Design and Application of Mini‐libraries of miRNA Probes for an Efficient and Versatile miRNA‐mRNA Cross‐linking

MicroRNAs constitute a class of endogenous, non‐coding RNAs that influence various processes within the cell. By base‐pairing to partially‐complementary sites located in the 3’ untranslated region of target messenger RNAs, microRNAs participate in post‐transcriptional regulation of the majority of human protein‐coding genes. Their dysregulation has been related to many pathological processes and diseases. Thus, an in‐depth understanding of the microRNA mechanisms of action is crucial. Here, we present a new concept of probe design to achieve an efficient and sequence‐independent miRNA‐mRNA cross‐linking. The new strategy is based on the utilization of a controlled mixture of probes for a chosen miRNA, in which a trioxsalen moiety is introduced at the N (4)‐position of a selected cytidine through short oligoethylene glycol‐based linkers. In vitro photo‐cross‐linking experiments with mini‐libraries of probes for microRNAs of interest showed variable cross‐linking efficiencies, demonstrating a general applicability of the presented approach.