Hi Miao,

Recently there have been two new additions to the family of CLIP protocols. These were enhanced-CLIP (e-CLIP) and infra-red CLIP (irCLIP). Both of these protocols omit radioisotopes. However, where as you "blind" cut above the molecular weight for crosslinked RBP:RNA complexes in the eCLIP protocol, irCLIP uses click-chemistry to attach an infra-red dye to the L3 Linker, which allows you to directly visualise cross-linked RBP:RNA complexes with a machine that can scan IR800 dyes.

Article irCLIP platform for efficient characterization of protein-RN...

Article Robust transcriptome-wide discovery of RNA-binding protein b...

You can try sCLIP, which doesn't use any radioactive labelling nor fluorescent labelling. It relies of aa highly sensitive HRP detection and it also uses a novel library prep method based on in vitro transcription.

https://academic.oup.com/nar/article/45/10/6074/3057353