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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.
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Southern Blot

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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.
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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,...

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Related Experiment Video

Updated: Apr 30, 2026

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

Accelerated Left-Handed DNA-PAINT Using Fluorogenic Probes.

Bas van Bommel¹, Helge Ewers¹

¹Institut für Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.

|April 29, 2026

Summary

This summary is machine-generated.

We developed a faster DNA-PAINT imaging method using left-handed DNA (L-DNA) probes. This approach reduces background noise and enhances multiplexing capabilities for super-resolution microscopy.

Keywords:

DNA-PAINT Fluorogenic DNA-PAINT Fluorogenic left-handed DNA-PAINT Single-molecule localization microscopy Super-resolution microscopy Volumetric DNA-PAINT

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Last Updated: Apr 30, 2026

Robust 3D DNA FISH Using Directly Labeled Probes

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Published on: August 15, 2013

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization

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Published on: December 10, 2012

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Area of Science:

Biophysics
Microscopy
Molecular Biology

Background:

Single-molecule localization microscopy (SMLM) achieves nanoscale resolution by localizing individual fluorescent molecules.
DNA-mediated point accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful SMLM technique known for multiplexing and accuracy.

Purpose of the Study:

To introduce a faster DNA-PAINT method utilizing left-handed DNA (L-DNA) probes.
To reduce background noise and improve volumetric imaging capabilities in DNA-PAINT.

Main Methods:

Development and application of left-handed DNA (L-DNA) probes for DNA-PAINT.
Integration of fluorogenic probes with L-DNA-PAINT for quenched emission from free binders.
Comparative analysis of binding kinetics, brightness, and localization precision between L-DNA and R-DNA probes.

Main Results:

L-DNA probes significantly reduce background noise from unspecific binding.
Fluorogenic L-DNA-PAINT enables volumetric imaging with quenched free binders.
L-DNA-PAINT allows for shorter integration times and faster localization accumulation.
Fluorogenic L-DNA and R-DNA probes exhibit indistinguishable binding kinetics, brightness, and precision.
Absence of cross-reactivity between fluorogenic left- and right-handed probes expands multiplexing options.

Conclusions:

L-DNA-PAINT offers a faster and lower-background alternative for super-resolution microscopy.
The combination of L-DNA probes and fluorogenic designs greatly enhances DNA-PAINT's experimental versatility.
This advancement facilitates reliable, high-resolution, multiplexed imaging in biological samples.