Purification of RNA G-Quadruplex Binding Proteins

G-quadruplex (G4) nucleic acids have been shown to regulate a wide range of cellular processes, including replication, telomere maintenance, epigenetic landscape, and various aspects of transcription and translation. In this method, we describe an experimental purification procedure for identifying RNA G-quadruplex-binding proteins from nuclear extracts. Using biotinylated oligonucleotides allows immobilization to streptavidin-coated magnetic beads and convenient washing during the pulldown. Importantly, the experimental protocol presented here can distinguish protein interactions with structured and unstructured RNA within the same oligonucleotide by controlling ionic conditions throughout the folding, RNA pulldown, and washing steps. The binding of individual candidate proteins can be determined by western blotting, while mass spectrometry can readily identify the whole RNA G-quadruplex-interacting proteome.