DNase1 footprinting

A method to study the sequence-specific binding of proteins to DNA. In the technique, a suitable uniquely end-labeled DNA fragment is allowed to interact with a given DNA-binding protein and then the complex partially digested with DNase I. Attached protein protects the DNA binding region from DNase attack. Subsequent molecular-weight analysis of the degraded DNA by electrophoresis and autoradiography identifies the region of protection as a gap in the otherwise continuous ladder of digestion products. The technique can be used to determine the site of interaction of most sequence-specific DNA-binding proteins but also has been extensively applied to the study of transcription factors.

PMID: 212715