nucleophilic RNAs. We used these probes to identify reactive genome-encoded RNAs, resulting in the discovery of a 42-nt catalytic RNA from an archaebacterium that reacts with a 2,3-disubstituted epoxide at N7 of a specific guanosine. Detailed characterization of the catalytic RNA revealed the structural requirements for reactivity. We developed this catalytic RNA into a general tool to selectively conjugate a small molecule to an RNA of interest. This strategy enabled up to 500-fold enrichment of target RNA from total mammalian RNA or from cell lysate. We demonstrated the utility of this approach by selectively capturing proteins in yeast cell lysate that bind the ASH1 mRNA.


Alternate JournalNat. Chem. Biol.
PubMed ID25306441
PubMed Central IDPMC4232462
Grant ListF32GM099359 / GM / NIGMS NIH HHS / United States
F32GM101751 / GM / NIGMS NIH HHS / United States
R01 GM065865 / GM / NIGMS NIH HHS / United States
R01 GM065865 / GM / NIGMS NIH HHS / United States
T32 HG002295 / HG / NHGRI NIH HHS / United States
/ / Howard Hughes Medical Institute / United States
/ / Howard Hughes Medical Institute / United States