Exonuclease III footprinting on immobilized DNA templates.

Patrizia Spitalny, Michael Thomm

Department of Microbiology, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.

Methods in molecular biology (Clifton, N.J.) 2009

filter terms:

DNA footprinting is a widely used method to locate the binding sites of protein on the DNA. It is based on the observation that a protein bound to DNA protects it from degradation by an enzyme or chemical reagent.Exonuclease III is a suitable probe to analyze the boundaries of a protein when it is necessary to eliminate any excess unbound DNA from the reaction to avoid background problems. In combination with biotin-labeled DNA that is bound to streptavidin-coated magnetic particles, information on the precise position of a DNA bound protein is available within a few hours. The position of the archaeal RNA polymerase at different stages of transcription in the Pyrococcus furiosus in vitro transcription system was analyzed by this method.

Citation

Patrizia Spitalny, Michael Thomm. Exonuclease III footprinting on immobilized DNA templates. Methods in molecular biology (Clifton, N.J.). 2009;543:49-56