Chapter 12, Problem 5EQ

Summary Introduction

To review:

The results of DNAse (deoxyribonuclease) footprinting to analyze:

Length of DNA (deoxyribonucleic acid) covered up by RNA (ribonucleic acid) polymerase II and the transcription factors.

Mechanism of binding of these proteins to the DNA if it was a part of a nucleosome; whether the DNA is in a nucleosomewhenRNA polymerase and transcription factors bind at the promoter.

Introduction:

DNAse footprinting is a common method used to study the interactions between DNA and proteins. The principle behind the method is that any DNA which is bound to protein is protected from the action of DNA digesting enzymes, since they make the DNA inaccessible for the DNAse. The DNAse enzyme cleaves the DNA that is freely available, which show up in the form of bands on an agarose gel. The gap in the gel defines the region where the protein and DNA are interacting.