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Updated: Jun 23, 2026

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins
Published on: June 4, 2021
Hydroxyl radical footprinting of protein-DNA complexes
Indu Jagannathan1, Jeffrey J Hayes
1Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.
Abstract:
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.

