DNase I Footprinting

Abstract

DNase I footprinting was developed by Galas and Schmitz in 1978 as a method to study the sequence-specific binding of proteins to DNA (1). In this technique a suitable uniquely end-labeled DNA fragment is allowed to interact with a given DNA-binding protein and then the complex is partially digested with DNase 1. The bound protein protects the region of the DNA with which it interacts from attack by the DNase. Subsequent molecular weight analysis of the degraded DNA by electrophoresis and autoradiography identifies the region of protection as a gap in the otherwise continuous background of digestion products (for examples, see Fig. 1). The technique can be used to determine the site of interaction of most sequence-specific DNAbinding proteins but has been most extensively applied to the study of transcription factors. Since the DNase I molecule is relatively large compared to other footprinting agents (see Chapters 3 and Chapters 7 in this volume), its attack on the DNA is more readily prevented by steric hindrance. Thus DNase I footprinting is the most likely of all the footprinting techniques to detect a specific DNA-protein interaction. This is clearly demonstrated by our studies on the transcription factor xUBF (see Fig. 1B). The xUBF interaction with the xenopus ribosomal DNA enhancer can be easily detected by DNase I footprinting but has not yet been detected by other footprinting techniques.