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Related Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
Southern Blot02:57

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

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Related Experiment Video

Updated: May 27, 2026

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

DNA Binding Hydroxyl Radical Probes.

Vicky J Tang1, Katie M Konigsfeld, Joe A Aguilera

  • 1Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610.

Radiation Physics and Chemistry (Oxford, England : 1993)
|November 30, 2011
PubMed
Summary
This summary is machine-generated.

Researchers developed a sensitive assay to detect hydroxyl radicals, key mediators of DNA damage from ionizing radiation. The coumarin system, when linked to a DNA-binding peptide, shows promise for detecting these damaging agents.

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Last Updated: May 27, 2026

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

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Published on: October 17, 2011

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Published on: November 1, 2019

Area of Science:

  • Biochemistry
  • Radiochemistry
  • Molecular Biology

Background:

  • Ionizing radiation induces DNA damage primarily through hydroxyl radicals.
  • Hydroxyl radicals are potent oxidizing agents formed during water radiolysis.
  • Sensitive detection methods for hydroxyl radicals are crucial for understanding radiation-induced DNA damage.

Purpose of the Study:

  • To develop sensitive assays for detecting hydroxyl radicals.
  • To evaluate the utility of hydroxylating aromatic chromophores for fluorescence-based detection.
  • To investigate the coumarin system, modified with a DNA-binding peptide, as a potential hydroxyl radical sensor.

Main Methods:

  • Examination of four different chromophores for fluorescent product generation upon hydroxylation.
  • Assessment of the coumarin system's properties and disadvantages.
  • Conjugation of the coumarin system to a cationic peptide ligand for enhanced DNA binding.

Main Results:

  • Hydroxylation of aromatic groups can yield fluorescent products, enabling detection.
  • The coumarin system demonstrated fewer disadvantages compared to other tested chromophores.
  • Linking coumarin to a cationic peptide ligand was explored for improved DNA interaction.

Conclusions:

  • The coumarin system shows potential as a basis for hydroxyl radical detection assays.
  • Cationic peptide conjugation may enhance the targeting and sensitivity of coumarin-based sensors.
  • Further development of this system could lead to improved methods for studying radiation biology.