Identifying Specific ProteinDNA Interactions Using SILAC-Based Quantitative Proteomics

A comprehensive identification of protein–DNA interactions that drive processes such as transcription and replication, both in prokaryotic and eukaryotic organisms, remains a major technical challenge. In this chapter, we present a SILAC-based DNA affinity purification method that can be used to identify specific interactions between proteins and functional DNA elements in an unbiased manner.