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Nucleic Acids Research 2006 34(6):e48; doi:10.1093/nar/gkl055
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Published online 31 March 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Methods Online

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins

Inna Shcherbakova, Somdeb Mitra, Robert H. Beer1 and Michael Brenowitz*

Department of Biochemistry, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, NY 10461, USA 1 Department of Chemistry, Fordham University 441 East Fordham Road, Bronx, NY 10458, USA

*To whom correspondence should be addressed. Tel: 00 1 718 430 3179; Fax: 00 1 718 430 8565; Email: brenowit{at}aecom.yu.edu

Received January 13, 2006. Revised February 14, 2006. Accepted February 24, 2006.

‘Footprinting’ describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions. The hydroxyl radical (·OH) is a particularly valuable footprinting probe by virtue of it being among the most reactive of chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved ·OH footprinting has been developed based on the Fenton reaction, Fe(II) + H2O2 -> Fe(III) + ·OH + OH–. This method can be implemented in laboratories using widely available three-syringe quench flow mixers and inexpensive reagents to study local changes in the solvent accessibility of DNA, RNA and proteins associated with their biological function.


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