A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites

Sumirtha Balaratnam, Curran Rhodes, Desta Doro Bume, Colleen Connelly, Christopher C Lai, James A Kelley, Kamyar Yazdani, Philip J Homan, Danny Incarnato, Tomoyuki Numata, John S Schneekloth*

*Bijbehorende auteur voor dit werk

OnderzoeksoutputAcademicpeer review

4 Citaten (Scopus)
23 Downloads (Pure)


The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ1 riboswitch system, assessing sixteen diverse PreQ1-derived probes for their ability to selectively modify the class-I PreQ1 riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ1, X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ1 aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ1 aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ1, which is similar in structure to guanine, interacts with human RNAs.

Originele taal-2English
Aantal pagina's15
TijdschriftNature Communications
Nummer van het tijdschrift1
StatusPublished - 6-okt-2021

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