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Title: Following Molecular Transitions with Single Residue Spatial and Millisecond Time Resolution

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 ({center_dot}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 {center_dot}OH footprinting is presented based on the Fenton reaction, Fe(II) + H2O2 {yields} Fe(III) + {center_dot}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.

Authors:
; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
960146
Report Number(s):
BNL-83132-2009-JA
TRN: US201016%%1290
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Methods in Cell Biology; Journal Volume: 84
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; CLEAVAGE; DNA; HYDROXYL RADICALS; KINETICS; NUCLEIC ACIDS; OXIDIZERS; POLYMERS; PROTEINS; RESIDUES; RESOLUTION; RNA; SOLVENTS; THERMODYNAMICS; TIME RESOLUTION; national synchrotron light source

Citation Formats

Shcherbakova,I., Mitra, S., Beer, R., and Brenowitz, M. Following Molecular Transitions with Single Residue Spatial and Millisecond Time Resolution. United States: N. p., 2008. Web. doi:10.1016/S0091-679X(07)84019-2.
Shcherbakova,I., Mitra, S., Beer, R., & Brenowitz, M. Following Molecular Transitions with Single Residue Spatial and Millisecond Time Resolution. United States. doi:10.1016/S0091-679X(07)84019-2.
Shcherbakova,I., Mitra, S., Beer, R., and Brenowitz, M. 2008. "Following Molecular Transitions with Single Residue Spatial and Millisecond Time Resolution". United States. doi:10.1016/S0091-679X(07)84019-2.
@article{osti_960146,
title = {Following Molecular Transitions with Single Residue Spatial and Millisecond Time Resolution},
author = {Shcherbakova,I. and Mitra, S. and Beer, R. and Brenowitz, M.},
abstractNote = {'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 ({center_dot}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 {center_dot}OH footprinting is presented based on the Fenton reaction, Fe(II) + H2O2 {yields} Fe(III) + {center_dot}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.},
doi = {10.1016/S0091-679X(07)84019-2},
journal = {Methods in Cell Biology},
number = ,
volume = 84,
place = {United States},
year = 2008,
month = 1
}
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