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JoVE General Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting JoVE 3244 10/17/2011 Ravichandra Bachu*1, Frances-Camille S. Padlan*2, Sara Rouhanifard2, Michael Brenowitz2, Jörg C. Schlatterer2 1Department of Chemistry, Hunter College, 2Department of Biochemistry, Albert Einstein College of Medicine This protocol describes how to quantify the Mg(II)-dependent formation of RNA tertiary structure by two methods of hydroxyl radical footprinting.