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Related Concept Videos

Radical Reactivity: Overview01:11

Radical Reactivity: Overview

Radicals, the highly reactive species, gain stability by undergoing three different reactions. The first reaction involves a radical-radical coupling, in which a radical combines with another radical, forming a spin‐paired molecule. The second reaction is between a radical and a spin‐paired molecule, generating a new radical and a new spin‐paired molecule. The third reaction is radical decomposition in a unimolecular reaction, forming a new radical and a spin‐paired molecule. These three...
Radical Autoxidation01:20

Radical Autoxidation

The oxidation of an organic compound in the presence of air or oxygen is called autoxidation. For example, cumene reacts with oxygen to form hydroperoxide. Autoxidation involves initiation, propagation, and termination steps. Many organic compounds are susceptible to autoxidation—especially ethers in the presence of oxygen, which form hydroperoxides. Even though this reaction is slow, old ether bottles contain small amounts of peroxide, which leads to laboratory explosions during ether...
Radical Formation: Overview01:03

Radical Formation: Overview

A bond can be broken either by heterolytic bond cleavage to form ions or homolytic bond cleavage to yield radicals. A fishhook arrow is used to represent the motion of a single electron in homolytic bond cleavage. There are two main sources from which radicals can be formed:
Radicals from spin-paired molecules:
Radicals can be obtained from spin-paired molecules either by homolysis or electron transfer. While two radicals are formed in the former, an electron is added in the latter, also known...
Radical Reactivity: Electrophilic Radicals01:02

Radical Reactivity: Electrophilic Radicals

Radicals adjacent to electron‐withdrawing groups are called electrophilic radicals. These radicals readily react with nucleophilic alkenes. For example, the malonate radical, in which the radical center is flanked by two electron‐withdrawing groups, reacts readily with butyl vinyl ether, which consists of an electron‐donating oxygen substituent. The reaction between electrophilic malonate radical and nucleophilic vinyl ether is favored because the radical has a low‐energy SOMO, which interacts...
Radical Reactivity: Nucleophilic Radicals01:16

Radical Reactivity: Nucleophilic Radicals

Radicals adjacent to electron-donating groups are called nucleophilic radicals. These radicals readily react with electrophilic alkenes. The SOMO–LUMO interactions are the driving force for the reaction, where the high-energy SOMO of the electron-rich, nucleophilic radicals interacts with the low-energy LUMO of the electron-deficient, electrophilic alkenes. Such SOMO–LUMO interactions are the basis of reactive radical traps, affecting the selectivity in radical reactions. For instance, consider...
Radical Formation: Elimination00:51

Radical Formation: Elimination

Another method of radical formation is the elimination process. It is the opposite of the addition route and is driven by the instability of the radical. For example, as depicted in Figure 1, dibenzoyl peroxide yields a pair of unstable radicals upon homolysis. Given its instability, this radical spontaneously undergoes elimination via a C–C bond cleavage to form a relatively more stable phenyl radical. The mechanism involves cleavage of the bond between the α and β positions with respect to...

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Related Experiment Video

Updated: Jun 4, 2026

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins
09:59

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

Published on: June 4, 2021

Hydroxyl-radical footprinting.

Michael Carey, Stephen T Smale

    CSH Protocols
    |March 2, 2011
    PubMed
    Summary
    This summary is machine-generated.

    Hydroxyl-radical footprinting precisely maps protein-DNA interactions by detecting DNA cleavage in the minor groove. This method reveals structural changes during protein binding with high resolution.

    More Related Videos

    Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting
    13:41

    Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting

    Published on: October 17, 2011

    Characterizing Cellular Proteins with In-cell Fast Photochemical Oxidation of Proteins
    09:03

    Characterizing Cellular Proteins with In-cell Fast Photochemical Oxidation of Proteins

    Published on: March 11, 2020

    Related Experiment Videos

    Last Updated: Jun 4, 2026

    Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins
    09:59

    Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

    Published on: June 4, 2021

    Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting
    13:41

    Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting

    Published on: October 17, 2011

    Characterizing Cellular Proteins with In-cell Fast Photochemical Oxidation of Proteins
    09:03

    Characterizing Cellular Proteins with In-cell Fast Photochemical Oxidation of Proteins

    Published on: March 11, 2020

    Area of Science:

    • Molecular Biology
    • Biochemistry
    • Structural Biology

    Background:

    • Protein-DNA interactions are crucial for cellular processes.
    • Understanding these interactions requires precise mapping techniques.
    • Existing methods like DNase I have limitations in resolution.

    Purpose of the Study:

    • To detail the hydroxyl-radical footprinting protocol.
    • To highlight its application in studying protein-DNA interactions.
    • To demonstrate its utility in identifying DNA structural changes upon binding.

    Main Methods:

    • Utilizing hydroxyl radicals generated by Fe(II) EDTA and hydrogen peroxide.
    • Employing ascorbic acid to regenerate Fe(II).
    • Analyzing DNA cleavage patterns to infer protein binding sites and effects.

    Main Results:

    • Hydroxyl radicals cleave DNA at the C4 sugar position in the minor groove.
    • Protein binding protects the sugar moiety from radical attack.
    • The small size of hydroxyl radicals allows for high-resolution mapping of minor groove interactions.

    Conclusions:

    • Hydroxyl-radical footprinting offers detailed insights into protein-DNA binding.
    • It is effective for studying minor groove interactions and DNA structural perturbations.
    • The method provides high resolution due to the non-sterically hindered nature of hydroxyl radicals.