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Overview

RNA pull-down is an in vitro affinity-based technique leveraging the biotin-streptavidin interaction system for the efficient enrichment and identification of RNA-binding proteins (RBPs). A biotin-labeled RNA probe is generated by in vitro transcription and subsequently incubated with whole-cell protein extracts, enabling the formation of sequence-specific RNA-protein complexes. These complexes are then captured by streptavidin-coated magnetic beads and magnetically separated from unbound components in the incubation mixture. Following stringent washes to eliminate non-specifically adsorbed contaminants, the target proteins are recovered via competitive elution (using free biotin) or denaturing elution (for downstream proteomic analysis). The eluted proteins are ultimately identified by Western blot (for validation of known RBPs) or liquid chromatography-tandem mass spectrometry (for discovery of novel interacting proteins), thereby enabling systematic profiling of the protein repertoire associated with the RNA of interest.

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