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

Chemistry. 2021 Jul 12;27(39):10193-10200. doi: 10.1002/chem.202101171. Epub 2021 Jun 4.


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 N4 -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.

Keywords: RNA; convertible nucleoside; cross-linking; miR-CLIP; oligonucleotides.

MeSH terms

  • 3' Untranslated Regions
  • Base Pairing
  • Gene Expression Regulation
  • Humans
  • MicroRNAs* / genetics
  • RNA, Messenger / genetics


  • 3' Untranslated Regions
  • MicroRNAs
  • RNA, Messenger