Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context.
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We thank T. Kodadek, G. Joyce, W. Ja, J. Childs-Disney, K. Sobczak and J. Cleveland for advice and critical review of the manuscript, and M.D.D. acknowledges J. and H. (nee McDougall) Disney. We also thank the platform for immortalization of human cells from the Institut de Myologie. This work was funded by the US National Institutes of Health (grants DP1NS096898 to M.D.D. and DP1NS096787 to R.Y.) and the Muscular Dystrophy Association (grant 380467 to M.D.D.). S.G.R. was partially supported by a postdoctoral fellowship from the Myotonic Dystrophy Foundation.
The authors declare no competing financial interests.
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Rzuczek, S., Colgan, L., Nakai, Y. et al. Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Nat Chem Biol 13, 188–193 (2017). https://doi.org/10.1038/nchembio.2251
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