Chemical Generation of Hydroxyl Radical for Oxidative 'Footprinting'.

Background: For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative 'footprinting' of macromolecules.

Objective: In this article, we start by reviewing the application of chemical generation of hydroxyl radical to the development of oxidative footprinting of DNA and RNA and the subsequent application of the method to oxidative footprinting of proteins. We next discuss a novel strategy for generating hydroxyl radicals by Fenton chemistry that immobilizes catalytic iron on a solid surface (Pyrite Shrink Wrap laminate) for the application of nucleic acid and protein footprinting.

Protein footprinting by pyrite shrink-wrap laminate.

The structure of macromolecules and their complexes dictate their biological function. In "footprinting", the solvent accessibility of the residues that constitute proteins, DNA and RNA can be determined from their reactivity to an exogenous reagent such as the hydroxyl radical (·OH). While ·OH generation for protein footprinting is achieved by radiolysis, photolysis and electrochemistry, we present a simpler solution.