Download MendeleyA chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites.
Balaratnam, S., Rhodes, C., Bume, D.D., Connelly, C., Lai, C.C., Kelley, J.A., Yazdani, K., Homan, P.J., Incarnato, D., Numata, T., Schneekloth Jr., J.S.(2021) Nat Commun 12: 5856-5856
- PubMed: 34615874
- DOI: https://doi.org/10.1038/s41467-021-25973-x
- Primary Citation of Related Structures:
7E9E, 7E9I - PubMed Abstract:
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 PreQ 1 riboswitch system, assessing sixteen diverse PreQ 1 -derived probes for their ability to selectively modify the class-I PreQ 1 riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ 1 , 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 PreQ 1 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 PreQ 1 aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ 1 , which is similar in structure to guanine, interacts with human RNAs.
Organizational Affiliation:
Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
