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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...
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

Quantitative, Real-time Analysis of Base Excision Repair Activity in Cell Lysates Utilizing Lesion-specific Molecular Beacons
15:01

Quantitative, Real-time Analysis of Base Excision Repair Activity in Cell Lysates Utilizing Lesion-specific Molecular Beacons

Published on: August 6, 2012

A two-color, self-controlled molecular beacon.

Sarah M Biner1, Robert Häner

  • 1Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.

Chembiochem : a European Journal of Chemical Biology
|November 15, 2011
PubMed
Summary

This study introduces a novel two-color molecular beacon. Its unique design with dual fluorophores offers a self-controlled system, reducing false positives in biological imaging and screening.

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Last Updated: May 27, 2026

Quantitative, Real-time Analysis of Base Excision Repair Activity in Cell Lysates Utilizing Lesion-specific Molecular Beacons
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07:10

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

Published on: July 8, 2025

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Analytical Chemistry

Background:

  • Molecular beacons are crucial for nucleic acid detection.
  • Existing methods can suffer from false positive signals.
  • Need for self-controlled detection systems in molecular diagnostics.

Purpose of the Study:

  • To develop a two-color molecular beacon with built-in self-control.
  • To utilize non-nucleosidic chromophores for enhanced quenching mechanisms.
  • To improve signal specificity in molecular imaging and screening.

Main Methods:

  • Design of a molecular beacon incorporating pyrene and PDI fluorophores.
  • Formation of a donor-acceptor complex for mutual quenching in the closed state.
  • Utilizing triplex stem formation for target hybridization-induced signal release.

Main Results:

  • Demonstrated successful two-color fluorescence read-out upon target hybridization.
  • Confirmed the self-quenching mechanism via donor-acceptor complex formation.
  • Showcased the elimination of false positive signals through the self-control feature.

Conclusions:

  • The developed two-color molecular beacon offers a robust self-controlled detection system.
  • This technology enhances reliability in fluorescence-based imaging and screening.
  • Potential for improved accuracy in molecular diagnostics and high-throughput screening.