For a complete understanding of the roles that RBPs play in cellular processes, it is necessary to understand at the atomic level how RNA binding domains in proteins engage with RNAs. RNA-protein interactions are generally characterized in two main ways in vivo: isolating proteins and sequencing the bound RNAs (CLIP methods), and identifying proteins bound to RNAs, for example, by mass spectrometry. Most of these approaches rely upon photo-induced cross-linking, which provides direct evidence of binding under native conditions. However, presently, native cross-linking-based methods suffer from two drawbacks: i) it is challenging to identify simultaneously sites of cross-linking on the RNA and protein, ii) cross-linking in an RNA-RBP motif typically proceeds inefficiently and in an unpredictable fashion.