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Labeling DNA Probes

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...

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Related Experiment Video

Updated: Jul 5, 2026

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Published on: August 6, 2014

Two color RNA intercalating probe for cell imaging applications.

Nathan Stevens¹, Naphtali O'Connor, Harshad Vishwasrao

¹Departments of Chemistry and Chemical Engineering, Columbia University, New York, New York 10027, USA.

Journal of the American Chemical Society

|May 21, 2008

Summary

This summary is machine-generated.

This study introduces a novel RNA probe with enhanced fluorescence. The probe is brighter and offers improved signal detection in cellular environments, enabling dual-color imaging.

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Area of Science:

Biochemistry
Molecular Biology
Fluorescence Spectroscopy

Background:

Phenanthridine derivatives are used as fluorescent probes for nucleic acids.
Enhancing fluorescence signal intensity and improving signal-to-background ratio are critical for sensitive detection.
Developing dual-color probes can provide simultaneous information on probe localization and target molecule presence.

Purpose of the Study:

To develop a brighter phenanthridine-based fluorescent probe for duplex RNA detection.
To enhance the probe's fluorescence signal intensity through covalent linkage with fluorescein.
To utilize time-resolved fluorescence for improved signal-to-background ratio in cellular imaging.

Main Methods:

Synthesis of a phenanthridine derivative with a covalently linked fluorescein molecule.
Steady-state and time-resolved fluorescence spectroscopy to characterize probe properties.
Fluorescence imaging of cells to assess probe performance in a biological context.

Main Results:

The novel probe exhibits approximately 77% energy transfer efficiency from fluorescein to phenanthridine.
The probe is over 5 times brighter than other phenanthridine derivatives when bound to RNA.
Time-resolved fluorescence increased the signal-to-background ratio from 7 to over 40 in cell growth medium.
Dual-color fluorescence imaging demonstrated simultaneous visualization of probe location and RNA.

Conclusions:

The developed fluorescein-phenanthridine conjugate is a highly sensitive and bright probe for duplex RNA.
Time-resolved fluorescence significantly enhances signal detection in complex biological samples.
The probe's dual-color capability allows for simultaneous tracking of probe localization and RNA presence, offering advanced cellular imaging applications.