1. Introduction
2. Global Analysis
3. Math Models
4. Dct Example
5. Software

Introduction

Proteins often bind to multiple sites in DNA elements. Such situations provide a possibility for cooperative protein-DNA binding, where occupancy of one site facilitates or hinders occupancy of another. In a DNAse 1 footprint experiment conducted over a suitable titration of protein concentrations, profiles of occupancy can be simultaneously visualized for several sites present on a single DNA template. This ability to follow individual site occupancies in the presence of adjacent sites, which is often not possible for the alternative gel-shift or filter binding studies, makes DNAse 1 footprinting a method of choice for estimating the free energy components involved in a protein-DNA system.

Purpose

The purpose of this document is to describe one such application in enough detail that the reader will be able to critically evaluate the quality of published protein-DNA binding data. Moreover, the reader will hopefully become inspired and enabled to conduct similar analyses in his/her own protein-DNA binding studies.

• It is indeed encouraging to learn that only a simple modification to the design usually employed for qualitiative DNAse 1 footprinting experiments is needed for designing quantitative experiments.
• The primary difficulty likely to be encountered by the average molecular biologist is understanding and implementing the data analysis portion of the experiment. This involves a simultaneous or global nonlinear regression analysis, which this document is meant to provide.

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