A cross-linking approach to map small molecule-RNA binding sites in cells

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

卷:29

Article

Velagapudi, Sai Pradeep¹  Li, Yue¹  Disney, Matthew D.¹ 

[1] Scripps Res Inst, Dept Chem, Jupiter, FL 33458 USA

关键词: RNA;    Small molecules;    Target validation;    Target profiling;    Oncogenic microRNA;   

DOI  :  10.1016/j.bmcl.2019.04.001

来源: Elsevier

【 摘 要 】

Methods to identify RNAs bound by small molecules in cells are sparse. Herein, an advance to identify the direct RNA targets of small molecules in cells is described. The approach, dubbed Chemical Cross-Linking and Isolation by Pull-down to Map Small Molecule-RNA Binding Sites (Chem-CLIP-Map-Seq), appends a cross-linker and a purification tag onto a small molecule. In cells, the compound binds to RNA and undergoes a proximity-based reaction. The cross-linked RNA is purified and then amplified using a universal reverse transcription (RT) primer and gene-specific PCR primers. At nucleotides proximal to the binding site, RT stops are observed. This approach has broad utility in identifying and validating the RNA targets and binding sites of small molecules in the context of a complex cellular system.

【 授权许可】

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