Related Experiment Video
Updated: Feb 9, 2026

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
Published on: February 17, 2023
Quantitative identification of proteins that influence miRNA biogenesis by RNA pull-down-SILAC mass spectrometry
Nila Roy Choudhury1, Gracjan Michlewski2
1Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh EH9 3BF, UK; Division of Infection and Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK.
Abstract:
RNA-binding proteins mediate and control gene expression. As some examples, they regulate pre-mRNA synthesis and processing; mRNA localisation, translation and decay; and microRNA (miRNA) biogenesis and function. Here, we present a detailed protocol for RNA pull-down coupled to stable isotope labelling by amino acids in cell culture (SILAC) mass spectrometry (RP-SMS) that enables quantitative, fast and specific detection of RNA-binding proteins that regulate miRNA biogenesis. In general, this method allows for the identification of RNA-protein complexes formed using in vitro or chemically synthesized RNAs and protein extracts derived from cultured cells.
Related Concept Videos
Peptide Identification Using Tandem Mass Spectrometry
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Mass Spectrometry: Overview
Tandem Mass Spectrometry
Mass Spectrometry: Isotope Effect
Mass Spectrometry of Amines
RNA Polymerase II Accessory Proteins

