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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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Robust 3D DNA FISH Using Directly Labeled Probes

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Trusted Codon Fingerprint: A Streamlined Platform for Deep and Reversible Bacterial Cell Labeling.

Zhaoguan Wang^1,2, Jingsong Cui³, Gaoxu Tan³

¹School of Chemical Engineering and Technology, Tianjin University, Tianjin 300354, China.

ACS Synthetic Biology

|September 22, 2025

Summary

This summary is machine-generated.

Trusted Codon Fingerprinting (TCF) offers a novel method for labeling engineered cells using synonymous codon substitutions. This system ensures efficient, erasable cell identification for improved synthetic biology applications.

Keywords:

DNA writing biotechnology cell labeling fingerprint strain engineering synthetic biology

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Area of Science:

Synthetic Biology
Molecular Biology
Genomics

Background:

Advances in synthetic biology necessitate robust methods for identifying and managing engineered cells.
Current cell labeling techniques may lack efficiency, precision, or erasability.

Purpose of the Study:

To develop a streamlined and erasable cell labeling platform for engineered cells.
To establish a unique identification system for synthetic entities using codon modifications.

Main Methods:

Leveraging synonymous codon substitutions within antibiotic-resistant genes on a plasmid to create unique "codon fingerprints."
Employing antibiotic selection and error-correcting codes to ensure accurate and efficient label writing.
Utilizing long-read sequencing and hash function computation for host cell genome identification.

Main Results:

Achieved 100% writing efficiency and successful host cell genome identification.
Demonstrated time- and labor-efficient recording and cyclic writing/erasure of cell labels in engineered *Escherichia coli*.
Validated the TCF system's ability to streamline the process of writing and managing cell labels.

Conclusions:

TCF provides a streamlined, erasable, and effective tool for labeling and identifying engineered cells.
The TCF system facilitates regulatory compliance and enhances identity management flexibility for engineered strains.
This platform significantly advances the traceability and oversight capabilities in synthetic biology.