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Updated: Jul 10, 2026

Direct Imaging of Laser-driven Ultrafast Molecular Rotation
Published on: February 4, 2017
Following molecular transitions with single residue spatial and millisecond time resolution
Inna Shcherbakova1, Somdeb Mitra, Robert H Beer
1Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
Abstract:
"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, respectively. The hydroxyl radical (*OH) is a uniquely insightful footprinting probe by virtue of it being among the most reactive 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 is presented based on the Fenton reaction, Fe(II) + H(2)O(2) --> Fe(III) + *OH + OH(-). It is implemented using a standard three-syringe quench-flow mixer. The utility of this method is demonstrated by its application to the studies on RNA folding. Its applicability to a broad range of biological questions involving the function of DNA, RNA, and proteins is discussed.
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