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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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Updated: Jun 28, 2025

Fluorescent End-Labeling and Encapsulation of Long RNAs for Single-Molecule FRET-TIRF Microscopy

Fluorescent End-Labeling and Encapsulation of Long RNAs for Single-Molecule FRET-TIRF Microscopy

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Bioorthogonal masked acylating agents for proximity-dependent RNA labelling.

Shubhashree Pani¹, Tian Qiu¹, Kaitlin Kentala¹

¹Department of Chemistry, The University of Chicago, Chicago, IL, USA.

Nature Chemistry

|April 9, 2024

Summary

Researchers developed a new method, bioorthogonal acylating agents for proximity labelling and sequencing (BAP-seq), to map RNA distribution within cells. This technique enables precise spatial analysis of RNA in various cellular compartments.

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Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

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Published on: November 22, 2014

Area of Science:

Molecular Biology
Cell Biology
Biochemistry

Background:

RNA localization is crucial for cellular functions and is tightly regulated.
Existing proximity labeling methods are effective for proteins but limited for unbiased RNA mapping.

Purpose of the Study:

To develop a novel method for unbiased spatial RNA mapping.
To create a platform for analyzing RNA distribution in specific subcellular locations.

Main Methods:

Development of novel α-alkoxy thioenol and chloroenol esters as potent acylating agents.
Utilizing subcellular-localized bioorthogonal esterase for controlled probe activation.
Implementing the bioorthogonal acylating agents for proximity labelling and sequencing (BAP-seq) for RNA analysis.

Main Results:

Demonstrated the ability to map RNA distribution in membrane-bound and membrane-less organelles.
Showcased the effectiveness of BAP-seq for precise spatial RNA analysis.
Validated the controlled-release acylating agent chemistry for proximity labeling.

Conclusions:

BAP-seq provides a robust and unbiased approach for mapping RNA localization.
The developed method expands the capabilities of proximity labeling technologies for RNA studies.
This platform offers a powerful tool to investigate cellular RNA organization.