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A biotin-labeled DNA probe is designed to target a specific genomic or regulatory region of interest. The labeled probe is subsequently captured by streptavidin-coated magnetic beads via the high-affinity biotin-streptavidin interaction. The immobilized DNA probe is then incubated with total protein extracts, allowing proteins that specifically recognize or bind the target DNA sequence to form a bead-DNA-protein ternary complex. Following stringent washes to remove non-specifically bound contaminants, the captured DNA-protein complexes are eluted under optimized conditions. The eluted proteins are subsequently identified and characterized by Western blot (for validation of known DNA-binding proteins) or mass spectrometry (for unbiased discovery of novel interacting proteins).

Chromatin Immunoprecipitation (ChIP) is a classical epigenetic technique for studying in vivo protein-DNA interactions, serving as a core tool for deciphering gene expression regulatory mechanisms, transcription factor binding sites, and epigenetic modification landscapes. By using specific antibodies to enrich DNA fragments bound to target proteins (such as transcription factors and histone modifications), ChIP provides an authentic reflection of in vivo protein-DNA binding. It is considered the gold standard for studying gene regulation, epigenetics, and chromatin structure. The core principle of ChIP is to “freeze” protein-DNA interactions in living cells via formaldehyde crosslinking, fragment chromatin into 200-1000 bp pieces, capture target protein-DNA complexes through specific antibody immunoprecipitation, reverse crosslinks to release and purify the DNA, and finally detect and analyze the enriched DNA fragments using qPCR, ChIP-seq, or ChIP-chip, thereby authentically reflecting in vivo protein-genome binding events.