Practice question

Studying protein-DNA interactions requires matrices presenting immobilized DNA or specific protein ligands to capture interacting partners. Affinity chromatography using DNA-cellulose, where double-stranded DNA is coupled to cellulose, or using biotinylated oligonucleotides bound to streptavidin agarose, allows selective retention of DNA-binding proteins via sequence-specific or non-specific electrostatic contacts. Sephadex and agarose alone separate by size, while silica adsorbs non-specifically. Ligand-based affinity matrices preserve native binding activity, enabling enrichment from nuclear extracts, followed by salt elution for subsequent analysis by electrophoretic mobility shift assays and transcription factor characterization.