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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...

FISH - Fluorescent In-situ Hybridization

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...

Southern Blot

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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Updated: May 8, 2026

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

Robust 3D DNA FISH using directly labeled probes.

Daniel J Bolland¹, Michelle R King, Wolf Reik

¹Nuclear Dynamics Programme, The Babraham Institute. daniel.bolland@babraham.ac.uk

Journal of Visualized Experiments : Jove

|August 28, 2013

Summary

This summary is machine-generated.

This study details a robust 3D DNA FISH protocol for analyzing nuclear organization. The optimized method ensures reproducibility and ease of use for high-throughput imaging of chromosomal regions.

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Last Updated: May 8, 2026

Robust 3D DNA FISH Using Directly Labeled Probes

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Published on: August 15, 2013

DNA-based Fish Species Identification Protocol

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Published on: April 28, 2010

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

Area of Science:

Molecular Biology
Genetics
Cell Biology

Background:

3D DNA FISH is crucial for understanding nuclear organization.
Existing protocols vary in robustness and ease of use.

Purpose of the Study:

To present an optimized protocol for 3D DNA FISH.
To enhance robustness, reproducibility, and ease of use.

Main Methods:

Directly labeled probes generated via nick-translation and chemical dye coupling.
Cell permeabilization using a freeze-thaw step.
Simultaneous probe and nuclear DNA denaturation via heating.

Main Results:

The protocol is robust, reproducible, and user-friendly.
Applicable to diverse cell types and probe formats (BACs, plasmids, fosmids, Whole Chromosome Paints).
Enables high-throughput automated imaging for analyzing up to three chromosomal regions.

Conclusions:

The described 3D DNA FISH protocol is a valuable tool for nuclear organization studies.
Facilitates efficient and reliable investigation of nuclear localization of chromosomal regions.