Hydroxyl radical footprinting of protein-DNA complexes.
This unit details the use of hydroxyl radicals to characterize protein-DNA interactions. This method may be used to assess the exact location of contacts between a protein and its cognate DNA and details of the complex structure. We describe several methods to prepare DNA templates for footprinting and ways to avoid many of the pitfalls associated with the use of hydroxyl radical footprinting. In addition, we describe in detail one example of the application of this technique.
Jagannathan
Indu
I
Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.
Hayes
Jeffrey J
JJ
D001483:Base Sequence; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D018983:DNA Footprinting / Q000379:methods*; D006801:Humans; D017665:Hydroxyl Radical / Q000378:metabolism*; D007553:Isotope Labeling; D008969:Molecular Sequence Data; D051718:MutS Homolog 2 Protein / Q000378:metabolism*
D017665:Hydroxyl Radical; D004247:DNA; C497172:MSH2 protein, human; D051718:MutS Homolog 2 Protein