Spin-column isolation of DNA–protein interactions from complex protein mixtures for AFM imaging

Applications of atomic force microscopy (AFM) to investigate structural–functional interactions between DNA and proteins, at the molecular level, should prove valuable for gaining a better understanding of gene expression. Specific genomic DNA–protein interactions occur within a sea of intracellular proteins. Successful AFM imaging requires isolating the specific DNA–protein complex free of background protein contamination. Using spin-column chromatography, we report the successful isolation and AFM imaging of transcription factor DNA complexes from DNA molecules incubated with crude cell lysates. This method should be applicable for the isolation and imaging of other specific DNA–protein complexes pertinent to functional genomic research.